[Chimera-users] writing Mol2 format

[chimera-users at cgl.ucsf.edu]

  Hi David,
Writing out Mol2 format can in principle be done, but there are a few
caveats.  If the original format is Mol2, the original information could
be retained and written back out.  I don't know how simple/hard this
would be to implement (feel free to chime in, other members of the team).

When the original format is not Mol2, there is less information in the
molecule data than is needed to write the file.  Chimera uses a fairly
rich set of atom types, but there is still not a one-to-one relationship
with all Mol2 types.  One would need to create a mapping between the types.
Also, I believe Chimera currently knows connectivity but not bond orders,
and does not retain any point charge information.

The online Chimera Programmer's Guide actually includes an example of
code required to write out a mol2 file.  I had forgotten about this when
visiting your office earlier.  It discusses a mapping between atom types
(if you use this, you should examine this mapping and make sure it
works the way you think it should).  The example code writes out all
bonds as single.

Check it out:
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html
click the "Examples" link
and then "Chimera's Object Model"
This example is "writeMol2.py"

If you have a molecule open in Chimera, you can view the type assignments
using Actions... Label... IDATM type  (version 1.1700).
A listing/explanation of Chimera types can be seen at
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html
  Best,
Elaine
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Elaine C. Meng, Ph.D.
Computer Graphics Lab and Babbitt Lab
meng at cgl.ucsf.edu
http://www.cgl.ucsf.edu/home/meng/index.html
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