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@cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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@cgl.ucsf.edu http://www.cgl.ucsf.edu On Wednesday, June 18, 2003, at 03:45 PM, chimera-users@cgl.ucsf.edu wrote:
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@cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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