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교내 인터넷 환경 : 자동 접속

교외에서 사용시 인증 필요(외부 유출, 절대 금지 - 학생 및 교사 대상 유료 계정)
★아이디 : yatap
★비밀번호: yatap0120

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DBpia는 국내 우수 학술기관이 발행한 저널과 논문을 제공하고 있습니다. 연구자에게 꼭 맞는 콘텐츠와 서비스를 한 곳에서 만나보세요.

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- 구글 내 다른 사이트와 연동 가능
- 짧은 단어의 경우, 알아서 번역하여 검색
- 생물학 이외 다양한 분야의 학술자료 검색

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- 생명과학 및 의학 논문 검색
- 영어 키워드 검색

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national center for biotechnology information

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PubMed® comprises more than 36 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

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- GenBank : accession number 찾기
- FASTA 클릭 : '염기서열' 복사

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National Center for Biotechnology Information

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The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.

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< 염기서열 검색 예시 >

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< 염기서열 검색 예시 >

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- 단순 서열 외 많은 정보 제공
- 노란색 별 : 신뢰성 있는 자료
- FASTA : 텍스트 형태 서열 제공
- Length : 길이
- Mass(Da) : 단백질의 질량
- Sequences( 숫자 -> Isoform 의미 )

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If you are not seeing anything on this page, it might be for multiple reasons:

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< 단백질 서열 검색 예시 >

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< 단백질 서열 검색 예시 >

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1. 번역물의 가공 - 번역 후 변형

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1. 번역물의 가공 - 번역 후 변형

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예) PKN1에 의해 인산화되는 모티프

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예) PKN1에 의해 인산화되는 모티프

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- 1차원의 아미노산 서열 정보 → 단백질 변화 예측
- 단백질의 인산화되는 모티프 검색
http://www.phosphonetworks.org

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예) 엑스파시 툴 사용

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예) 엑스파시 툴 사용

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- 무료 : 다양한 프로테오믹스 소프트웨어 툴 제공
- https://web.expasy.org/translate/
- NetPhos 툴 추천 : https://services.healthtech.dtu.dk/service.php?NetPhos-3.1

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3. 세포 내 단백질의 위치

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3. 세포 내 단백질의 위치

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- 단백질의 서열 정보 →단백질의 위치 검색
- 프리딕트_프로테인 : http://www.predictprotein.org/

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예) 엑스파시 툴, 세포 내 단백질의 위치 예측

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예) 엑스파시 툴, 세포 내 단백질의 위치 예측

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- 1차 아미노산 서열을 이용한 3D 모델링
- PyRosetta : http://www.pyrosetta.org/

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- 단백질 데이터 은행 (안드로이드, ios 모바일 앱 지원)
- 구조생물학 연구 연합(RCSB, Research Col-laboratory for Structural Bioinformatics)에서 관리
- 이미 밝혀진 단백질 구조 정보 확인 가능

- PDB ID 코드 : 4자리, 0~9까지 수와 A~Z까지의 대문자 조합
예) 인슐린 ID 코드 : 3INS

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부록) 3D 단백질 구조 뷰어

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부록) 3D 단백질 구조 뷰어

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Rasmol : http://www.rasmol.org/doc/rasmol.html

PyMOL : http://www.rasmol.org/doc/rasmol.html

Jmol : http://jmol.sourceforge.net

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Running RasMol on the Apple Macintosh/PPC
To start RasMol on the Macintosh, double click on the RasMol icon using Finder. When RasMol first starts, the program displays two windows, the top window (with the black background) is the graphics or canvas window and the window underneath it (with the white background) is the RasMol command line window. RasMol on the Macintosh may also be started by double clicking on a file owned/created by the application with the signature 'RSML'. This will start up RasMol and pass the selected file to be loaded. There is no way of specifying the file format on the command line with a Macintosh so RasMol attempts to determine the file format by inspecting the file's type signature. Files with type signature 'RSML' are assumed to be RasMol scripts, files of type 'mMOL' are assumed to be MDL Mol files and all other types (principally 'TEXT') are assumed to be in PDB format. Unlike other versions of RasMol it is impossible to specify both a script and a coordinate file simultaneously.
Dragging and dropping multi-file 'movie' scripts onto aliases or copies of the RasMol application file may fail due to confusion about which is the correct script folder. Double-clicking on a script may lead to similar problems if copies are present.

RasMol's Window
On all platforms RasMol displays two windows, the main graphics orcanvas window with a black background and a command line orterminal window. At the top of the graphics window (or at the top of the screen for the Macintosh) is the RasMol menu bar. The contents of the menu bar change from platform to platform to support the local user interface guidelines; however, all platforms support the 'File', 'Display', 'Colours', 'Export', 'Options' and 'Settings' pull-down menus. The Main graphics window also has two scroll bars, one on the right and one at the bottom, that may be used to rotate the molecule interactively.
While the mouse pointer is located within the graphics area of the main display window, the mouse pointer is drawn as a cross-hair cursor, to enable the 'picking' of objects being displayed; otherwise the mouse pointer is drawn as an arrowhead. Any characters that are typed at the keyboard while the display window is in 'focus' (meaning active or foreground) are redirected to the command line in the terminal window. Hence you do not need continually to switch focus between the command line and graphics windows.

The display window may be resized at any point during the session. This has the effect of simply rescaling the image displayed on the canvas. RasMol imposes limits on the size of the display window such that the window must be large enough to display the menu and scroll bars and yet small enough to fit on a single screen. Attempts to enlarge the screen may fail owing to insufficient memory on the host machine, in which case RasMol reports the error message 'Renderer Error: Unable to allocate frame buffer!' or some similar error.

On eight bit displays, when the number of colours required by the program exceeds the number of free colours on the screen, the program uses its own colourmap. This has the effect of temporarily displaying all windows other than the display window in false colours while the mouse pointer is within the display windows. If the mouse pointer is moved outside the display windows, the original colours of the other windows return, and the image on the canvas is shown in 'false colour'. Once the number of colours required by the program drops again, the presentation of colours returns to normal.

Mouse Controls
Here is a summary of RasMol's mouse click-and-drag controls. The ' set mouse' command mode defaults to 'set mouse rasmol', which gives the controls summarized below. However, there are also 'set mouse insight' and 'set mouse quanta' modes (not shown below).

Action

Windows

Macintosh

Scroll Bars
The scroll bar across the bottom of the canvas area is used to rotate the molecule about the y-axis, i.e. to spin the nearest point on the molecule left or right; and the scroll bar to the right of the canvas rotates the molecule about the x-axis,i.e. the nearest point up or down. Each scroll bar has an 'indicator' to denote the relative orientation of the molecule, which is initially positioned in the centre of the scroll bar. These scroll bars may be operated in either of two ways. The first is by clicking any mouse button on the dotted scroll bar background to indicate a direct rotation relative to the current indicator position; the second is by clicking one of the arrows at either end of the scroll bar to rotate the molecule in fixed sized increments. Rotating the molecule by the second method may cause the indicators on the scroll bars to wrap around from one end of the bar to the other. A complete revolution is indicated by the indicator travelling the length of the scroll bar. The angle rotated by using the arrows depends upon the current size of the display window.
Picking
In order to identify a particular atom or bond being displayed, RasMol allows the users to 'pick' objects on the screen. The mouse is used to position the cross-hair cursor over the appropriate item, and then any of the mouse buttons is depressed. Provided that the pointer is located close enough to a visible object, the program determines the identity of the nearest atom to the point identified.

The program will display, in the terminal window, the atom's type, serial number, residue name and residue number. If the atom is a member of a named chain, the chain identifier is also displayed. Two examples of the output generated by selecting an atom are displayed below:

     Atom:  CA 349       Group:  SER 70
     Atom:  O  526       Hetero:  HOH 205    Chain:  P
The first line describes the alpha carbon of the serine-70 amino acid in a protein. The unique Protein Data Bank serial number for this atom is 349. The following line describes the oxygen atom in a water molecule attached to the P chain of the main molecule. The word 'Hetero' distinguishes heterogeneous molecules (such as cofactors) from the residues in the main molecule, noted by 'Group'. [These two atoms are referred to by the two atom expressions 'SER70.CA' and 'HOH205:P.O', respectively, when using the RasMol commands ' select' and 'restrict'.]
Clicking the mouse on an atom can be used not only to identify it, but also to find the coordinates, the distances between two atoms (or to display a distance monitor), the bond angle defined by three atoms, the torsion angle defined by four atoms, to toggle labels on or off, to specify the centre of rotation, or to specify a bond as the axis of rotation. See the 'set picking' command for details.

Dials Box
If RasMol detects a 'dials box' attached to the user's workstation, it also allows the molecule to be manipulated interactively by the dials. Once RasMol starts up, it labels the LED displays above each dial, 'ROTATE X', 'ROTATE Y', 'ROTATE Z' and 'ZOOM' across the top row from left to right, and 'TRANS X', 'TRANS Y', 'TRANS Z' and 'SLAB' from left to right across the bottom row. Rotating any of the knobs will automatically transform and redisplay the molecule interactively. The dials only have effect while the mouse pointer is within the display window. If more than one application is using the dials box at a time, care must be taken to remember the dial labels assigned by each program, as each application may overwrite the dial-label LEDS.

The 'ZOOM' dial allows the interactive zooming of the molecule between 10% and 200% of the original default magnification. Rotating the dial clockwise magnifies the molecule and anticlockwise shrinks it. A complete revolution of the dial corresponds to a 100% change in scale.

The 'SLAB' dial, which is only effective when slabbing is enabled, allows the user to move the front z-clipping plane from the nearest point on the molecule to the furthest. A complete rotation of the SLAB dial corresponds to moving the clipping plane half the distance between the front and back of the molecule. Turning the SLAB knob clockwise moves the clipping plane closer to the viewer (increasing the number of objects displayed), and turning it anticlockwise moves it further away (preventing more objects from being displayed). Slabbing mode is enabled by typing the command 'slab on' on the command line or toggling the slab option on the options menu.

Translation along the X and Y axis allows the centre of the molecule to be moved within the canvas area of the screen. Rotation and zooming are still performed relative to the centre of rotation and the molecule, respectively, which may often not be at the centre of the canvas. The TRANS Z dial currently has no effect.

Command Line Interface
RasMol allows the execution of interactive commands typed at the RasMol prompt in the terminal window. Characters typed into either the terminal or the display window are processed on the command line. Each command must be given on a separate line terminated by a newline or carriage return character. Keywords are case insensitive and may be entered in both lower and upper case letters. All whitespace (space, tab and formfeed) characters are ignored, except to separate the keyword and the arguments of a command. Blank lines (those containing only whitespace) are ignored. There is an internal restriction that command lines are limited to a maximum of 256 characters. Strings may be delimited by matching single or double quotation marks. Placing a hash '#' character anywhere outside quotes terminates the line. RasMol will ignore the rest of the line, which may be used to comment on the command.
If a syntax error is detected on entering an interactive command, RasMol indicates the location of the error on the command line by placing the '^' character under the offending word or character, and writing an error message on the following line. If a command is not recognised by RasMol, the program will generate an 'Unrecognised command!' error and redisplay the main prompt. If surplus information is given at the end of a command line, RasMol will execute the recognised command, but issue the warning message 'Warning: Ignoring rest of command!'. Some commands may prompt the user for more information. These commands display a different prompt and are discussed in the command reference.

