Hi Pascal, I cannot reproduce this (I tried your example with almost every PyMOL version from 1.2 to 1.7). Which version do you use? Are you sure those settings are actually used and not changed by some other script? And do you load the original 1EHZ file or a processed PDB, which might already have the wrong atom names?
Cheers, Thomas Pascal Auffinger wrote, On 07/16/14 08:14: > > Dear pymol users, > > I came across a problem with pymol writing out pdbfiles > containing MG atoms like in 1EHZ. > > I used the following options since a long time: > > set retain_order, on > set pdb_retain_ids, on > set pdb_use_ter_records, off > set pdb_no_end_record, on > set pdb_conect_all,off > set pdb_unbond_cations, on > set pdb_literal_names, on > set pdb_truncate_residue_name, on > set pdb_reformat_names_mode, 3 > > Yet, these options transform the following lines > extracted from 1EHZ > > HETATM 1654 MG MG A 590 70.566 35.530 1.665 1.00 65.44 > MG > HETATM 1655 MN MN A 530 80.714 57.068 31.271 1.00 34.23 > MN > HETATM 1656 MG MG A 510 57.346 47.575 47.279 1.00 62.77 > MG > HETATM 1657 MN MN A 520 49.923 44.427 50.131 1.00 89.20 > MN > HETATM 1658 MG MG A 540 77.110 64.307 25.357 1.00 40.08 > MG > HETATM 1659 MG MG A 560 62.649 46.629 27.595 1.00 47.02 > MG > HETATM 1660 MG MG A 570 73.331 43.321 11.207 1.00 50.39 > MG > HETATM 1661 MG MG A 580 69.222 44.815 33.339 1.00 61.74 > MG > HETATM 1662 MN MN A 550 72.301 48.513 33.894 1.00 56.51 > MN > > into > > HETATM 1654 MN MN A 530 80.714 57.068 31.271 1.00 34.23 > MN > HETATM 1655 MG MG A 510 57.346 47.575 47.279 1.00 62.77 > MG > HETATM 1656 MN MN A 520 49.923 44.427 50.131 1.00 89.20 > MN > HETATM 1657 MG MG A 540 77.110 64.307 25.357 1.00 40.08 > MG > HETATM 1658 MG MG A 560 62.649 46.629 27.595 1.00 47.02 > MG > HETATM 1659 MG MG A 570 73.331 43.321 11.207 1.00 50.39 > MG > HETATM 1660 MG MG A 580 69.222 44.815 33.339 1.00 61.74 > MG > HETATM 1661 MN MN A 550 72.301 48.513 33.894 1.00 56.51 > MN > > Thus, MG^^is transformed into ^MG^ which is a problem and would for > example prevent to distinguish > CA^^ as a calcium atom > from ^CA^ which would be a C-alpha based solely on atom names. > > Are my settings OK ? > Did I do something wrong ? > Should I change them to get an output respecting pdb standards ? > > Thanks a lot for helping, > > Pascal > > ----- > Pascal Auffinger > IBMC/CNRS > 15 rue René Descartes > 67084 Strasbourg Cedex > > p.auffin...@ibmc-cnrs.unistra.fr > ----- -- Thomas Holder PyMOL Schrödinger, Inc. ------------------------------------------------------------------------------ Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds _______________________________________________ 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
