[Chimera-users] Grouping models

Eric Pettersen pett at cgl.ucsf.edu
Wed May 19 12:06:12 PDT 2010

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 Pettersen
                         UCSF Computer Graphics Lab

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