Whenever RasMol outputs diagnostic or error messages to the screen owing to selecting options from the menu or picking objects on the screen, the current command line is cleared. The prompt is redisplayed after any text has been displayed.

Command Line Editing
RasMol allows basic editing of the command line. Pressing either backspace, delete or ^H (Control-H) will delete the previous character, and the key ^D may be used to delete the character under the cursor. Several characters may be used to move the cursor along the command line. The characters ^B, ^F, ^A and ^E move the cursor back a single character, forward a single character, to the beginning of the line and to the end of the line, respectively. When the cursor is not at the end of the command line, typed characters are inserted into the line and do not overwrite existing characters. After a command line has been edited, a newline or carriage return will enter the entire line, regardless of where the cursor is positioned. Because RasMol is unable to move the cursor up to the previous line, care must be taken when editing commands that wrap over several lines. In the event that another process overwrites or corrupts the command line, the character ^L may be used to redisplay the line on the screen.
RasMol maintains a history of recently used commands, so that the user never needs to type the same commands repeatedly. Typing ^P (Control-P) on the command line will display the previous command in the history and ^N will display the following command. These commands may be edited using the features described below. Moving forward or backward through the command history undoes the modifications made to the current line. The number of commands retained in the history depends upon their length. RasMol can retain more short command lines and fewer long ones.

Users with the Microsoft Windows version or the X windows version and with 'vt100' or compatible terminals (such as an 'xterm') can use the cursor control characters on the keyboard to abbreviate the control keys. The right and left cursor keys have the same affect as ^F and ^B, moving the cursor forward and back a single character, respectively. Similarly, the up and down cursor keys have the same function as ^P and ^N, producing the previous and next entries in the command history, respectively.

Users with the Macintosh version can use the four 'arrow keys' to move up and down through previous command line entries; and back and forth within a single command line statement. Hitting 'return' or 'enter' at any time will result in the execution of the current, e.g. selected or edited, command line contents.

Dimensions within RasMol
All dimensions in RasMol, such as radii and distances, may be specified in either 'RasMol units' or Ångstroms (Å). The RasMol units were first introduced to allow reasonably sized values to be specified for most of the operations performed in RasMol. A single RasMol unit corresponds to 1/250th of an Ångstrom; therefore the most frequently used values are in the hundreds. For this reason, if RasMol is given a distance parameter that does not contain a decimal point, it is assumed to be in RasMol units. For example, the command 'spacefill 300' specifies a sphere radius of 300 RasMol units, or 1.2 Å.

However, dimensions within RasMol can also be specified in Ångstroms by placing a decimal point in the number. For example, 'spacefill 1.2' specifies a sphere radius of 1.2 Å. This is particularly useful for the cut-off distance parameter inwithin expressions.
Start-up Initialisation Files
Each time RasMol is started, it searches for an initialisation file of commands to run before the command prompt is presented to the user. The file is called .rasmolrc on UNIX systems, andRASMOL.INI on VMS and Microsoft Windows Systems. The format and execution of this file is identical to that of the RasMol script command.

RasMol first looks for the initialisation file in the current directory and if it is not found will look for it in the user's home directory. On all systems the environment variable HOME may be used to name the user's home directory. If no personal initialisation file is found the program looks for the file rasmolrc (or RASMOLRC) in the RasMol system directory pointed to by the environment variable RASMOLPATH. This directory should also contain the on-line help file rasmol.hlp. On UNIX systems RASMOLPATH is typically set to be '/usr/local/lib/rasmol'.

Inter-Process Communication
RasMol supports Inter Process Communication (IPC) in one form or another on all platforms. Under Microsoft Windows, IPC is implemented using Dynamic Data Exchange (DDE), on the MacIntosh IPC is implemented using Apple Events and on X Windows systems IPC is implemented using John Ousterhaut's Tcl/Tk communication protocol.

When RasMol starts up on an X window system it registers itself with the X window Server as a Tcl interpreter. From within a Tcl application such as 'wish', you can use the Tcl command 'winfo interps' to determine the currently register interpreters on that display. The first instance of RasMol registers itself as 'rasmol', the second as 'rasmol #2', the third as 'rasmol #3' and so on. The Tcl interpreter can easily send a command to rasmol using the built-in 'send' command. RasMol interprets the string parameter to the send command not as a Tcl function to execute but as a RasMol command. Hence, typing 'send {rasmol} {background red}' into the wish interpreter will cause RasMol's display window to change colour. Using the same encoding as Microsoft's DDE Execute protocol, multiple commands may be sent in a single 'send' by placing the consecutive commands in square brackets. RasMol will execute all of the commands in a 'send' before refreshing the screen.

Under Microsoft Windows, RasMol supports a complete DDE protocol. The simplest layers of the protocol may be accessed by sending a DDE Execute command to application 'RasWin' and any topic. This will start a DDE conversation with the most recently launched instance of RasMol. Although any topic name can be used, the use of 'System' and/or 'RemoteControl' are recommended. Once again the contents of the execute package consists of a string for RasMol to execute. If the first non-whitespace character is an open bracket, the string is interpreted to be a sequence of consecutive commands enclosed in square brackets; otherwise the string consists of just a single command. Commands in square brackets may optionally be separated by whitespace and/or semi- colons. RasMol can also act as a 'data server' supporting hot, cold and warm links. Currently supported DDE items include 'Name', 'Image', 'Pick', 'Count' which denotes the Molecule name, the currently displayed image (in Microsoft DIB format), the atom expression of the last picked atom (or an empty string) and the number of selected atoms, respectively. Using a hot or warm link on the 'Pick' item, for example, allows an application such as Microsoft Word, Excel or Visual Basic to respond each time the user clicks on an atom in RasMol.

RasMol on the Apple Macintosh supports AppleEvents. Currently the only supported AppleEvents are the four 'core' events, Open Application, Open Document, Print Document and Quit. However, because OpenDocument determines its actions by the file's type signature this can be used to implement generic IPC. Because RasMol for the Macintosh treats all files of type 'RSML' as scripts, the sending application need only place all the commands to be executed in a temporary file, set the type of the file to 'RSML' and then send RasMol an OpenDocument AppleEvent with the file as parameter.

Command Reference
RasMol allows the execution of interactive commands typed at the 'RasMol>' prompt in the terminal window. Each command must be given on a separate line. Keywords are case insensitive and may be entered in either upper or lower case letters. All whitespace characters are ignored except to separate keywords and their arguments.
All commands may be prefixed by a parenthesized 'atom expression' to temporarily select certain atoms just for the execution of that one command. After execution of the command, the previous selection is restored except for the commands 'select' , 'restrict' and 'script'.

The commands/keywords currently recognised by RasMol are given below.
Backbone

Syntax:  backbone {<boolean>}
         backbone <value>
         backbone dash

The RasMol 'backbone' command permits the representation of a polypeptide backbone as a series of bonds connecting the adjacent alpha carbons of each amino acid in a chain. The display of these backbone 'bonds' is turned on and off by the command parameter in the same way as with the 'wireframe' command. The command 'backbone off' turns off the selected 'bonds', and 'backbone on' or with a number turns them on. The number can be used to specify the cylinder radius of the representation in either Ångstrom or RasMol units. A parameter value of 500 (2.0 Ångstroms) or above results in a "Parameter value too large" error. Backbone objects may be coloured using the RasMol 'colour backbone' command.

The backbone may be displayed with dashed lines by use of the 'backbone dash' command.
Background

Syntax:  background <colour>

Bond

Syntax:  bond <number>  <number> +
         bond <number>  <number> pick
         bond rotate {<boolean>}

The RasMol command 'bond <number> <number> +' adds the designated bond to the drawing, increasing the bond order if the bond already exists. The command 'bond <number> <number> pick' selects the two atoms specified by the atom serial numbers as the two ends of a bond around which the 'rotate bond <angle>' command will be applied. If no bond exists, it is created.

Rotation around a previously picked bond may be specified by the 'rotate bond <angle>' command, or may also be controlled with the mouse, using the 'bond rotate on/off' or the equivalent 'rotate bond on/off' commands.
Bulgarian

Syntax:  Bulgarian

The RasMol 'Bulgarian' command sets the menus and messages to the Bulgarian versions.
Cartoon

Syntax:  cartoon {<number>}

The RasMol 'cartoon' command does a display of a molecule 'ribbons' as Richardson (MolScript) style protein 'cartoons', implemented as thick (deep) ribbons. The easiest way to obtain a cartoon representation of a protein is to use the 'Cartoons' option on the 'Display' menu. The 'cartoon' command represents the currently selected residues as a deep ribbon with width specified by the command's argument. Using the command without a parameter results in the ribbon's width being taken from the protein's secondary structure, as described in the 'ribbons' command. By default, the C-termini of beta-sheets are displayed as arrow heads. This may be enabled and disabled using the 'set cartoons' command. The depth of the cartoon may be adjusted using the 'set cartoons <number>' command. The 'set cartoons' command without any parameters returns these two options to their default values.
Centre

Syntax:  centre {<expression>} {translate|center}
         center {<expression>} {translate|center}

Alternatively the centring may be given as a comma separated triple of [CenX, CenY, CenZ] offsets in RasMol units (1/250 of an Ångstrom) from the centre of gravity. The triple must be enclosed in square brackets.
Chinese

Syntax:  Chinese

The RasMol 'Chinese' command sets the menus and messages to the Chinese versions.
Clipboard

Syntax:  clipboard

The RasMol 'clipboard' command places a copy of the currently displayed image on the local graphics 'clipboard'. Note: this command is not yet supported on UNIX or VMS machines. It is intended to make transfering images between applications easier under Microsoft Windows or on an Apple Macintosh.
Colour

Syntax:  colour {<object>} <colour>
         color {<object>} <colour>

Allowed objects are 'atoms', 'bonds', 'backbone', 'ribbons', 'labels', 'dots', 'hbonds', 'map', and 'ssbonds'. If no object is specified, the default keyword 'atom' is assumed. Some colour schemes are defined for certain object types. The colour scheme 'none' can be applied to all objects except atoms and dots, stating that the selected objects have no colour of their own, but use the colour of their associated atoms ( i.e. the atoms they connect). 'Atom' objects can also be coloured by 'alt', 'amino', 'chain', 'charge', 'cpk', 'group', 'model', 'shapely', 'structure', 'temperature' or 'user'. Hydrogen bonds can also be coloured by 'type' and dot surfaces can also be coloured by 'electrostatic potential'. For more information type 'help colour <colour>'. Map objects may be coloured by specific color of by nearest atom.
ColourMode

