[Chimera-users] python scripting for multiscale model

Thomas Goddard goddard at cgl.ucsf.edu
Mon Oct 5 11:29:32 PDT 2009

Hi Pat,

   There is not a command equivalent for the multi-scale dialog.  The 
unit cell dialog in the latest Chimera daily builds can make multiple 
unit cells (Number of Cells field under Options), but again it has no 
equivalent command.  I have enhanced the "sym" command so that you can 
specify various symmetry groups for making copies, and intend that this 
command to do the job of multi-scale and unit cell.  It handles some 
symmetries in current daily builds (cyclic, dihedral, helical, 
icoshahedral) but not yet unit cell symmetries.  I can add that if you like.

   The "crystalcontacts" command can place all copies of your asymmetric 
unit that contact the original asymmetric unit.  If that is what you 
need the command would look like

   cryst #0 5 copies true

which would open copies of #0 related by crystal symmetry that have 
atom-to-atom contact distances less than 5 Angstroms to #0.  It also 
makes a kind of crazy diagram showing balls representing neighboring 
asymmetric units which you can close.  This command was for the PDB to 
check entries for bad steric clashes.


-------- Original Message --------
Subject: [Chimera-users] python scripting for multiscale model
From: Pat Weinkam
To: chimera-users
Date: 10/2/09 12:42 PM

> Hi,
> I am a new postdoc with Andrej Sali.  I am looking to use the multiscale 
> model tool to recreate a 3x3x3 set of unit cells around my pdb file.  I 
> can use the GUI to do this just fine but I would like to incorporate 
> this into a python script.  Is such a thing available?  It would be 
> greatly appreciated.  
> Thanks!
> Pat

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