Hi Marko and Rui, The TER records can also be prevented with "set pdb_use_ter_records, off".
https://pymolwiki.org/index.php/pdb_use_ter_records Cheers, Thomas On 28 Nov 2016, at 05:03, Rui Sousa <rui.so...@univ-nantes.fr> wrote: > Hi Marko, > > For the order of the atoms, check if "retain_order" is set to 1; if not, > use "set retain_order, 1" before importing your PDB file. For the rest > of your problem, what exactly is being changed from the imported PDB > file and the saved one? Apart from the addition of TER, which is a > fairly trivial problem to solve. > > Best regards, > > Rui > > Le 28/11/2016 10:41, Marko Sever a écrit : >> Hello everybody, >> >> I'm working with a protein-protein complex and am fixing some stuff. >> >> When I save the fixed complex as a pdb the PDB format is not the same as it >> was in the imported pdb files (there it was the same as the CHARMM default >> pdb format). >> >> In the saved pdb it changed the line position of atoms in the pdb file. >> Residues are ok but atoms in a given residue are mixed up. It also added >> addition TER's which I had to manually delete. >> >> So how would I specify the output PDB format to be the same as in the >> original imported pdbs (before manipulation), so same as CHARMM pdb format. >> >> Please help, >> >> Marko -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ _______________________________________________ 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