Syntax:  colourmode {<boolean>}
         colormode {<boolean>}

Connect

Syntax:  connect {<boolean>}

The RasMol 'connect' command is used to force RasMol to (re)calculate the connectivity of the current molecule. If the original input file contained connectivity information, this is discarded. The command 'connect false' uses a fast heuristic algorithm that is suitable for determining bonding in large bio-molecules such as proteins and nucleic acids. The command "connect true" uses a slower more accurate algorithm based upon covalent radii that is more suitable to small molecules containing inorganic elements or strained rings. If no parameters are given, RasMol determines which algorithm to use based on the number of atoms in the input file. Greater than 255 atoms causes RasMol to use the faster implementation. This is the method used to determine bonding, if necessary, when a molecule is first read in using the 'load' command.
Defer

Syntax:  defer <name> <command to defer>

Define

Syntax:  define <identifier> <expression>

The RasMol 'define' command allows the user to associate an arbitrary set of atoms with a unique identifier. This allows the definition of user-defined sets. These sets are declared statically, i.e. once defined the contents of the set do not change, even if the expression defining them depends on the current transformation and representation of the molecule.
Depth

Syntax:  depth {<boolean>}
         depth <value>

The RasMol 'depth' command enables, disables or positions the back-clipping plane of the molecule. The program only draws those portions of the molecule that are closer to the viewer than the clipping plane. Integer values range from zero at the very back of the molecule to 100 which is completely in front of the molecule. Intermediate values determine the percentage of the molecule to be drawn.
Dots

Syntax:  dots {<boolean>}
         dots <value>

Echo

Syntax:  echo {<string>}

The RasMol 'echo' command is used to display a message in the RasMol command/terminal window. The string parameter may optionally be delimited in double quote characters. If no parameter is specified, the 'echo' command displays a blank line. This command is particularly useful for displaying text from within a RasMol 'script' file.
English

Syntax:  English

The RasMol 'English' command sets the menus and messages to the English versions.
Execute

Syntax:  execute <name>

The RasMol 'execute' command:

1. saves the old poise of the molecule (translation, rotation and zoom)

2. executes the specified macro suppressing both screen updates and recording

3. animates motion of the newly rendered molecule linearly
French

Syntax:  French

The RasMol 'French' command sets the menus and messages to the French versions.
HBonds

Syntax:  hbonds {<boolean>}
         hbonds <value>

The RasMol 'hbond' command is used to represent the hydrogen bonding of the protein molecule's backbone. This information is useful in assessing the protein's secondary structure. Hydrogen bonds are represented as either dotted lines or cylinders between the donor and acceptor residues. The first time the 'hbond' command is used, the program searches the structure of the molecule to find hydrogen bonded residues and reports the number of bonds to the user. The command 'hbonds on' displays the selected 'bonds' as dotted lines, and the 'hbonds off' turns off their display. The colour of hbond objects may be changed by the 'colour hbond' command. Initially, each hydrogen bond has the colours of its connected atoms.
Help

Syntax:  help {<topic> {<subtopic>}}
         ? {<topic> {<subtopic>}}

The RasMol 'help' command provides on-line help on the given topic.
Italian

Syntax:  Italian

The RasMol 'Italian' command sets the menus and messages to the Italian versions.
Japanese

Syntax:  Japanese

The RasMol 'Japanese' command sets the menus and messages to the Japanese versions.
Label

Syntax:  label {<string>}
         label <boolean>

The RasMol 'label' command allows an arbitrary formatted text string to be associated with each currently selected atom. This string may contain embedded 'expansion specifiers' which display properties of the atom being labelled. An expansion specifier consists of a '%' character followed by a single alphabetic character specifying the property to be displayed (similar to C's printf syntax). An actual '%' character may be displayed by using the expansion specifier '%%'.

Atom labelling for the currently selected atoms may be turned off with the command 'label off'. By default, if no string is given as a parameter, RasMol uses labels appropriate for the current molecule. RasMol uses the label '%n%r:%c.%a' if the molecule contains more than one chain, '%e%i' if the molecule has only a single residue (a small molecule) and '%n%r.%a' otherwise.

The colour of each label may be changed using the 'colour label' command. By default, each label is drawn in the same colour as the atom to which it is attached. The size and spacing of the displayed text may be changed using the 'set fontsize' command. The width of the strokes in the displayed text may be changed using the 'set fontstroke' command.

The following table lists the current expansion specifiers:

    %a      Atom Name
    %b %t   B-factor/Temperature
    %c %s   Chain Identifier
    %e      Element Atomic Symbol
    %i      Atom Serial Number
    %n      Residue Name
    %r      Residue Number
    %M      NMR Model Number (with leading "/")
    %A      Alternate Conformation Identifier (with leading ";")

Load

Syntax:  load {<format>} <filename>

The 'load' command selects all the atoms in the molecule, centres it on the screen and renders it as a CPK coloured wireframe model. If the molecule contains no bonds ( i.e. contains only alpha carbons), it is drawn as an alpha carbon backbone. If the file specifies fewer bonds than atoms, RasMol determines connectivity using the 'connect' command.
Map

Syntax:  map {<map_selector>} {<map_subcommand> <parameters>}

The RasMol 'map' commands manipulate electron density maps in coordination with the display of molecules. These commands are very memory intensive and may not work on machines with limited memory. Each molecule may have as many maps as available memory permits. Maps may be read from files or generated from Gaussian density distributions around atoms.

'map colour', to colour a map according to a given colour scheme, 'map generate', to generate a map from selected atoms based on pseudo-Gaussians, 'map level', to set the contouring level for selected maps, 'map load', to load a map from a file, 'map mask' to designate a mask for the selected maps, 'map resolution', to set the resolution for contouring selected maps, 'map restrict', to select one or more maps and to disable all others, 'map save', to save map information to a file, 'map scale', 'control the scaling of pseudo-Gaussians when generating maps', 'map select', to select one or more maps, 'map show', to display information about one or more maps or about the parameters to be used in generating or loading the next map, 'map spacing', to set the spacing betwen contour lines of selected maps, 'map spread', to set the variance of the Gaussians for map generation as a fraction of the atomic radius, and 'map zap' to delete previously generated or loaded maps.

The effect of 'map generate' and 'map load' commands is modified by the 'map mask' command which limits the portion of the display space that can be considered for display of maps.
Map colour

Syntax:  map {<map_selector>} colour <colour_scheme>

Map generate

Syntax:  map {<map_selector>} generate {LRsurf} dots
         map {<map_selector>} generate {LRsurf} mesh
         map {<map_selector>} generate {LRsurf} surface

For example, if the resolution is given as 1., and the atom in question is a Carbon with a van der Waals radius of 468 RasMol units (1.87 Ångstroms), the inferred spead is .6667, and the standard deviation of the Gaussian is taken as 1.25 Ångstroms.

If the spread has been set to zero, the spread for each atom is determined from the van der Waals radius and the probe atom radius to simulate the effect of a Lee-Richards surface.

If no specific map was given by the map selector, the new map is given the next available map number.

If a specific map was given by the map selector, the new map replaces that map. If more than one map was given by the map selector, the new map replaces the lowest numbered of the selected maps. In any case the new map becomes the currently selected map.

The map is displayed as dots, mesh or a surface, depending on the last map rendering mode selected or the mode selected on the command itself.
Map level

Syntax:  map {<map_selector>} level {MEAN} <number>

The RasMol 'map level' command sets the contour level to be used in creating subsequent representations of generated or loaded maps. If the keyword MEAN in used the level is relative to the mean of the map data. Otherwise the level is absolute.

In general, a lower level results in a map containing more of the displayed volume, while a higher level results in a map containing less of the displayed volume.
Map load

Syntax:  map {<map_selector>} load <filename>

The RasMol 'map load' command loads a map file into RasMol. The valid formats are CCP4 map format and imgCIF format.

If no specific map was given by the map selector, the new map is given the next available map number.

If a specific map was given by the map selector, the new map replaces that map. If more than one map was given by the map selector, the new map replaces the lowest numbered of the selected maps. In any case the new map becomes the currently selected map.

The map is displayed as dots, mesh or a surface depending on the last map rendering mode selected.
Map mask

Syntax:  map {<map_selector>} mask selected
         map {<map_selector>} mask <number>
         map {<map_selector>} mask none

The RasMol 'map mask' command specifies a mask to be used to limit the display space to be used for making representations of other maps or removes an earlier mask specification.

The 'selected' option indicates that the mask is to be created from the currently selected atoms. The '<number>' option indicates that the mask is to be copied from the map of the number specified. The 'none' option removes the previously specified mask, if any.

The map selector specifies the map or maps to which the specified mask will the applied. For example, 'map next mask selected' specifies that the currently selected atoms are to be used to generate a mask to be applied to any maps created by subsequent 'map load' or 'map generate' commands.

Any map may be used as a mask. The portions of the mask map greater than than or equal to the average value of the mask map allow the values of the map being masked to be used as given. The portions of the mask map lower than the average value of the mask map cause the values of the map being masked to be treated as if they were equal to the lowest data value of the map being masked.
Map resolution

Syntax:  map {<map_selector>} resolution <number>

The RasMol 'map resolution' command specifies the resolution in RasMol units or, if a number containing a decimal point is given, the resolution in Ångstroms to be used in generating and in representing maps.
Map restrict

Syntax:  map {<map_selector>} restrict

Map save

Syntax:  map {<map_selector>} save <filename>

The RasMol 'map save' command saves an imgCIF map file.

If no specific map was given by the map selector, the currently selected maps and their masks are written to the file, one map and mask pair per data block.
Map scale

Syntax:  map {<map_selector>} scale <boolean>

Map select

Syntax:  map {<map_selector>} select {atom {within} {add} {search_radius}}

Map show

Syntax:  map {<map_selector>} show

The RasMol 'map show' command causes information about the maps specified by the map selector to be written to the command window.
Map spacing

Syntax:  map {<map_selector>} spacing <number>

The RasMol 'map spacing' command specifies the spacing to be used between contour lines in creating representations of maps. The spacing is typically given in Ångstroms with a decimal point, but may also be specified in RasMol units (250ths of an Angstom) as an integer. For maps loaded in grid coordinates that spacing is parallel to the cell edges. The default spacing is one half Ångstrom.
Map spread

Syntax:  map {<map_selector>} spread <number>

The RasMol 'map spread' command specifies the reciprocal of the number of standard deviations per radius to be used in generating maps as sums of Gaussians centered on atomic positions. The default spread is one two thirds ( i.e. each radius covers 1.5 standard deviations).

