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