[Chimera-users] Chimera and building molecules

Grant Jacobs gjacobs at bioinfotools.com
Tue Aug 31 16:05:38 PDT 2004

I recall a command-line tool from my student days ('88-'92) that I 
used for molecular construction and editing. I wish I could remember 
the name of it as I'd love to track down the code for this. It was 
available on VMS before BIOSYM started up. I believe BIOSYM included 
it in their package, but this component was actually free. (I could 
be wrong as this is a long, fuzzy memory!)

I recall the command line interface as being simple and very easy to 
use. I vaguely recall you could just type in an amino acid sequence, 
assign secondary structure and you were done. Side chains could be 
"mutated". DNA could be built also. I doubt this program could handle 
anything other than "standard" amino acids and bases, but if I had 
the code I could try fiddling (for my own use at any rate).

If anyone is able to name the program, I'd be interested in tracking it down.

Part of the reason I mention this here is that this is another way 
forward - find an external program start from there.


>Dear Ben,
>We definitely agree that molecule-building would be a very
>useful addition to Chimera.  Toward this functionality,
>Chimera includes hydrogen addition; also, the "bond" command
>has been implemented (and will be available in the next release).
>Chimera also includes the "swapaa" and "swapna" commands
>which "mutate" one sidechain or base to another, although they
>are not very sophisticated.
>I am not certain what you are referring to in MIDAS, which
>only had very rudimentary building capabilities and no ability
>to add hydrogens.  The "addgrp" command did allow definition of
>new amino acid sidechains, but was quite unwieldy and not
>usable for building in general.  Similarly, "addaa" could
>append one of the standard amino acids to the end of a peptide
>but was not generalizable to other types of molecules.
>If you could clarify how you were applying these tools,
>we might be able to prioritize developments accordingly.
>Thank you,
>Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
>Computer Graphics Lab and Babbitt Lab
>Department of Pharmaceutical Chemistry
>University of California, San Francisco
>                      http://www.cgl.ucsf.edu/home/meng/index.html
>Chimera-users mailing list
>Chimera-users at cgl.ucsf.edu

Grant Jacobs Ph.D.                                     BioinfoTools
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