If the spread has been set to zero, the spread for each atom is determined from the van der Waals radius and the probe atom radius to simulate the effect of a Lee-Richards surface.
Map zap

Syntax:  map {<map_selector>} zap

The RasMol 'map zap' command removes the data and representations of the maps specified by the map selector. The map numbers of maps that have not been removed are not changed.
Molecule

Syntax:  molecule <number>

Monitor

Syntax:  monitor <number>  <number>
         monitor {<boolean>}

Distance monitors are turned off with the command 'monitors off'. By default, monitors display the distance between its two end points as a label at the centre of the monitor. These distance labels may be turned off with the command 'set monitors off', and re-enabled with the command 'set monitors on'. Like most other representations, the colour of a monitor is taken from the colour of its end points unless specified by the 'colour monitors' command.
Notoggle

Syntax:  notoggle {<boolean>}

Pause

Syntax:  pause
         wait

The RasMol 'pause' command is used in script files to stop the script file for local manipulation by a mouse, until any key is pushed to restart the script file. 'Wait' is synonymous with 'pause'. This command may be executed in RasMol script files to suspend the sequential execution of commands and allow the user to examine the current image. When RasMol executes a 'pause' command in a script file, it suspends execution of the rest of the file, refreshes the image on the screen and allows the manipulation of the image using the mouse and scroll bars, or resizing of the graphics window. Once a key is pressed, control returns to the script file at the line following the 'pause' command. While a script is suspended the molecule may be rotated, translated, scaled, slabbed and picked as usual, but all menu commands are disabled. The 'pause' can probably be used most effectively with 'echo' commands in education pre-scripted demonstrations, where a description of the current image is presented to the user/student. Typically the command before a 'pause' should be 'echo Press any key to continue'.
Play

Syntax:  play {from

As of release 2.7.5, RasMol support play from scripts and data files.
Print

Syntax:  print

The RasMol 'print' command sends the currently displayed image to the local default printer using the operating system's native printer driver. Note: this command is not yet supported under UNIX or VMS. It is intended to take advantage of Microsoft Windows and Apple Macintosh printer drivers. For example, this allows images to be printed directly on a dot matrix printer.
Quit

Syntax:  quit
         exit

Record

Syntax:  record {from

The RasMol 'record' command specifies the recording medium to hold the movie. Since we are working on computers, the medium is specified as a template for a set of files, each marked with the playback frame start time in milliseconds (rather than as seconds to avoid embedding a decimal point) as part of the name. The place in the name to be replaced with the playback frame start time in milliseconds is marked by the characters "ssssss" with an appropriate number of digits. RasMol accepts either upper or lower case s's or decimal digits to mark the place for the time. The record off commands remove the specified medium from use. If no medium is specified, record off suspends recording and record on resumes recording with the next available time on the same medium. The screen is the default medium and is, by default, on. Writing to disk must be explicitly specified so that the disk does not get filled up unintentionally. The type of a recording medium may be an image type such as gif, pict or png to record the actual screen images or script to record the RasMol commands used to generate the frames.

'record from 600'

'record until 1800'

would result in a 20 minute movie segment intended to start 10
Refresh

Syntax:  refresh

The RasMol 'refresh' command redraws the current image. This is useful in scripts to ensure application of a complex list of parameter changes.
Renumber

Syntax:  renumber {{-} <value>}

The RasMol 'renumber' command sequentially numbers the residues in a macromolecular chain. The optional parameter specifies the value of the first residue in the sequence. By default, this value is one. For proteins, each amino acid is numbered consecutively from the N terminus to the C terminus. For nucleic acids, each base is numbered from the 5' terminus to the 3' terminus. All chains in the current database are renumbered and gaps in the original sequence are ignored. The starting value for numbering may be negative.
Reset

Syntax:  reset

The RasMol 'reset' command restores the original viewing transformation and centre of rotation. The scale is set to its default value, 'zoom 100', the centre of rotation is set to the geometric centre of the currently loaded molecule, 'centre all', this centre is translated to the middle of the screen and the viewpoint set to the default orientation.
Restrict

Syntax:  restrict {<expression>}

The RasMol 'restrict' command both defines the currently selected region of the molecule and disables the representation of (most of) those parts of the molecule no longer selected. All subsequent RasMol commands that modify a molecule's colour or representation affect only the currently selected region. The parameter of a 'restrict' command is a RasMol atom expression that is evaluated for every atom of the current molecule. This command is very similar to the RasMol 'select' command, except 'restrict' disables the 'wireframe', 'spacefill' and 'backbone' representations in the non-selected region.
Ribbons

Syntax:  ribbons {<boolean>}
         ribbons <value>

The RasMol 'ribbons' command displays the currently loaded protein or nucleic acid as a smooth solid "ribbon" surface passing along the backbone of the protein. The ribbon is drawn between each amino acid whose alpha carbon is currently selected. The colour of the ribbon is changed by the RasMol 'colour ribbon' command. If the current ribbon colour is 'none' (the default), the colour is taken from the alpha carbon at each position along its length.
Rotate

Syntax:  rotate <axis> {-} <value>
         rotate bond {<boolean>}
         rotate molecule {<boolean>}
         rotate all {<boolean>}

Alternatively, this command may be used to specify which rotations the mouse or dials will control. If 'rotate bond true' is selected, the horizontal scroll bar will control rotation around the axis selected by the 'bond src dst pick' command. If 'rotate all true' is selected, and multiple molecules have been loaded, then all molecules will rotate together. In all other cases, the mouseand dials control the the rotation of the molecule selected by the 'molecule n' command.
Russian

Syntax:  Russian

The RasMol 'Russian' command sets the menus and messages to the Russian versions.
Save

Syntax:  save {pdb} <filename>
         save mdl <filename>
         save alchemy <filename>
         save xyz <filename>

Save the currently selected set of atoms in a Protein Data Bank (PDB), MDL, Alchemy(tm) or XYZ format file. The distinction between this command and the RasMol 'write' command has been dropped. The only difference is that without a format specifier the 'save' command generates a 'PDB' file and the 'write' command generates a 'GIF' image.
Script

Syntax:  script <filename>

Scripts may also be created with a text editor.
Select

Syntax:  select {<expression>}

Define the currently selected region of the molecule. All subsequent RasMol commands that manipulate a molecule or modify its colour or representation only affect the currently selected region. The parameter of a 'select' command is a RasMol expression that is evaluated for every atom of the current molecule. The currently selected (active) region of the molecule are those atoms that cause the expression to evaluate true. To select the whole molecule use the RasMol command 'select all'. The behaviour of the 'select' command without any parameters is determined by the RasMol 'hetero' and 'hydrogen' parameters.
Set

Syntax:  set <parameter> {<option>}

The RasMol 'set' command allows the user to alter various internal program parameters such as those controlling rendering options. Each parameter has its own set or permissible parameter options. Typically, omitting the paramter option resets that parameter to its default value. A list of valid parameter names is given below.
Show

Syntax:  show information
         show centre
         show phipsi
         show RamPrint
         show rotation
         show selected { group | chain | atom }
         show sequence
         show symmetry
         show translation
         show zoom

The RasMol 'show' command display details of the status of the currently loaded molecule. The command 'show information' lists the molecule's name, classification, PDB code and the number of atoms, chains, groups it contains. If hydrogen bonding, disulphide bridges or secondary structure have been determined, the number of hbonds, ssbonds, helices, ladders and turns are also displayed, respectively. The command 'show centre' shows any non-zero centering values selected by the 'centre [CenX, CenY, CenZ]' command. The command 'show phipsi' shows the phi and psi angles of the currently selected residues and the omega angles of cis peptide bonds. The command 'show RamPrint' (or 'show RPP' or 'show RamachandranPrinterPlot') shows a simple Ramachandran printer plot in the style of Frances Bernstein's fisipl program. The command 'show rotation' (or 'show rot' or 'show 'rotate') shows the currently selected values of z, y, x and bond rotations, if any. The command 'show selected' (or 'show selected group' or 'show selected chain' or 'show selected atom' ) shows the groups (default), chains or atoms of the current selection. The command 'show sequence' lists the residues that comprise each chain of the molecule. The command 'show symmetry' shows the space group and unit cell of the molecule. The command 'show translation' shows any non-zero translation values selected by the 'translate <axis> <value>' command. The command 'show zoom' shows any non-zero zoom value selected by the 'zoom <value>' command.
Slab

Syntax:  slab {<boolean>}
         slab <value>

The RasMol 'slab' command enables, disables or positions the z-clipping plane of the molecule. The program only draws those portions of the molecule that are further from the viewer than the slabbing plane. Integer values range from zero at the very back of the molecule to 100 which is completely in front of the molecule. Intermediate values determine the percentage of the molecule to be drawn.
Spacefill

Syntax:  spacefill {<boolean>}
         spacefill temperature
         spacefill user
         spacefill <value>

Spanish

Syntax:  Spanish

The RasMol 'Spanish' command sets the menus and messages to the Spanish versions.
SSBonds

Syntax:  ssbonds {<boolean>}
         ssbonds <value>

The RasMol 'ssbonds' command is used to represent the disulphide bridges of the protein molecule as either dotted lines or cylinders between the connected cysteines. The first time that the 'ssbonds' command is used, the program searches the structure of the protein to find half-cysteine pairs (cysteines whose sulphurs are within 3 Ångstroms of each other) and reports the number of bridges to the user. The command 'ssbonds on' displays the selected "bonds" as dotted lines, and the command 'ssbonds off' disables the display of ssbonds in the currently selected area. Selection of disulphide bridges is identical to normal bonds, and may be adjusted using the RasMol 'set bondmode' command. The colour of disulphide bonds may be changed using the 'colour ssbonds' command. By default, each disulphide bond has the colours of its connected atoms.
Star

Syntax:  star {<boolean>}
         star temperature
         star user
         star <value>

The RasMol 'star' command is used to represent all of the currently selected atoms as stars (six strokes, one each in the x, -x, y, -y, z and -z directions). The commands 'select not bonded' followed by 'star 75' are useful to mark unbonded atoms in a 'wireframe' display with less overhead than provided by 'spacefill 75'. This can be done automatically for all subsequent wireframe displays with the command 'set bondmode not bonded'.
Stereo

Syntax:  stereo on
         stereo <number>
         stereo off

The RasMol 'stereo' command provides side-by-side stereo display of images. Stereo viewing of a molecule may be turned on (and off) either by selecting 'Stereo' from the 'Options' menu, or by typing the commands 'stereo on' or 'stereo off'.

Starting with RasMol version 2.7.2.1, the 'Stereo' menu selection and the command 'stereo' without arguments cycle from the initial state of 'stereo off' to 'stereo on' in cross-eyed mode to 'stereo on' in wall-eyed mode and then back to 'stereo off'.

