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 ------------------------------------------------------------------------------ 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