[Chimera-users] writing Mol2 format

chimera-users at cgl.ucsf.edu chimera-users at cgl.ucsf.edu
Thu Jun 19 10:56:10 PDT 2003

The only thing I would add is that writing Mol2 is certainly on our "to 
do" list, but there are many things on that list.  So it will happen, 
but the time frame is uncertain.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Wednesday, June 18, 2003, at 03:45 PM, 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
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> 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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