The separation angle between the two views may be adjusted with the 'set stereo [-] <number>' command, where positive values result in crossed eye viewing and negative values in relaxed (wall-eyed) viewing. The inclusion of '[-] <number>' in the 'stereo' command, as for example in 'stereo 3' or 'stereo -5', also controls angle and direction.
Strands

Syntax:  strands {<boolean>}
         strands <value>

The RasMol 'strands' command displays the currently loaded protein or nucleic acid as a smooth "ribbon" of depth-cued curves passing along the backbone of the protein. The ribbon is composed of a number of strands that run parallel to one another along the peptide plane of each residue. The ribbon is drawn between each amino acid whose alpha carbon is currently selected. The colour of the ribbon is changed by the RasMol 'colour ribbon' command. If the current ribbon colour is 'none' (the default), the colour is taken from the alpha carbon at each position along its length. The central and outermost strands may be coloured independently using the 'colour ribbon1' and 'colour ribbon2' commands, respectively. The number of strands in the ribbon may be altered using the RasMol 'set strands' command.
Structure

Syntax:  structure

The RasMol 'structure' command calculates secondary structure assignments for the currently loaded protein. If the original PDB file contained structural assignment records (HELIX, SHEET and TURN) these are discarded. Initially, the hydrogen bonds of the current molecule are found, if this hasn't been done already. The secondary structure is then determined using Kabsch and Sander's DSSP algorithm. Once finished the program reports the number of helices, strands and turns found.
Surface

Syntax:  surface molecule <value>
         surface solvent  <value>

The RasMol 'surface' command renders a Lee-Richards molecular surface resulting from rolling a probe atom on the selected atoms. The value given specifies the radius of the probe. If given in the first form, the evolute of the surface of the probe is shown (the solvent excluded surface). If given in the second form, the envelope of the positions of the center of the probe is shown (the solvent accessible surface).
Trace

Syntax:  trace {<boolean>}
         trace <value>
         trace temperature

The RasMol 'trace' command displays a smooth spline between consecutive alpha carbon positions. This spline does not pass exactly through the alpha carbon position of each residue, but follows the same path as 'ribbons', 'strands' and 'cartoons'. Note that residues may be displayed as 'ribbons', 'strands', 'cartoons' or as a 'trace'. Enabling one of these representations disables the others. However, a residue may be displayed simultaneously as backbone and as one of the above representations. This may change in future versions of RasMol. Prior to version 2.6, 'trace' was synonymous with 'backbone'.

'Trace temperature' displays the backbone as a wider cylinder at high temperature factors and thinner at lower. This representation is useful to X-ray crystallographers and NMR spectroscopists.
Translate

Syntax:  translate <axis> {-} <value>

UnBond

Syntax:  unbond <number>  <number>
         unbond

The RasMol command 'unbond <number> <number>' removes the designated bond from the drawing.
Wireframe

Syntax:  wireframe {<boolean>}
         wireframe <value> {}

The RasMol 'wireframe' command represents each bond within the selected region of the molecule as a cylinder, a line or a depth-cued vector. The display of bonds as depth-cued vectors (drawn darker the further away from the viewer) is turned on by the command 'wireframe' or 'wireframe on'. The selected bonds are displayed as cylinders by specifying a radius either as an integer in RasMol units or containing a decimal point as a value in Ångstroms. A parameter value of 500 (2.0 Ångstroms) or above results in an "Parameter value too large" error. Bonds may be coloured using the 'colour bonds' command. If the selected bonds involved atoms of alternate conformers then the bonds are narrowed in the middle to a radius of .8 of the specified radius (or to the radius specifed as the optional second parameter).

Non-bonded atoms, which could become invisible in an ordinary 'wireframe' display can be marked by a preceding 'set bondmode not bonded' command. If nearly co-linear bonds to atoms cause them to be difficult to see in a wireframe display, the 'set bondmode all' command will add markers for 'all' atoms in subsequent 'wireframe' command executions.
Write

Syntax:  write {<format>} <filename>

The distinction between this command and the RasMol 'save' command has been dropped. The only difference is that without a format specifier the 'save' command generates a 'PDB' file and the 'write' command generates a 'GIF' image.
Zap

Syntax:  zap

Deletes the contents of the current database and resets parameter variables to their initial default state.
Zoom

Syntax:  zoom {<boolean>}
         zoom <value>

Change the magnification of the currently displayed image. Boolean parameters either magnify or reset the scale of current molecule. An integer parameter specifies the desired magnification as a percentage of the default scale. The minimum parameter value is 10; the maximum parameter value is dependent upon the size of the molecule being displayed. For medium sized proteins this is about 500.

Internal Parameters
RasMol has a number of internal parameters that may be modified using the 'set' command. These parameters control a number of program options such as rendering options and mouse button mappings.
A complete list of internal parameter names is given below.
Set Ambient

Syntax:  set ambient {<value>}

This parameter is commonly used to correct for monitors with different "gamma values" (brightness), to change how light or dark a hardcopy image appears when printed or to alter the feeling of depth for wireframe or ribbon representations.
Set Axes

Syntax:  set axes <boolean>

Set Backfade

Syntax:  set backfade <boolean>

Set Background

Syntax:  set background {<colour>}

Set BondMode

Syntax:  set bondmode and
         set bondmode or
         set bondmode all
         set bondmode none
         set bondmode not bonded

When using the 'select' and 'restrict' commands, a given bond will be selected if i) the bondmode is 'or' and either of the connected atoms is selected, or ii) the bondmode is 'and' and both atoms connected by the bond are selected. Hence an individual bond may be uniquely identified by using the command 'set bondmode and' and then uniquely selecting the atoms at both ends.

The 'bondmode [all | none | not bonded]' commands add 'star 75' or 'spacefill 75' markers for the designated atoms to 'wireframe' displays. Stars are used when the specified wireframe radius is zero.
Set Bonds

Syntax:  set bonds <boolean>

Set BoundBox

Syntax:  set boundbox <boolean>

Set Cartoon

Syntax:  set cartoon {<boolean>}
         set cartoon {<number>}

The RasMol 'cartoon' parameter is used to control display of the cartoon version of the 'ribbons' display. By default, the C-termini of beta-sheets are displayed as arrow heads. This may be enabled and disabled using the 'set cartoons <boolean>' command. The depth of the cartoon may be adjusted using the 'cartoons <number>' command. The 'set cartoons' command without any parameters returns these two options to their default values.
Set CisAngle

Syntax:  set cisangle {<value>}

The RasMol 'cisangle' parameter controls the cutoff angle for identifying cis peptide bonds. If no value is given, the cutoff is set to 90 degrees.
Set Display

Syntax:  set display selected
         set display normal

Set FontSize

Syntax:  set fontsize {<value>} { FS | PS }

Set FontStroke

Syntax:  set fontstroke {<value>}

The RasMol 'set fontstroke' command is used to control the size of the stroke width of the characters that form atom labels. This value is the radius in pixels of cylinders used to form the strokes. The special value of "0" is the default used for the normal single pixel stroke width, which allows for rapid drawing and rotation of the image. Non-zero values are provided to allow for more artistic atom labels for publication at the expense of extra time in rendering the image.

The character sets used by RasMol rendered with fixed spacing with single-pixel-width strokes and with proportional spacing with 2-pixel-radius cylinder strokes are shown in the following sample:

Set HBonds

Syntax:  set hbonds backbone
         set hbonds sidechain

The RasMol 'hbonds' parameter determines whether hydrogen bonds are drawn between the donor and acceptor atoms of the hydrogen bond, 'set hbonds sidechain' or between the alpha carbon atoms of the protein backbone and between the phosphorous atoms of the nucleic acid backbone, 'set hbonds backbone'. The actual display of hydrogen bonds is controlled by the 'hbonds' command. Drawing hydrogen bonds between protein alpha carbons or nucleic acid phosphorous atoms is useful when the rest of the molecule is shown in only a schematic representation such as 'backbone', 'ribbons' or 'strands'. This parameter is similar to the RasMol 'ssbonds' parameter.
Set Hetero

Syntax:  set hetero <boolean>

The RasMol 'hetero' parameter is used to modify the 'default' behaviour of the RasMol 'select' command, i.e. the behaviour of 'select' without any parameters. When this value is 'false', the default 'select' region does not include any heterogeneous atoms (refer to the predefined set 'hetero' ). When this value is 'true', the default 'select' region may contain hetero atoms. This parameter is similar to the RasMol 'hydrogen' parameter which determines whether hydrogen atoms should be included in the default set. If both 'hetero' and 'hydrogen' are 'true', 'select' without any parameters is equivalent to 'select all'.
Set HourGlass

Syntax:  set hourglass <boolean>

Set Hydrogen

Syntax:  set hydrogen <boolean>

The RasMol 'hydrogen' parameter is used to modify the "default" behaviour of the RasMol 'select' command, i.e. the behaviour of 'select' without any parameters. When this value is 'false', the default 'select' region does not include any hydrogen, deuterium or tritium atoms (refer to the predefined set 'hydrogen' ). When this value is 'true', the default 'select' region may contain hydrogen atoms. This parameter is similar to the RasMol 'hetero' parameter which determines whether heterogeneous atoms should be included in the default set. If both 'hydrogen' and 'hetero' are 'true', 'select' without any parameters is equivalent to 'select all'.
Set Kinemage

Syntax:  set kinemage <boolean>

Set Menus

Syntax:  set menus <boolean>

The RasMol 'set menus' command enables the canvas window's menu buttons or menu bar. This command is typically only used by graphical user interfaces or to create as large an image as possible when using Microsoft Windows.
Set Monitor

Syntax:  set monitor <boolean>

Set Mouse

Syntax:  set mouse rasmol
         set mouse insight
         set mouse quanta

Set Picking

Syntax:  set picking <boolean>
         set picking off
         set picking none
         set picking ident
         set picking distance
         set picking monitor
         set picking angle
         set picking torsion
         set picking label
         set picking centre
         set picking center
         set picking coord
         set picking bond
         set picking atom
         set picking group
         set picking chain

The RasMol 'set picking' series of commands affects how a user may interact with a molecule displayed on the screen in RasMol.

Measuring Distances, Angles and Torsions: Interactive measurement of distances, angles and torsions is achieved using the commands: 'set picking distance', 'set picking monitor', 'set picking angle' and 'set picking torsion', respectively. In these modes, clicking on an atom results in it being identified on the rasmol command line. In addition every atom picked increments a modulo counter such that in distance mode, every second atom displays the distance (or distance monitor) between this atom and the previous one. In angle mode, every third atom displays the angle between the previous three atoms and in torsion mode every fourth atom displays the torsion between the last four atoms. By holding down the shift key while picking an atom, this modulo counter is not incremented and allows, for example, the distances of consecutive atoms from a fixed atom to be displayed. See the 'monitor' command for how to control the display of distance monitor lines and labels.
Set Play

Syntax:  set play.fps {<value>}

In the current release of RasMol, the play timing is not controlled by this parameter.
Set Radius

Syntax:  set radius {<value>}

The RasMol 'set radius' command is used to alter the behaviour of the RasMol 'dots' command depending upon the value of the 'solvent' parameter. When 'solvent' is 'true', the 'radius' parameter controls whether a true van der Waals' surface is generated by the 'dots' command. If the value of 'radius' is anything other than zero, that value is used as the radius of each atom instead of its true vdW value. When the value of 'solvent' is 'true', this parameter determines the 'probe sphere' (solvent) radius. The parameter may be given as an integer in rasmol units or containing a decimal point in Ångstroms. The default value of this parameter is determined by the value of 'solvent' and changing 'solvent' resets 'radius' to its new default value.
Set Record

Syntax:  set record.aps {<value>}
         set record.fps {<value>}
Syntax:  set record.dwell {<value>}

The RasMol 'set record.aps' gives the maximum on-screen velocity in Ångstroms per second in animating translations, rotations and zooms (default 10 A/second).

The RasMol 'set record.dwell' command sets the time in seconds to dwell on a change in appearance (default .5 sec).
Set ShadePower

Syntax:  set shadepower {<value>}

The 'shadepower' parameter (adopted from RasTop) determines the shade repartition (the contrast) used in rendering solid objects. This value between 0 and 100 adjusts shading on an object surface oriented along the direction to the light source. Changing the shadepower parameter does not change the maximum or the minimum values of this shading, as does changing the 'ambient' parameter. A value of 100 concentrates the light on the top of spheres, giving a highly specular, glassy rendering (see the 'specpower' parameter). A value of 0 distributes the light on the entire object.

