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

chimera-users at cgl.ucsf.edu chimera-users at cgl.ucsf.edu
Tue Apr 8 09:51:47 PDT 2003

	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.
	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...


On Monday, April 7, 2003, at 04:36  PM, Eric Pettersen wrote:

>> 	Now to a comment.  After some tinkering, I finally managed to output 
>> a
>> new PDB file that contained models from several other PDB files.  
>> This,
>> however, wasn't exactly an easy of intuitive thing to do.  My first
>> thought had been to use the 'Write PDB' command in the Model Panel.
>> However, that button automatically greys itself out when more than one
>> model is selected.  I finally stumbled upon the command line command
>> 'pdbrun cat > file'.  So, I was able to do what I wanted, but I had to
>> go through a rather backdoor method.  Any chance that things like
>> 'Write PDB' will be enabled when more than one model is selected?
> 	I could enable 'write PDB' with multiple models selected.  I guess my 
> question is why do you want multiple PDB models in a single file?  
> What will you do with that file?  Knowing how you want to use the file 
> will help me decide if simply enabling the button is the way to go or 
> if some other interface is more appropriate.  If I enabled it, the 
> models would be separated by END records.
>> 	And what about a method of adding more atoms, other than just
>> hydrogen?  (I also know of 'backdoor' ways that I can do this, but I'd
>> love to see Chimera become a more fully featured molecular modeler, 
>> and
>> to that end, I'm quite happy to give all kinds of input.)
> 	I'm currently working on smarter hydrogen addition (avoiding steric 
> conflicts and maintaining hydrogen-bonding interactions).  I should be 
> done with that in time for our next release.  I intend to work on some 
> limited structure-building features after that.  So a preliminary 
> version might be available two releases from now.
> 	Even I'm not aware of backdoor ways to add non-hydrogen atoms!  I 
> guess the swapaa command _sort_ of does this, but it's not at all 
> generic.  Are you writing Python code to do this?
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         pett at cgl.ucsf.edu
>                         http://www.cgl.ucsf.edu

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