[Chimera-users] Grouping models

[Eric Pettersen]

On May 18, 2010, at 5:19 PM, Thomas Goddard wrote:

> 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.

I guess the trick is that there is no standard for writing multiple  
different structures to a single PDB file.  The dialog produces a file  
that has the models separated by MODEL/ENDMDL records -- which is  
definitely non-standard as far as the PDB spec goes unless the models  
are different conformers of the same structure.  Chimera will likely  
not be able to read such a file back in correctly unless the  
"conformers of same structure" bit is true (the CONECT records will be  
a problem because multiple structurally-different atoms will have the  
same serial number).

I suppose there's no reason not to allow the same leeway in the write  
command, but the user really needs to know what they're doing or  
things will all go sideways.

--Eric


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


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