This implementation of shadepower differs from the one in RasTop only in the choice of range (0 to 100 versus -20 to 20 in RasTop).
Set Shadow

Syntax:  set shadow <boolean>

Set SlabMode

Syntax:  set slabmode <slabmode>

The RasMol 'slabmode' parameter controls the rendering method of objects cut by the slabbing (z-clipping) plane. Valid slabmode parameters are "reject", "half", "hollow", "solid" and "section".
Set Solvent

Syntax:  set solvent <boolean>

The RasMol 'set solvent' command is used to control the behaviour of the RasMol 'dots' command. Depending upon the value of the 'solvent' parameter, the 'dots' command either generates a van der Waals' or a solvent accessible surface around the currently selected set of atoms. Changing this parameter automatically resets the value of the RasMol 'radius' parameter. The command 'set solvent false', the default value, indicates that a van der Waals' surface should be generated and resets the value of 'radius' to zero. The command 'set solvent true' indicates that a 'Connolly' or 'Richards' solvent accessible surface should be drawn and sets the 'radius' parameter, the solvent radius, to 1.2 Ångstroms (or 300 RasMol units).
Set Specular

Syntax:  set specular <boolean>

The RasMol 'set specular' command enables and disables the display of specular highlights on solid objects drawn by RasMol. Specular highlights appear as white reflections of the light source on the surface of the object. The current RasMol implementation uses an approximation function to generate this highlight.
Set SpecPower

Syntax:  set specpower {<value>}

Set SSBonds

Syntax:  set ssbonds backbone
         set ssbonds sidechain

The RasMol 'ssbonds' parameter determines whether disulphide bridges are drawn between the sulphur atoms in the sidechain (the default) or between the alpha carbon atoms in the backbone of the cysteines residues. The actual display of disulphide bridges is controlled by the 'ssbonds' command. Drawing disulphide bridges between alpha carbons is useful when the rest of the protein is shown in only a schematic representation such as 'backbone', 'ribbons' or 'strands'. This parameter is similar to the RasMol 'hbonds' parameter.
Set Stereo

Syntax:  set stereo <boolean>
         set stereo [-] <number&gt

The RasMol 'set stereo' parameter controls the separation between the left and right images. Turning stereo on and off doesn't reposition the centre of the molecule.
Set Strands

Syntax:  set strands {<value>}

Set Transparent

Syntax:  set transparent <boolean>

Set UnitCell

Syntax:  set unitcell <boolean>

The RasMol 'unitcell' parameter controls the display of the crystallographic unit cell on the current display. The crystal cell is only enabled if the appropriate crystal symmetry information is contained in the PDB, CIF or mmCIF data file. The RasMol command 'show symmetry' display details of the crystal's space group and unit cell axes. The 'set unitcell' command is similar to the commands 'set axes' and 'set boundbox' that display orthogonal coordinate axes and the bounding box, respectively.
Set VectPS

Syntax:  set vectps <boolean>

Set Write

Syntax:  set write <boolean>

The RasMol 'write' parameter controls the use of the 'save' and 'write' commands within scripts, but it may only be executed from the command line. By default, this value is 'false', prohibiting the generation of files in any scripts executed at start-up (such as those launched from a WWW browser). However, animators may start up RasMol interactively: type 'set write on' and then execute a script to generate each frame using the source command.

Atom Expressions
RasMol atom expressions uniquely identify an arbitrary group of atoms within a molecule. Atom expressions are composed of either primitive expressions, predefined sets, comparison operators, 'within' expressions, or logical (boolean) combinations of the above expression types.
The logical operators allow complex queries to be constructed out of simpler ones using the standard boolean connectives 'and', 'or' and 'not'. These may be abbreviated by the symbols "&", "|" and "!", respectively. Parentheses (brackets) may be used to alter the precedence of the operators. For convenience, a comma may also be used for boolean disjunction.

The atom expression is evaluated for each atom, hence 'protein and backbone' selects protein backbone atoms, not the protein and [nucleic] acid backbone atoms!

Examples:backbone and not helixwithin( 8.0, ser70 )not (hydrogen or hetero)not *.FE and hetero8, 12, 16, 20-28arg, his, lys
Example Expressions
The following table gives some useful examples of RasMol atom expressions.

Expression Interpretation * All atoms cys Atoms in cysteines hoh Atoms in heterogeneous water molecules as? Atoms in either asparagine or aspartic acid *120 Atoms at residue 120 of all chains *p Atoms in chain P *.n? Nitrogen atoms cys.sg Sulphur atoms in cysteine residues ser70.c? Carbon atoms in serine-70 hem*p.fe Iron atoms in the Heme groups of chain P *.*;A All atoms in alternate conformation A */4 All atoms in model 4
Primitive Expressions
The second type of primitive expression specifies a sequence of fields that must match for a given atom. The first part specifies a residue (or group of residues) and an optional second part specifies the atoms within those residues. The first part consists of a residue name, optionally followed by a residue number and/or chain identifier.

A residue name typically consists of up to three alphabetic characters, which are case insensitive. Hence the primitive expressions 'SER' and 'ser' are equivalent, identifying all serine residues. Residue names that contain non-alphabetic characters, such as sulphate groups, may be delimited using square brackets, i.e. '[SO4]'.

The residue number is intended to be the residue's position in the macromolecule sequence, but negative sequence numbers, gaps in numbering, or even reverse numbering are permitted in the PDB format. Care must be taken when specifying both residue name and number. If the group at the specified position isn't the specified residue then no atoms are selected.

The second part consists of a period character followed by an atom name. An atom name may be up to four alphabetic or numeric characters. An optional semicolon followed by an alternate conformation identifier may be appended. An optional slash followed by a model number may also be appended.

An atom name may be up to four alphabetic or numeric characters.

An asterisk may be used as a wild card for a whole field and a question mark as a single character wildcard.
Comparison Operators
Parts of a molecule may also be distinguished using equality, inequality and ordering operators on their properties. The format of such comparison expression is a property name, followed by a comparison operator and then an integer value.

The atom properties that may be used in RasMol are 'atomno' for the atom serial number, 'elemno' for the atom's atomic number (element), 'resno' for the residue number, 'radius' for the spacefill radius in RasMol units (or zero if not represented as a sphere) and 'temperature' for the PDB isotropic temperature value.

Examples:    resno < 23
             temperature >= 900
             atomno == 487

Within Expressions Predefined Sets
RasMol atom expressions may contain predefined sets. These sets are single keywords that represent portions of a molecule of interest. Predefined sets are often abbreviations of primitive atom expressions. In some cases the use of predefined sets allows selection of areas of a molecule that could not otherwise be distinguished. A list of the currently predefined sets is given below. In addition to the sets listed here, RasMol also treats element names (and their plurals) as predefined sets containing all atoms of that element type, i.e. the command 'select oxygen' is equivalent to the command 'select elemno=8'.

AT Acidic AcyclicAliphatic Alpha AminoAromatic Backbone BasicBonded Buried CGCharged Cyclic CystineHelix Hetero HydrogenHydrophobic Ions LargeLigand Medium NeutralNucleic Polar ProteinPurine Pyrimidine SelectedSheet Sidechain SmallSolvent Surface TurnWater
AT Set Acidic Set
The set of acidic amino acids. These are the residue types Asp and Glu. All amino acids are classified as either 'acidic', 'basic' 'or' 'neutral'. This set is equivalent to the RasMol atom expressions "asp, glu" and "amino and not (basic or neutral)".
Acyclic Set Aliphatic Set
This set contains the aliphatic amino acids. These are the amino acids Ala, Gly, Ile, Leu and Val. This set is equivalent to the RasMol atom expression "ala, gly, ile, leu, val".
Alpha Set Amino Set
This set contains all the atoms contained in amino acid residues. This is useful for distinguishing the protein from the nucleic acid and heterogeneous atoms in the current molecule database.
Aromatic Set Backbone Set
This set contains the four atoms of each amino acid that form the polypeptide N-C-C-O backbone of proteins, and the atoms of the sugar phosphate backbone of nucleic acids. Use the RasMol predefined sets 'protein' and 'nucleic' to distinguish between the two forms of backbone. Atoms in nucleic acids and proteins are either 'backbone' or 'sidechain'. This set is equivalent to the RasMol expression "(protein or nucleic) and not sidechain".
Basic Set
The set of basic amino acids. These are the residue types Arg, His and Lys. All amino acids are classified as either 'acidic', 'basic' or 'neutral'. This set is equivalent to the RasMol atom expressions "arg, his, lys" and "amino and not (acidic or neutral)".
Bonded Set
This set contain all the atoms in the current molecule database that are bonded to at least one other atom.
Buried Set CG Set
This set contains the atoms in the complementary nucleotides cytidine and guanosine (C and G, respectively). All nucleotides are classified as either the set 'at' or the set 'cg' This set is equivalent to the RasMol atom expressions "c,g" and "nucleic and not at".
Charged Set
This set contains the charged amino acids. These are the amino acids that are either 'acidic' or 'basic'. Amino acids are classified as being either 'charged' or 'neutral'. This set is equivalent to the RasMol atom expressions "acidic or basic" and "amino and not neutral".
Cyclic Set
The set of atoms in amino acids containing a cycle or rings. All amino acids are classified as either 'cyclic' or 'acyclic'. This set consists of the amino acids His, Phe, Pro, Trp and Tyr. The members of the predefined set 'aromatic' are members of this set. The only cyclic but non-aromatic amino acid is proline. This set is equivalent to the RasMol atom expressions "his, phe, pro, trp, tyr" and "aromatic or pro" and "amino and not acyclic".
Cystine Set
This set contains the atoms of cysteine residues that form part of a disulphide bridge, i.e. half cystines. RasMol automatically determines disulphide bridges, if neither the predefined set 'cystine' nor the RasMol 'ssbonds' command have been used since the molecule was loaded. The set of free cysteines may be determined using the RasMol atom expression "cys and not cystine".
Helix Set Hetero Set
This set contains all the heterogeneous atoms in the molecule. These are the atoms described by HETATM entries in the PDB file. These typically contain water, cofactors and other solvents and ligands. All 'hetero' atoms are classified as either 'ligand' or 'solvent' atoms. These heterogeneous 'solvent' atoms are further classified as either 'water' or 'ions'.
Hydrogen Set
This predefined set contains all the hydrogen, deuterium and tritium atoms of the current molecule. This predefined set is equivalent to the RasMol atom expression "elemno=1".
Hydrophobic Set Ions Set Large Set Ligand Set
This set contains all the heterogeneous cofactor and ligand moieties that are contained in the current molecule data file. This set is defined to be all 'hetero' atoms that are not 'solvent' atoms. Hence this set is equivalent to the RasMol atom expression "hetero and not solvent".
Medium Set
All amino acids are classified as either 'small', 'medium' or 'large'. This set is equivalent to the RasMol atom expression "amino and not (large or small)".
Neutral Set Nucleic Set Polar Set Protein Set Purine Set Pyrimidine Set
The set of pyrimidine nucleotides. These are the bases cytidine and thymidine (C and T, respectively). All nucleotides are either 'purines' or 'pyrimidines'. This set is equivalent to the RasMol atom expressions "c,t" and "nucleic and not purine".
Selected Set
This set contains the set of atoms in the currently selected region. The currently selected region is defined by the preceding 'select' or 'restrict' command and not the atom expression containing the 'selected' keyword.
Sheet Set Sidechain Set
This set contains the functional sidechains of any amino acids and the base of each nucleotide. These are the atoms not part of the polypeptide N-C-C-O backbone of proteins or the sugar phosphate backbone of nucleic acids. Use the RasMol predefined sets 'protein' and 'nucleic' to distinguish between the two forms of sidechain. Atoms in nucleic acids and proteins are either 'backbone' or 'sidechain'. This set is equivalent to the RasMol expression "(protein or nucleic) and not backbone".
Small Set
All amino acids are classified as either 'small', 'medium' or 'large'. This set is equivalent to the RasMol atom expression "amino and not (medium or large)".
Solvent Set
This set contains the solvent atoms in the molecule coordinate file. These are the heterogeneous water molecules, phosphate and sulphate ions. All 'hetero' atoms are classified as either 'ligand' or 'solvent' atoms. All 'solvent' atoms are classified as either 'water' or 'ions'. This set is equivalent to the RasMol atom expressions "hetero and not ligand" and "water or ions".
Surface Set
This set contains the atoms in those amino acids that tend (prefer) to be on the surface of proteins, in contact with solvent molecules. This set refers to the amino acids preference and not the actual solvent accessibility for the current protein. All amino acids are classified as either 'surface' or 'buried'. This set is equivalent to the RasMol atom expression "amino and not buried".
Turn Set Water Set
This set contains all the heterogeneous water molecules in the current database. A large number of water molecules are sometimes associated with protein and nucleic acid structures determined by X-ray crystallography. These atoms tend to clutter an image. All 'hetero' atoms are classified as either 'ligand' or 'solvent' atoms. The 'solvent' atoms are further classified as either 'water' or 'ions'.
Set Summary
The table below summarises RasMol's classification of the common amino acids.

