The ‘selected’ option indicates that the mask is to be created from the currently selected atoms. The display window may be resized at any point during the session. If no parameters are given, RasMol determines which algorithm to use based on the number of atoms in the input file. A single question mark may also be used to abbreviate the keyword “help”. The 24 currently predefined colour names are listed below with their corresponding RGB triplet and hexadecimal value.

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All nucleotides are either ‘ purines ‘ or ‘ pyrimidines ‘.

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.

Changing this parameter automatically resets the value of the RasMol ‘ radius ‘ parameter. In order to leave RasMol, the user can type the command quit rasmol 2.7.5 exit at the RasMol prompt, and the program will return the user to the familiar unix prompt.

2.5 Department of Energy, the U. When stereo is turned on, the image is not properly recentred. The place in the name to be replaced with the playback frame start time in milliseconds is marked by the characters “ssssss” with an rasmol 2.7.5 number of digits.

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 rrasmol in ‘false colour’.

Jean-Pierre Demailly provided French translations of menus and messages in January The ” record until ” command allows an upper limit to be set on recording time in seconds. All bonds rasmol 2.7.5 for rotation are remembered so that they can be properly reported when writing a script, but only the most 2.7.5 selected bond may be actively rotated.


Rasmok program only draws those portions of the molecule that are further from the viewer than the slabbing plane. The place in the name at which to look for the playback frame start time in milliseconds is marked by the characters “ssssss” with an appropriate number rasmol 2.7.5 digits.

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The ‘ cartoon ‘ command represents the currently selected residues as a deep ribbon with width specified by the command’s argument. If both ‘ hetero ‘ and ‘ hydrogen ‘ are ‘ true ‘, ‘ select ‘ without any parameters is equivalent to ‘ select all ‘. However, the current implementation of RasMol incorrectly cartoons spheres that are intersected by more than one other sphere. Overall, RasMol makes a good impression; however, what struck us during rasmol 2.7.5 testing was the lack of a zoom function, which seems a bit odd for a viewer.

It is also possible to specify the initial graphics window size or position or both rasmol 2.7.5 size and the position with the options ‘-height nnnn ‘, ‘-width nnnn ‘, ‘-xpos nnnn ‘ and ‘-ypos nnnn ‘. Measuring Distances, Angles and Torsions: 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.

For proteins, each amino acid is numbered consecutively from the N terminus to the C terminus. A residue name typically consists of up to three alphabetic characters, which are case insensitive.

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A value of concentrates the light on the top of spheres, giving a highly specular, glassy rendering see the ‘ specpower ‘ parameter.

The screen is the default medium and is, by default, on. This value is the radius in pixels of cylinders used to form the strokes. It controls the percentage intensity of the darkest shade of an object. When this value is ‘ false ‘, the rrasmol ‘ select ‘ region does not include any hydrogen, deuterium or tritium atoms refer to the rasmol 2.7.5 raemol ‘ hydrogen ‘. Medium Set All amino acids are classified as either ‘ small ‘, ‘ medium ‘ or ‘ large ‘.


The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a rasmok of rasmol 2.7.5 schemes and molecule representations. The command ‘ hbonds on ‘ displays the selected ‘bonds’ as dotted lines, and the ‘ hbonds off ‘ turns off rasmol 2.7.5 display.

Distance monitors may also be added to a molecule interactively with the mouse, using the ‘ set picking monitor ‘ command. By default, radmol no string is given as a parameter, RasMol uses labels appropriate for the current molecule.


An optional slash followed by a model number raxmol also rasoml appended. These commands are very memory intensive and may not work on machines with limited memory. The ribbon is composed of a number rasmol 2.7.5 strands that run parallel to one another along the peptide plane of each residue. This is particularly useful for running RasMol as a background or batch process.

Water Set This set contains all the heterogeneous water molecules in the current database.