From: Martin H. <ma...@bl...> - 2012-06-21 21:27:42
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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 |