Colour Schemes
The RasMol 'colour' command allows different objects (such as atoms, bonds and ribbon segments) to be given a specified colour. Typically this colour is either a RasMol predefined colour name or an RGB triple. Additionally RasMol also supports 'alt', 'amino', 'chain', 'charge', 'cpk', 'group', 'model', 'shapely', 'structure', 'temperature' or 'user' colour schemes for atoms, and 'hbond type' colour scheme for hydrogen bonds and 'electrostatic potential' colour scheme for dot surfaces. The 24 currently predefined colour names are listed below with their corresponding RGB triplet and hexadecimal value.
Note that the rendering of the hexadecimal-equivalent colours shown here will depend on many factors. Thus, they only approximate how RasMol will render the RGB colours on your computer.

If you frequently wish to use a colour not predefined, you can write a one-line script. For example, if you make the file 'grey.col' containing the line, 'colour [180,180,180] #grey', then the command 'script grey.col' colours the currently selected atom set grey.
Alt Colours
The RasMol 'alt' (Alternate Conformer) colour scheme codes the base structure with one colour and applies a limited number of colours to each alternate conformer. In a RasMol built for 8-bit colour systems, 4 colours are allowed for alternate conformers. Otherwise, 8 colours are available.
Amino Colours Chain Colours Charge Colours
The RasMol 'charge' colour scheme colour codes each atom according to the charge value stored in the input file (or beta factor field of PDB files). High values are coloured in blue (positive) and lower values coloured in red (negative). Rather than use a fixed scale this scheme determines the maximum and minimum values of the charge/temperature field and interpolates from red to blue appropriately. Hence, green cannot be assumed to be 'no net charge' charge.
CPK Colours
The RasMol 'cpk' colour scheme is based upon the colours of the popular plastic spacefilling models which were developed by Corey, Pauling and later improved by Kultun. This colour scheme colours 'atom' objects by the atom (element) type. This is the scheme conventionally used by chemists. The assignment of the most commonly used element types to colours is given below.

Note that except for green, white, blue, andorange, these colour names are not the ones specified as " Predefined colours" in RasMol; thus, they can only be specified on the command line as RGB triplets.

In the CPK colouring scheme, RasMol will attempt to assign a colour to each element from the periodic table from a list of 16 colours (the colour codes listed are to help in understanding the mapping and are not used by RasMol):

In the CPKnew colouring scheme, RasMol uses brighter colours:

1a

2a

3b

4b

5b

6b

7b

8

1b

2b

3a

4a

5a

6a

7a

0

H
1 W

He
2 Pk

Li
3 FB

Be
4 DP

B
5 G

C
6 LG

N
7 SB

O
8 R

F
9 Go

Ne
10 DP

Na
11 Bl

Mg
12 FG

Al
13 DG

Si
14 Go

P
15 Or

S
16 Y

Cl
17 G

Ar
18 DP

Fr
87 DP

Ra
88 DP

Ac
89 DP

For X-ray crystallographic models of proteins and nucleic acids ( i.e. without hydrogens) the display can be 'brightened' by converting the O, C, and N atoms from the RasMol defaultcpk colors to "true red, white and blue" using RasMol's predefined colour scheme. Use the following sequence of commands to try it:

 select all select oxygen colour red select carbon colour white select nitrogen colour blue select all
Extension of this idea to other atoms and colour schemes is straightforward. Group Colours
If a chain has a large number of heterogeneous molecules associated with it, the macromolecule may not be drawn in the full range of the spectrum. When RasMol performs group colouring it decides the range of colours it uses from the residue numbering given in the PDB file. Hence the lowest residue number is displayed in blue and the highest residue number is displayed as red. Unfortunately, if a PDB file contains a large number of heteroatoms, such as water molecules, that occupy the high residue numbers, the protein is displayed in the blue-green end of the spectrum and the waters in the yellow-red end of the spectrum. This is aggravated by there typically being many more water molecules than amino acid residues. The solution to this problem is to use the command 'set hetero off' before applying the group colour scheme. This can also be achieved by toggling 'Hetero Atoms' on the 'Options' menu before selecting 'Group' on the 'Colour' menu. This command instructs RasMol to only use non-hetero residues in the group colour scaling.
NMR Model Colours
The RasMol 'model' colour scheme codes each NMR model with a distinct colour. The NMR model number is taken as a numeric value. High values are coloured in blue and lower values coloured in red. Rather than use a fixed scale this scheme determines the maximum value of the NMR model number and interpolates from red to blue appropriately.
Shapely Colours
The RasMol 'shapely' colour scheme colour codes residues by amino acid property. This scheme is based upon Bob Fletterick's "Shapely Models". Each amino acid and nucleic acid residue is given a unique colour. The 'shapely' colour scheme is used by David Bacon's Raster3D program. This colour scheme is similar to the 'amino' colour scheme.
Structure Colours Temperature Colours
The RasMol 'temperature' colour scheme colour codes each atom according to the anisotropic temperature (beta) value stored in the PDB file. Typically this gives a measure of the mobility/uncertainty of a given atom's position. High values are coloured in warmer (red) colours and lower values in colder (blue) colours. This feature is often used to associate a "scale" value [such as amino acid variability in viral mutants] with each atom in a PDB file, and colour the molecule appropriately.
User Colours
The RasMol 'user' colour scheme allows RasMol to use the colour scheme stored in the PDB file. The colours for each atom are stored in COLO records placed in the PDB data file. This convention was introduced by David Bacon's Raster3D program.
HBond Type Colours

      Offset    Colour    Triple
        +2      white     [255,255,255]
        +3      magenta   [255,0,255]
        +4      red       [255,0,0]
        +5      orange    [255,165,0]
        -3      cyan      [0,255,255]
        -4      green     [0,255,0]
      default   yellow    [255,255,0]

Potential Colours

     25 < V          red       [255,0,0]
     10 < V <  25    orange    [255,165,0]
      3 < V <  10    yellow    [255,255,0]
      0 < V <   3    green     [0,255,0]
     -3 < V <   0    cyan      [0,255,255]
    -10 < V <   3    blue      [0,0,255]
    -25 < V < -10    purple    [160,32,240]
          V < -25    white     [255,255,255]

Amino Acid Codes
The following table lists the names, single letter and three letter codes of each of the amino acids.
Booleans
A boolean parameter is a truth value. Valid boolean values are 'true' and 'false', and their synonyms 'on' and 'off'. Boolean parameters are commonly used by RasMol to either enable or disable a representation or option.
File Formats
Protein Data Bank Files

If you do not have the PDB documentation, you may find the following summary of the PDB file format useful. The Protein Data Bank is a computer-based archival database for macromolecular structures. The database was established in 1971 by Brookhaven National Laboratory, Upton, New York, as a public domain repository for resolved crystallographic structures. The Bank uses a uniform format to store atomic coordinates and partial bond connectivities as derived from crystallographic studies. In 1999 the Protein Data Bank moved to the Research Collaboratory for Structural Biology.

PDB file entries consist of records of 80 characters each. Using the punched card analogy, columns 1 to 6 contain a record-type identifier, the columns 7 to 70 contain data. In older entries, columns 71 to 80 are normally blank, but may contain sequence information added by library management programs. In new entries conforming to the 1996 PDB format, there is other information in those columns. The first four characters of the record identifier are sufficient to identify the type of record uniquely, and the syntax of each record is independent of the order of records within any entry for a particular macromolecule.

The only record types that are of major interest to the RasMol program are the ATOM and HETATM records which describe the position of each atom. ATOM/HETATM records contain standard atom names and residue abbreviations, along with sequence identifiers, coordinates in Ångstrom units, occupancies and thermal motion factors. The exact details are given below as a FORTRAN format statement. The "fmt" column indicates use of the field in all PDB formats, in the 1992 and earlier formats or in the 1996 and later formats.

FORMAT(6A1,I5,1X,A4,A1,A3,1X,A1,I4,A1,3X,3F8.3,2F6.2,1X,I3,2X,A4,2A2)

Residues occur in order starting from the N-terminal residue for proteins and 5'-terminus for nucleic acids. If the residue sequence is known, certain atom serial numbers may be omitted to allow for future insertion of any missing atoms. Within each residue, atoms are ordered in a standard manner, starting with the backbone (N-C-C-O for proteins) and proceeding in increasing remoteness from the alpha carbon, along the side chain.

HETATM records are used to define post-translational modifications and cofactors associated with the main molecule. TER records are interpreted as breaks in the main molecule's backbone.

If present, RasMol also inspects HEADER, COMPND, HELIX, SHEET, TURN, CONECT, CRYST1, SCALE, MODEL, ENDMDL, EXPDTA and END records. Information such as the name, database code, revision date and classification of the molecule are extracted from HEADER and COMPND records, initial secondary structure assignments are taken from HELIX, SHEET and TURN records, and the end of the file may be indicated by an END record.
RasMol Interpretation of PDB fields
Atoms located at 9999.000, 9999.000, 9999.000 are assumed to be Insight pseudo atoms and are ignored by RasMol. Atom names beginning ' Q' are also assumed to be pseudo atoms or position markers.

