[Chimera-users] Grouping models

Thomas Goddard goddard at cgl.ucsf.edu
Tue May 18 17:19:59 PDT 2010

Hi Thomas,

   I don't understand well enough what you are doing.  You can move 
several models at once with commands like

   turn y 30 models #15-25 coord #1

which will rotate models 15 through 25 about the y axis of model 1 by 30 
degrees.  I'm not sure if a Chimea command can save multiple PDB models 
in a single file.  It looks like the "write" command can't do that.  I'm 
not sure why it would be limited since the Chimera Save PDB... dialog 
can save multiple models.  Probably Elaine or Eric can explain that. 
You could use the "combine" command to make one molecule from several 
molecules using multiple chains, but PDB format is limited to 62 chains 
(single letter upper/lowercase/number chain identifier).  The combined 
molecule could then be saved with the "write" command.


> Hi Tom,
> we are working at the interphase of EM and atomic structures and would
> like to do some interactive docking/prediction/validations etc . So our
> wish would be if we can use chimera in an automatic fashion to load
> atomic coordinates and simulate the structures by positioning them at
> various positions within a volumetric box (such as applying a rotation,
> turn around x, etc). The problem that we have is that we have to load
> many structures (>60 !) at the same time as we are working with a highly
> oligomeric complex. It would be great, if we can use a chimera
> command-line based option to do the modifications of coordinates on a
> sub-group of the loaded structures (Q: can we group several models
> easily ?) and save the new coos in a single file. For now, we would need
> to do it by hand, as we couldn't find a command line based saving
> options into a single pdb-file .... but this can be quite tedious, if
> one would like to test hundreds of possibilities. Do you have a
> procedure that you would recommend for generating such simulations (for
> now, we treat the structures as rigid bodies) ?
> Best,
> -Thomas

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