The RasMol backbone command permits the representation of a polypeptide backbone as a series of bonds connecting. 10 Jun We’ll assume that you know how to use RasMol’s pull-down menus, the mouse, and RasMol’s command-line interface. We won’t explain the. 27 Apr In Chime, commands are typed into one slot, and Chime’s replies (“messages”) come back into a different slot or box. In contrast, in RasMol.

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The following formats are useful for further processing: This has the effect of simply rescaling the image displayed rasmol commands the canvas. The colour of each label may be changed using the ‘ colour label ‘ command.

rasmol commands The ‘ background ‘ command is synonymous with the RasMol ‘ set background ‘ command. The ‘ set unitcell ‘ command is similar to the commands rasmol commands set axes ‘ and ‘ set boundbox ‘ that display orthogonal coordinate axes and the bounding box, respectively.

The map spread is set to two thirds of the rasmol commands resolution. The mouse may also rasmol commands used to toggle the display of an atom label on a given atom.

If a non-zero spread has ccommands given the radius of the atom is multiplied by the spread to find the standard deviation. Rasmol commands no parameter is specified, the ‘ echo ‘ command displays a blank line.

Use rasmol commands copyright notice does not imply publication or disclosure. When this value is ‘ false ‘, the default ‘ select ‘ region does not include any hydrogen, deuterium or tritium atoms refer to the predefined set ‘ hydrogen ‘. The parameter of a ‘ select ‘ command is a RasMol expression that is evaluated for every atom of the current molecule. The colour of disulphide bonds may be changed using the ‘ colour ssbonds ‘ command.

Commonly Used RasMol Commands

If the molecule rasmol commands no bonds i. Hydrogen bonds are represented as either dotted lines or cylinders between the donor and acceptor residues. The command ‘ dots on ‘ deletes any existing dot surface and generates a dots surface around the currently selected atom set with a default dot density of Bonds may be coloured using the ‘ colour bonds ‘ command.

The width of the strokes in the displayed text may be rasmol commands using the ‘ set fontstroke ‘ command. Predefined sets are often abbreviations of primitive atom expressions. Non-zero values are rasmol commands to allow for more artistic atom labels for publication at the expense of extra time in rendering the image. Map rasmol commands may be coloured by specific color of by nearest atom.

Nucleic Set The set of all atoms rasmol commands nucleic acids, which consists of the four nucleotide bases adenosine, cytidine, guanosine and thymidine A, C, G and T, respectively.

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. When the ‘ set picking chain ‘ command is given, picking any atom will cause selection of all atoms which agree in chain identifier with rasmol commands picked atom. The bounding box is orthogonal to the data file’s original coordinate axes.

Bernstein and Frances C. Parentheses brackets may be used to alter the precedence of the operators.

Guide to “Movie” Script Creation for RasMol and Chime

The default width of protein alpha helices and beta sheets is 1. This may be enabled and disabled using the ‘ set cartoons ‘ command. Rasmol commands atoms tend rasmol commands clutter an image. A list of the currently predefined sets is given below.

This value corresponds to the height of the displayed character in pixels. Rasmol commands to version 2.

RasMol V Manual

If given rasmol commands the second form, the envelope of the positions of the center of the probe is shown the solvent accessible surface. This command should not be mistaken for commabds RasMol ‘ zap ‘ command which deletes the currently stored molecule, returning the program to its initial state.

The ‘ set mouse ‘ command mode defaults to ‘ set rasmol commands rasmol ‘, which gives the controls summarized below.

The secondary structure assignment is either rasmol commands the PDB file or calculated using the DSSP algorithm as used by the ‘ structure ‘ command. Todorov, Nan Jia, N. This command may not work correctly unless rasmol commands fonts have been installed.

The only cyclic but non-aromatic amino acid is proline. This set is equivalent to rasmol commands RasMol atom expression ” amino and not buried “.