[Chimera-users] Selecting subassemblies

[Thomas Goddard]

Hi Brian,

   Documentation for the Chimera Multiscale Models tool that is 
described in that paper is in the Chimera User's Guide:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html

The subsection on selecting components would be relevant.  Here's a 
little tutorial on display of viruses using this tool.

http://www.cgl.ucsf.edu/chimera/tutorials/virus-howto/showvirus.html

In practice I would select the outer capsid of bluetongue virus (2btv) 
by selecting one chain with the mouse (ctrl-click on it) then use the 
keyboard shortcut that extends the selection to all chains with the same 
sequence (shortcut "xc" - extend to equiv chains).  When the paper was 
written that didn't exist.

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html

If I forgot about shortcut xc my next quickest route would be to select 
the two inner chains using ctrl-click, then shift-ctrl-click through 
holes in the outer capsid, then press the Copies button on the 
multiscale dialog then menu Select / Invert on the main window.  If I 
really didn't know much about the capsid I'd probably select one chain 
of each different color in the outer layer (ctrl-click, then 
shift-ctrl-click to add more) then press the Copies button.

All of this presumes you don't have any hierarchy info.  The paper 
describes how with a script it is possible to define a hierarchy of 
structures (trimers, outer capsid, inner capsid, whole capsid). 
Unfortunately a script is still needed to do that.  The script for that 
is in the above Chimera User Guide documentation under Structural Hierarchy.

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/bluetongue.py

You open the script file in Chimera (File / Open) to show the capsid 
with the hierarchy, then select one chain (ctrl-click), then press the 
Up button on the multiscale dialog to promote to the trimer, all 
trimers, ....  That script had to work around an error in the 2btv PDB 
file which has since been fixed by the PDB.  So the original script 
doesn't work unless the script is edited to remove "given = True".  I've 
made that change in the online development documentation.

	Tom




Brian and Lanie Grech wrote:
> Hi everyone
> 
>  
> 
> In reference to the publication in the March 2005 edition of Structure, 
> titled “Software extension to UCSF Chimera for interactive visualization 
> of large molecular assemblies”. Under the subheading “Selecting 
> subassemblies”, page 480, it talks about two methods to select part of 
> the outer capsid layer of the model of bluetongue virus and not the 
> inner capsid layers. I am unable to find the documentation explaining 
> how to do this, could someone please direct me to the documentation or 
> explain how to do this.
> 
>  
> 
> Regards
> 
> Brian Grech
> 
> 
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