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

chimera-users at cgl.ucsf.edu chimera-users at cgl.ucsf.edu
Mon Apr 7 16:36:28 PDT 2003

> 	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
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