[Chimera-users] Chimera and building molecules

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 31 11:10:19 PDT 2004

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


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