[PyMOL] how to keep the atom order when convert mol2 file to pdb in pymol
Hi, Everyone. I always using pymol to prepare the pdb files for MD simulations. However, when I merge the extra small molecular (substrate optimized from the Gaussian09, mol2 formats) and the protein file (PDB formats) into the a single pdb, I found the atom order of substrate is not the same as the original mol2 files. It seems the pymol would put the the hydrogen atom after the heavy atom. It also rearrange the atom when convert the mol2 file to mol2 file when using the pymol. (The attachments, from the test1 to test2 by using pymol) However the rearrangement of the atom is not very convenient for the following actions. I wonder how to keep the original atom order when convert to other formats by using pymol. （I using PYMOL 1.7.0 in Ubuntu 14.04） Thanks very much. Chen test2_from_pymol.pdb Description: Binary data test2_from_pymol.mol2 Description: Binary data test1.mol2 Description: Binary data -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev___ 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
Re: [PyMOL] how to keep the atom order when convert mol2 file to pdb in pymol
http://www.pymolwiki.org/index.php/Retain_order see if this helps João On Fri, Aug 12, 2016 at 5:25 PM, windy wrote: > Hi, > >Everyone. > >I always using pymol to prepare the pdb files for MD simulations. > However, when I merge the extra small molecular (substrate optimized from > the Gaussian09, mol2 formats) and the protein file (PDB formats) into the a > single pdb, I found the atom order of substrate is not the same as the > original mol2 files. > >It seems the pymol would put the the hydrogen atom after the heavy > atom. It also rearrange the atom when convert the mol2 file to mol2 file > when using the pymol. (The attachments, from the test1 to test2 by using > pymol) > >However the rearrangement of the atom is not very convenient for the > following actions. I wonder how to keep the original atom order when > convert to other formats by using pymol. （I using PYMOL 1.7.0 in Ubuntu > 14.04） > >Thanks very much. > > Chen > > > > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. http://sdm.link/zohodev2dev > ___ > 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 > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev___ 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
[PyMOL] how to keep the atom order when convert mol2 file to pdb in pymol
Hello Did you try to use the following command* before to save your pdb file? * set retain_order,[0,1] : http://www.pymolwiki.org/index.php/Retain_order Stephane -- Message: 4 Date: Sat, 13 Aug 2016 00:25:06 +0800 (CST) From: windy Subject: [PyMOL] how to keep the atom order when convert mol2 file to pdb in pymol To: pymol-users Message-ID: <2b26344c.24a.1567f924065.coremail.chxp_m...@163.com> Content-Type: text/plain; charset="gbk" Hi, Everyone. I always using pymol to prepare the pdb files for MD simulations. However, when I merge the extra small molecular (substrate optimized from the Gaussian09, mol2 formats) and the protein file (PDB formats) into the a single pdb, I found the atom order of substrate is not the same as the original mol2 files. It seems the pymol would put the the hydrogen atom after the heavy atom. It also rearrange the atom when convert the mol2 file to mol2 file when using the pymol. (The attachments, from the test1 to test2 by using pymol) However the rearrangement of the atom is not very convenient for the following actions. I wonder how to keep the original atom order when convert to other formats by using pymol. ?I using PYMOL 1.7.0 in Ubuntu 14.04? Thanks very much. Chen -- next part -- An HTML attachment was scrubbed... -- next part -- A non-text attachment was scrubbed... Name: test2_from_pymol.pdb Type: application/octet-stream Size: 3714 bytes Desc: not available -- next part -- A non-text attachment was scrubbed... Name: test2_from_pymol.mol2 Type: application/octet-stream Size: 1518 bytes Desc: not available -- next part -- A non-text attachment was scrubbed... Name: test1.mol2 Type: application/octet-stream Size: 1710 bytes Desc: not available -- -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users End of PyMOL-users Digest, Vol 123, Issue 4 *** -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev ___ 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
