From: Marko S. <Mar...@ki...> - 2016-11-28 09:41:30
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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 |
From: Rui S. <Rui...@un...> - 2016-11-28 10:04:44
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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 > ------------------------------------------------------------------------------ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Thomas H. <tho...@sc...> - 2016-11-28 15:01:48
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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...@un...> 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. |
From: Spencer B. <spe...@gm...> - 2016-11-28 15:31:34
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It would be nice to have a setting that adds TER records only where the chain or segi change (as opposed to whenever the residue numbers are non-sequential). I believe that better captures the original intent for terminating polymers. Of course, the real answer is that everyone should switch to mmCIF. On Mon, Nov 28, 2016 at 4:01 PM, Thomas Holder < tho...@sc...> wrote: > 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...@un...> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Ezra P. <ezr...@rc...> - 2016-11-28 16:16:25
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PDB format dictates that TER records are present at the end of a polymer chain. Chain breaks or non-sequential numbering do not introduce TER records. A TER record is required between the polymer and non-polymer chain - even with same chain ID. TER records should not be between non-polymers... Of course, there have been many different flavors of PDB files produced by different programs... http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER On 11/28/2016 10:31 AM, Spencer Bliven wrote: > It would be nice to have a setting that adds TER records only where the chain > or segi change (as opposed to whenever the residue numbers are > non-sequential). I believe that better captures the original intent for > terminating polymers. Of course, the real answer is that everyone should > switch to mmCIF. > > On Mon, Nov 28, 2016 at 4:01 PM, Thomas Holder <tho...@sc... > <mailto:tho...@sc...>> wrote: > > 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 > <https://pymolwiki.org/index.php/pdb_use_ter_records> > > Cheers, > Thomas > > On 28 Nov 2016, at 05:03, Rui Sousa <Rui...@un... > <mailto:Rui...@un...>> 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 (PyM...@li... > <mailto:PyM...@li...>) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > <https://lists.sourceforge.net/lists/listinfo/pymol-users> > Archives: http://www.mail-archive.com/pym...@li... > <http://www.mail-archive.com/pym...@li...> > > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |