RASMOL COMMANDS PDF

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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Guide to “Movie” Script Creation for RasMol and Chime

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. The program is aimed at display, teaching and generation of publication quality images.

This set is equivalent to the RasMol atom rasmol commands ” amino and commznds hydrophobic “. If the mouse pointer rasmol commands moved outside rasmol commands display windows, the original colours of the other windows rasmol commands, and the image on the canvas is shown in ‘false colour’.

The second type of primitive commands specifies a sequence of fields that must match for a given atom.

Set Summary Rasmol commands table below summarises RasMol’s classification of the common amino acids. These sets are declared statically, i. Some colour schemes are defined for certain object types.

Since we are working on computers, the medium is specified as a set of files, each marked with the playback frame start time in milliseconds as part of the name. Script files are often also annotated rasmol commands the RasMol ‘ echo ‘ command. The second part consists of a period rxsmol followed by rasmol commands atom name.

The display of these backbone ‘bonds’ is commandd on and off by the command parameter in the same way as with the ‘ wireframe ‘ command. The specular highlights on the surfaces of solid objects may be altered by using the specular reflection coefficient, which is altered using the RasMol ‘ set specpower ‘ command. If no bond exists, it is created. Map rasmol commands may be coloured by specific color of by rasmol commands atom.

Hence “ball and stick” models are rendered correctly but not large spacefilling spheres models. The specular highlights are enabled and disabled by the RasMol ‘ set specular ‘ command. More functions rasmol commands utilize this capability may be added at a later date.

One possible use is a standard RasMol script prefix that may be concatenated with an appropriate PDB file on-the-fly. If the original input file contained connectivity information, this is discarded. The colour may be given as either a colour name rasmol commands a comma separated triple of Red, Green and Blue RGB components enclosed in square brackets.

Additional functions are controlled by holding a rasmol commands key on the keyboard. If both ‘ hydrogen ‘ and ‘ hetero ‘ are ‘ true ‘, ‘ select ‘ without any parameters is equivalent to ‘ select all ‘. If either file is not found, the program displays the error message ‘Error: Changing this parameter automatically resets the value of the RasMol ‘ radius ‘ rasmol commands.

If no specific map was given by the map selector, the new rasmol commands is given the next available map number. Atoms, groups and chains may be selected as if with the ‘ select ‘ commandwith the ‘ rasmol commands picking atom ‘, ‘ set picking group ‘, ‘ set picking chain ‘ commands. Notices This software has been created from several sources. The command ‘ dots off ‘ deletes any existing dot surface. Each commnds may have as many maps as available memory permits. Atoms may also be labelled with arbitrary text strings.

The ‘ set cartoons ‘ command without any parameters returns these two options to their default values. The ‘ set commnads ‘ command mode defaults to ‘ set mouse rasmol ‘, which gives ccommands controls summarized below. In either case a standard deviation rasmol commands by the most recently specified spread or resolution is used. The format of such comparison rasmol commands is a property name, followed by a comparison operator and then rasmol commands integer value.

Commonly Used RasMol Commands

The colour may be given as either a colour name or a comma separated triple of Rasmol commands, Green, Blue RGB components enclosed in square brackets. For depth-cued objects this is the intensity of objects furthest from the viewer. Up to 20 molecules may be loaded at a time.

The currently selected region is defined by the rasmol commands ‘ select ‘ or ‘ restrict ‘ command rasml not the atom expression containing the ‘ selected ‘ keyword. Centring Rotation with the Mouse: Some commands which use the toggle feature are: Alternate conformers and multiple NMR models may be specially coloured and identified rasmol commands atom labels. This command is similar to the RasMol command ‘ ribbons ‘ which renders the biomolecular ribbon as ramsol smooth shaded surface.

All subsequent RasMol commands that manipulate a molecule or modify rasmol commands colour or representation only affect the currently selected region. In any case the new map becomes the currently selected map. When this value is ‘ false ‘, the default ‘ select ‘ region does not include any heterogeneous atoms refer to the predefined set ‘ hetero ‘. If given in the second form, the envelope of the positions of the center of the probe is shown the solvent accessible surface.

If given in the first form, the rsmol of the surface of the probe is shown the solvent ccommands surface.

This spline does rasmol commands pass exactly through the alpha carbon position of each residue, but follows the same path as ‘ ribbons ‘, ‘ strands ‘ and ‘ cartoons ‘. Acidic Set The set of acidic amino acids. This command can be followed by an optional filename. Rasmol commands colour of disulphide bonds may be changed using the ‘ rasmol commands ssbonds ‘ command.

Unlike other versions of RasMol it is impossible to specify both a script and a coordinate file simultaneously.

Jean-Pierre Demailly provided French translations of menus and messages in January This command is used to produce both union-of-spheres and ball-and-stick models of a molecule. When wider strokes are rasmol commands, a larger font size is recommend, e. By default the dotted lines are drawn between the accepting oxygen and the donating nitrogen.