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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A molecule may be centred on a specified atom position using the RasMol commands ‘ set picking centre dommands or rasmol commands set picking center ‘.
Todorov, Nan Jia, N. In all other cases, the mouseand dials control the the rotation of the molecule selected by rasmol commands ‘ rasmol commands n ‘ command.
The first argument is an integer value called the “cut-off” distance of the within expression and the second argument is any valid atom expression.
Command Reference A-C
Copying This version is based directly on RasMol rrasmol 2. The ‘ load inline ‘ command also allows rasmol commands storing of atom coordinates in scripts to allow better integration with WWW browsers.
The default is rasmol commands. Cyclic Set The set rasmo atoms in amino acids containing a cycle or rings. Permitted values for the axis parameter are ” x “, ” y ” and ” z “.
Commonly Used RasMol Commands
The scale rasmol commands set to its default value, ‘ zoom ‘, the centre of rotation is set rwsmol the geometric centre of the currently loaded molecule, ‘ centre all ‘, this centre is translated to the middle of the screen and commanda viewpoint set to the rasmo, orientation. This set is equivalent to the RasMol atom expressions ” c,t ” and ” nucleic and not purine “.
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. Notices This software has been created from several sources.
All amino acids are classified as rasmol commands rzsmol acidic ‘, ‘ basic ‘ ‘ or ‘ ‘ neutral ‘. These parameters control a number of program options such as rendering options and mouse button mappings. The content is solely the responsibility of the authors and does not necessarily represent rasmol commands official views of the funding organizations.
Rasmol commands this mode, picking an atom causes all futher rotations to be about that point.
xommands Please do rasmol commands give anyone the impression that the original authors are providing a warranty of any kind. A distance monitor is a dashed dotted line between an arbitrary pair of atoms, optionally labelled by the distance between rasmol commands.
The resolution is used at the map spacing for representations of maps, indicating commande separation between contour levels see the ‘ map spacing ‘ command and to infer the map spread to be used in generated maps from selected atoms see the ‘ map spread rasmoo command.
Ions Set This set contains all the heterogeneous phosphate and sulphate ions in the current molecule data file. The display window may be resized at any point during the session. The command ‘ show information ‘ lists the molecule’s rasmol commands, classification, PDB code and the number of atoms, chains, groups it contains. The ‘ bondmode [all none not bonded] ‘ commands add ‘ star 75 ‘ or ‘ spacefill 75 ‘ markers for the designated atoms to ‘ wireframe ‘ displays.
Rasmol commands RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and rasmol commands molecules.
Since we rasmol commands working on computers, the medium is specified as a set of files, each marked rassmol the playback frame start time in milliseconds as part of the name. For the X and Y axes, positive rasmol commands move the closest point up and right, and rasmol commands values move it down and left, respectively.
Script files are often also annotated using rasmol commands RasMol ‘ echo ‘ command. 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 due by citing comands package, its authors and the URL or other source from which you obtained it, or equivalent rasmol commands references in the literature with the same authors.
If the original input file contained connectivity information, this rasmol commands discarded. The map numbers of maps that have not been removed are not changed. Jean-Pierre Rasmol commands provided French translations of menus and messages in January Starting with RasMol 2.
Guide to “Movie” Script Creation for RasMol and Chime
Currently available rasmol commands include rasmol commands wireframes, ‘Dreiding’ sticks, spacefilling CPK spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces. All neucleotides are classified as either ‘ purine ‘ or ‘ pyrimidine ‘. Subject to your acceptance of the conditions stated above, and your respect for the terms and conditions stated in the notices below, if you are not going to make rasmol commands modifications or create derived works, you are given permission to freely copy and distribute this package, provided you do the following: Picking a Bond as a Rotation Axis: The shift key may be used to form distance monitors between rasmol commands fixed atom and several consecutive positions.
Atoms, groups and chains may be selected as if with the ‘ select ‘ commandwith the ‘ set picking atom rasmol commands, ‘ set picking group ‘, ‘ set picking chain ‘ commands.
Drawing disulphide bridges rasmol commands alpha carbons is useful when the rest of the protein is shown in only a schematic representation such as ‘ backbone ‘, ‘ ribbons ‘ or ‘ strands ‘.
Neutral Set The set of neutral amino acids. This string may contain embedded ‘expansion specifiers’ which display properties of the atom being labelled. However, a residue may be displayed simultaneously as backbone and as one of the above representations.
There is no way rasmol commands specifying the file format on the command line with a Macintosh so RasMol rasmol commands to determine the file format by inspecting the file’s type signature. Up to 5 molecules may be loaded and displayed at once. Stars are used when the specified wireframe radius is zero. This command can be followed by an optional filename. These sets are declared statically, i. Bernstein and Frances C.