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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Commonly Used RasMol Commands

Map objects may be coloured by specific color of by nearest rasmol commands. This set is equivalent to the RasMol expression ” protein or nucleic and not backbone “. The first time the ‘ hbond ‘ command is used, the program searches rasmol commands structure of the molecule to find hydrogen bonded residues and reports the number of bonds to the user. The bond cannot be used for rotation if it is rasmol commands of a ring of any size.

This value between rasmol commands and adjusts the reflection coefficient used in specular highlight calculations. The first type is used to identify a given residue number or range of rasmol commands numbers.

If hydrogen bonding, disulphide bridges or secondary structure have been determined, the number of hbonds, ssbonds, helices, ladders and turns are also displayed, commanvs. Script files are often also annotated using the RasMol ‘ echo ‘ command.

Guide to “Movie” Script Creation for RasMol and Chime

The command ‘ star true ‘, the default, represents each atom as a star with strokes length equal to van der Waals radius. If no medium is specified, play off suspends playing and play rasmpl resumes rasmol commands.

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Bernstein RasMol 2. Predefined Sets RasMol atom expressions may contain predefined sets. By default, rasmol commands set display normal ‘, RasMol displays the molecule in the representation specified by the user.

RasMol Script Creation Guide

For example, this may be used to generate depth-cued images that fade to white, rather than black. Rasmol commands 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 Bernstein rasmol rasmol. The starting value for numbering may be negative. rasmol commands

The colour of hbond objects may be changed by the ‘ colour hbond ‘ command. Predefined sets are often abbreviations of primitive atom expressions. The distinction rasmo rasmol commands command rasmol commands the RasMol ‘ write ‘ command has been dropped. A load command executed inside a script file may specify the keyword ‘ inline ‘ instead of a conventional filename.

razmol If a non-zero spread has been given the radius of the atom is multiplied by the spread rasmol commands find the standard deviation. The RasMol command ‘ show symmetry ‘ display details of the crystal’s space rasmol commands and unit cell axes. The command ‘ show phipsi ‘ shows the phi and psi angles of the currently selected residues and the omega angles of cis peptide bonds.

In the default rasmol commands map scale true, each Gaussian has a height proportional element type of rasmol commands atom. The display of these backbone ‘bonds’ is turned on and off by the command parameter in the same way as with the ‘ wireframe ‘ command. Up to 5 molecules may be loaded and displayed at once. This command is particularly useful for displaying ocmmands from within a RasMol ‘ script ‘ file.

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Commonly Used RasMol Commands

If no medium is specified, record off suspends recording and record on resumes recording with the next available rasmol commands on the same medium.

This product is not to be used in the planning, construction, maintenance, operation or use of any nuclear facility nor the flight, navigation or communication rasmol commands aircraft or ground support equipment. This means any lines following ‘ exit ‘ are never interpreted by RasMol.

Initially, the hydrogen bonds rasmol commands the rasmol commands molecule are rasmol commands, if this hasn’t been done already. A single question mark may also be used to abbreviate the keyword “help”.

The ‘ load inline ‘ command also allows the storing of atom coordinates in scripts to allow better integration with WWW browsers. In addition to whatever other steps you may be obliged to take to respect the intellectual property rights of the various parties involved, if you do make use of the software and documents in this package, please give credit where credit is rasmol commands by citing this package, its authors and the URL or other source from which you obtained it, or equivalent primary references in the literature with the same authors.

By default, the C-termini of beta-sheets are displayed as arrow heads.