When a data file contains an NMR structure, multiple conformations may be placed in a single PDB file delimited by pairs of MODEL and ENDMDL records. RasMol displays all the NMR models contained in the file.

Residue names "CSH", "CYH" and "CSM" are considered pseudonyms for cysteine "CYS". Residue names "WAT", "H20", "SOL" and "TIP" are considered pseudonyms for water "HOH". The residue name "D20" is consider heavy water "DOD". The residue name "SUL" is considered a sulphate ion "SO4". The residue name "CPR" is considered to be cis-proline and is translated as "PRO". The residue name "TRY" is considered a pseudonym for tryptophan "TRP".

RasMol uses the HETATM fields to define the sets hetero, water, solvent and ligand. Any group with the name "HOH", "DOD", "SO4" or "PO4" (or aliased to one of these names by the preceding rules) is considered a solvent and is considered to be defined by a HETATM field.

RasMol only respects CONECT connectivity records in PDB files containing fewer than 256 atoms. This is explained in more detail in the section on determining molecule connectivity. CONECT records that define a bond more than once are interpreted as specifying the bond order of that bond, i.e. a bond specified twice is a double bond and a bond specified three (or more) times is a triple bond. This is not a standard PDB feature.
PDB Colour Scheme Specification
RasMol also accepts the supplementary COLO record type in the PDB files. This record format was introduced by David Bacon's Raster3D program for specifying the colour scheme to be used when rendering the molecule. This extension is not currently supported by the PDB. The COLO record has the same basic record type as the ATOM and HETATM records described above.

Colours are assigned to atoms using a matching process. The Mask field is used in the matching process as follows. First RasMol reads in and remembers all the ATOM, HETATM and COLO records in input order. When the user-defined ('User') colour scheme is selected, RasMol goes through each remembered ATOM/HETATM record in turn, and searches for a COLO record that matches in all of columns 7 through 30. The first such COLO record to be found determines the colour and radius of the atom.

Column

Content

1-6

'COLOR' or 'COLOUR'

7-30

Mask (described below)

31-38

Red component

39-46

Green component

47-54

Blue component

55-60

Sphere radius in Ångstroms

61-70

Comments

Note that the Red, Green and Blue components are in the same positions as the X, Y, and Z components of an ATOM or HETA record, and the van der Waals radius goes in the place of the Occupancy. The Red, Green and Blue components must all be in the range 0 to 1.

In order that one COLO record can provide colour and radius specifications for more than one atom (e.g. based on residue, atom type, or any other criterion for which labels can be given somewhere in columns 7 through 30), a 'don't-care' character, the hash mark "#" (number or sharp sign) is used. This character, when found in a COLO record, matches any character in the corresponding column in a ATOM/HETATM record. All other characters must match identically to count as a match. As an extension to the specification, any atom that fails to match a COLO record is displayed in white.
Multiple NMR Models CIF and mmCIF Format Files
CIF is the IUCr standard for presentation of small molecules and mmCIF is intended as the replacement for the fixed-field PDB format for presentation of macromolecular structures. RasMol can accept data sets in either format.

There are many useful sites on the World Wide Web where information tools and software related to CIF, mmCIF and the PDB can be found. The following are good starting points for exploration:

The International Union of Crystallography (IUCr) provides access to software, dictionaries, policy statements and documentation relating to CIF and mmCIF at: IUCr, Chester, England (www.iucr.org/iucr-top/cif/) with many mirror sites.

The Nucleic Acid Database Project provides access to its entries, software and documentation, with an mmCIF page giving access to the dictionary and mmCIF software tools at Rutgers University, New Jersey, USA (http://ndbserver.rutgers.edu/NDB/mmcif) with many mirror sites.

This version of RasMol restricts CIF or mmCIF tag values to essentially the same conventions as are used for the fixed-field PDB format. Thus chain identifiers and alternate conformation identifiers are limited to a single character, atom names are limited to 4 characters, etc. RasMol interprets the following CIF and mmCIF tags:
A search is made through multiple data blocks for the desired tags, so a single dataset may be composed from multiple data blocks, but multiple data sets may not be stacked in the same file. Machine-Specific Support
In the following sections, support for 'Monochrome X-Windows', 'Tcl/Tk IPC', 'UNIX sockets based IPC', 'Compiling RasWin with Borland and MetroWerks' are described.
Monochrome X-Windows Support
RasMol supports the many monochrome UNIX workstations typically found in academia, such as low-end SUN workstations and NCD X-terminals. The X11 version of RasMol (when compiled in 8 bit mode) now detects black and white X-Windows displays and enables dithering automatically. The use of run-time error diffusion dithering means that all display modes of RasMol are available when in monochrome mode. For best results, users should experiment with the set ambient command to ensure the maximum contrast in resulting images.
Tcl/Tk IPC support
Version 4 of Tk graphics library changed the protocol used to communicate between Tk applications. RasMol version 2.6 was modified such that it could communicate with both this new protocol and the previous version 3 protocol supported by RasMol v2.5. Although Tcl/Tk 3.x applications may only communicate with other 3.x applications and Tcl/Tk 4.x applications with other 4.x applications, these changes allow RasMol to communicate between processes with both protocols (potentially concurrently).
UNIX sockets based IPC Compiling RasWin with Borland and MetroWerks
A number of changes were made to the source code in the transition from version 2.5 to 2.6 to allow the Microsoft Windows version of RasMol to compile using the Borland C/C++ compiler. These fixes include name changes for the standard library and special code to avoid a bug in _fmemset. Additional changes were made in the transition from 2.6 to 2.7 to allow compilation with the MetroWerks compilers.
Bibliography
Molecular Graphics

[1] Nelson Max, "Computer Representation of Molecular Surfaces", IEEE Computer Graphics and Applications, pp.21-29, August 1983.

[2] Arthur M. Lesk, "Protein Architecture: A Practical Approach", IRL Press Publishers, 1991.

Molecular Graphics Programs

[3] Per J. Kraulis, "MOLSCRIPT: A Program to Produce both Detailed and Schematic Plots of Protein Structures", Journal of Applied Crystallography, Vol.24, pp.946-950, 1991.

[4] David Bacon and Wayne F. Anderson, "A Fast Algorithm for Rendering Space-Filling Molecule Pictures", Journal of Molecular Graphics, Vol.6, No.4, pp.219-220, December 1988.

[5] David C. Richardson and Jane S. Richardson, "The Kinemage: A tool for Scientific Communication", Protein Science, Vol.1, No.1,pp.3-9, January 1992.

[6] Mike Carson, "RIBBONS 2.0", Journal of Applied Crystallography, Vol.24, pp.958-961, 1991.

[7] Conrad C. Huang, Eric F. Pettersen, Teri E. Klein, Thomas E. Ferrin and Robert Langridge, "Conic: A Fast Renderer for Space-Filling Molecules with Shadows", Journal of Molecular Graphics, Vol.9, No.4, pp.230-236, December 1991.

Molecular Biology Algorithms

[8] Wolfgang Kabsch and Christian Sander, "Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features", Biopolymers, Vol.22, pp.2577-2637, 1983.

[9] Michael L. Connolly, "Solvent-Accessible Surfaces of Proteins and Nucleic Acids", Science, Vol.221, No.4612, pp.709-713, August 1983.

[10] Khaled Belhadj-Mostefa, Ron Poet and E. James Milner-White, "Displaying Inter-Main Chain Hydrogen Bond Patterns in Proteins", Journal of Molecular Graphics, Vol.9, No.3, pp.194-197, September 1991.

[11] Mike Carson, "Ribbon Models of Macromolecules", Journal of Molecular Graphics, Vol.5, No.2, pp.103-106, June 1987.

[12] Mike Carson and Charles E. Bugg, "Algorithm for Ribbon Models of Proteins", Journal of Molecular Graphics, Vol.4, No.2, pp.121-122, June 1986.

[13] H. Iijima, J. B. Dunbar Jr. and G. Marshall, "Calibration of Effective van der Waals Atomic Contact Radii for Proteins and Peptides", Proteins: Structure, Functions and Genetics, Vol.2, pp.330-339,1987.

Graphics Algorithms

[14] J. Foley, A. van Dam, S. Feiner and J. Hughes, "Computer Graphics: Principles and Practice", 2nd Edition, Addison Wesley Publishers, 1990.

[15] J. Cleary and G. Wyvill, "Analysis of an Algorithm for Fast Ray Tracing using Uniform Space Subdivision", The Visual Computer, Vol.4, pp.65-83, 1988.

[16] Thomas Porter,"Spherical Shading", Computer Graphics Vol.12, ACM SIGGRAPH, pp.282-285, 1978.

[17] Jean-Michel Cense, "Exact Visibility Calculation for Space-Filling Molecular Models", Journal of Molecular Graphics, Vol.9, No.3, pp.191-193, September 1991.

[18] Chris Schafmeister, "Fast Algorithm for Generating CPK Images on Graphics Workstations", Journal of Molecular Graphics, Vol.8, No.4, pp.201-206, December 1990.

[19] Bruce A. Johnson, "MSURF: A Rapid and General Program for the Representation of Molecular Surfaces", Journal of Molecular Graphics, Vol.5, No.3, pp.167-169, September 1987.

File Formats

[20] Frances C. Bernstein et al., "The Protein Data Bank: A Computer-Based Archival File for Macromolecular Structures", Journal of Molecular Biology, Vol.112, pp.535-542, 1977.

[21] Arthur Dalby, James G. Nourse, W. Douglas Hounshell, Ann K. I. Gushurst, David L. Grier, Burton A. Leland and John Laufer, "Description of Several Chemical File Formats Used by Computer Programs Developed at Molecular Design Limited", Journal of Chemical Information and Computer Sciences, Vol.32, No.3, pp.244-255, 1992.

[22] Adobe Systems Inc., "PostScript Language Reference Manual", Addison-Wesley Publishers, Reading, Mass., 1985.

[23] Philip E. Bourne et al., "The Macromolecular Crystallographic Information File (mmCIF)", Meth. Enzymol. (1997) 277, 571-590.

[24] Sydney R. Hall, "The STAR File: a New Format for Electronic Data Transfer and Archiving", Journal of Chemical Information and Computer Sciences, Vol. 31, 326-333, 1991.

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Updated 17 April 2009.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
yaya@bernstein-plus-sons.com

# data[].attributes.attachment_link.description
To start RasMol on the Macintosh, double click on the RasMol icon using Finder. When RasMol first starts, the program displays two windows, the top window (with the black background) is the graphics or canvas window and the window underneath it (with the white background) is the RasMol command line window.

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Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

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Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

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- 알고 싶은 유전자 또는 유전자의 위치를 검색

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예) UCSC, 게놈의 성질과 기능, 다른 종과의 비교

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예) UCSC, 게놈의 성질과 기능, 다른 종과의 비교

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예) 육탄당 인산화 효소-1 (hexokinase 1, HK 1), track