Re: [PyMOL] PyMOL MOPAC format

[Thomas Holder]

Hi Martin,

I don't know the MOPAC format and couldn't find a specification ad hoc.
But the attached script will produce output which is equivalent to your



Cheers,
   Thomas

On 06/21/2012 11:27 PM, Martin Hediger wrote:

example. Use the "zero" argument to specify the selection of "+0" flagged atoms.

Dear PyMOL users
I'm using MOPAC to do quantum chemical calculations of enzymes.
I'm wondering if PyMOL could be used to output a PDB file in MOPAC format.
An example of this format is here:

     C(     1 LEU  24)   9.04500000 +0   4.94400000 +0  19.45600000 +0          
           0.4527
     O(     2 LEU  24)   8.05600000 +1   5.59200000 +1  19.15100000 +1          
          -0.5188
     H(     3 LEU  24)  10.04000000 +1   5.40500000 +1  19.57200000 +1          
           0.1090
     N(     4 ASP  25)   9.08100000 +1   3.59500000 +1  19.71600000 +1          
          -0.4910
     C(     5 ASP  25)   7.89300000 +1   2.76600000 +1  19.57800000 +1          
          -0.0307
     C(     6 ASP  25)   7.70800000 +0   1.88300000 +0  20.81000000 +0          
           0.3465
     O(     7 ASP  25)   8.44900000 +1   0.95600000 +1  21.12200000 +1          
          -0.4321
     C(     8 ASP  25)   7.97500000 +1   1.90500000 +1  18.33900000 +1          
          -0.4663
     C(     9 ASP  25)   6.66900000 +1   1.15400000 +1  18.28400000 +1          
           0.7179
     O(    10 ASP  25)   5.64600000 +1   1.70700000 +1  18.79700000 +1          
          -0.7657
     O(    11 ASP  25)   6.69700000 +1   0.02300000 +1  17.72800000 +1          
          -0.6565
     H(    12 ASP  25)   7.03100000 +1   3.43800000 +1  19.54700000 +1          
           0.1841
     H(    13 ASP  25)   8.81500000 +1   1.20200000 +1  18.39200000 +1          
           0.1979
     H(    14 ASP  25)   8.10000000 +1   2.50700000 +1  17.43400000 +1          
           0.1919
     H(    15 ASP  25)   9.95700000 +1   3.14300000 +1  19.95300000 +1          
           0.2791
     H(    16 ASP  25)   6.98200000 +1   2.29500000 +1  21.52500000 +1          
           0.1043

What I'm especially interested in is the "+0" and "+1" flags, which
sometimes are required but are quite inconvenient to find for single
atoms in a large file, it's also very error prone. The parenthesis after
the atom type can be omitted, also the very last column (0.4527, ...)
Would it be possible to write a PyMOL plugin, where single atoms could
be added to a selection (using point-and-click) and when saving to the
MOPAC file, the selected atoms would be written with the "+0" flags?
Any hints on what part of the API to look at are very appreciated.

Best regards
Martin

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

mopac.py
Description: application/chimera

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net