[Chimera-users] Re: [chimera-dev] Mailing list, etc.?

chimera-users at cgl.ucsf.edu chimera-users at cgl.ucsf.edu
Tue Apr 8 10:51:25 PDT 2003

On Tuesday, April 8, 2003, at 09:51 AM, Geoffrey H Wathen wrote:

> 	Currently, I'm exploring using Chimera to visualize chemical 
> interactions.  I know that this can be done using multiple pdb files, 
> and the 'Save Session' command.  (Indeed, this might be a better way 
> to have Chimera handle it, as it seems that Chimera doesn't like 
> finding hydrogen bonds between models in a single PDB file.)  The one 
> thing that is lacking in this approach is the ability to talk to other 
> applications that can read PDB files, but, clearly, not the Chimera PY 
> session files.

Hi Geoff,
	I guess I'll enable 'write PDB' for multiple models and offer the 
option of writing to a single file or to multiple files distinguished 
by model number.
	FindHBond doesn't offer to find cross-sub-model hydrogen bonds since 
the only standard PDB files that have multiple models are ones 
containing different conformers of the same structure -- rather than 
heterogeneous models.  I could allow cross-sub-model hydrogen bonds if 
you felt there was a real need even after the 'write PDB' change above.

> 	As to the 'backdoor' method I'm using to add atoms, it's nothing so 
> glamorous as programming in Python.  Indeed, it's simply manually 
> writing in the atom's code into the PDB file.  By making it a separate 
> model (using the END command), I can manipulate it separately from the 
> rest of the PDB file, move it into the proper location, then write the 
> PDB file out again.  I can then edit the PDB file to remove the END 
> command, and the atom is part of the overall structure.  I am also 
> working on a better way to do this by writing a program that will 
> allow me to work within a better dimensional framework for placing the 
> new atom, then will write out a PDB file.  We'll see how it goes...

Never underestimate the ingenuity of frustrated users. :-)  Obviously, 
the structure editing I'll be adding will be somewhat easier than this 
to use, but it's still a couple of releases down the line -- so keep 
using what works!  I am impressed. :-)

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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