Re: [PyMOL] Saving the Connolly surface of a PDB
Jason Vertrees wrote: > Hi Francios, > > Someone recently asked about this and the answer was that this should > be a setting, but isn't currently available. If I have time, I'll try > to sneak this in the upcoming PyMOL v1.4 release. Is there a workaround for the moment? For example, asking Pymol what is the current rotation and translation the model being displayed has undergone compared to the initial PDB that was read in? With such a possibility, it would allow one to know how to rigid body transform the input PDB in order to have it aligned with the surface Pymol is writing to a .obj file. Thanks a lot, Francois. > Cheers, > > -- Jason > > On Fri, Feb 25, 2011 at 3:05 AM, Francois Berenger wrote: >> Hello, >> >> Is it possible to save the Connolly surface >> computed by Pymol without any rotation and translation >> added compared to the PDB from which the atom coordinates were read? >> >> I looked at the .obj file output and find there was some centering >> done and also some rotation added. >> >> Thanks a lot, >> F. >> >> -- >> Free Software Download: Index, Search & Analyze Logs and other IT data in >> Real-Time with Splunk. Collect, index and harness all the fast moving IT data >> generated by your applications, servers and devices whether physical, virtual >> or in the cloud. Deliver compliance at lower cost and gain new business >> insights. http://p.sf.net/sfu/splunk-dev2dev >> ___ >> 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 >> > > > -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ 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] Saving the Connolly surface of a PDB
Hello, Is it possible to save the Connolly surface computed by Pymol without any rotation and translation added compared to the PDB from which the atom coordinates were read? I looked at the .obj file output and find there was some centering done and also some rotation added. Thanks a lot, F. -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ 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] Saving the Connolly surface of a PDB
Jason Vertrees wrote: > Hi Francios, > > Someone recently asked about this and the answer was that this should > be a setting, but isn't currently available. If I have time, I'll try > to sneak this in the upcoming PyMOL v1.4 release. Please, send me an e-mail if it is done some day. Other software, like Jmol, don't suffer from such bug so this is just preventing people from using Pymol on some applications. As the surface is computed for a PDB that was read in, I don't see why it is exported after undergoing some rotation and a translation that has nothing to do with the input PDB. Regards, F. > Cheers, > > -- Jason > > On Fri, Feb 25, 2011 at 3:05 AM, Francois Berenger wrote: >> Hello, >> >> Is it possible to save the Connolly surface >> computed by Pymol without any rotation and translation >> added compared to the PDB from which the atom coordinates were read? >> >> I looked at the .obj file output and find there was some centering >> done and also some rotation added. >> >> Thanks a lot, >> F. >> >> -- >> Free Software Download: Index, Search & Analyze Logs and other IT data in >> Real-Time with Splunk. Collect, index and harness all the fast moving IT data >> generated by your applications, servers and devices whether physical, virtual >> or in the cloud. Deliver compliance at lower cost and gain new business >> insights. http://p.sf.net/sfu/splunk-dev2dev >> ___ >> 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 >> > > > -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ 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] Question about the .obj file saved by Pymol
Hello, If I use "save myscene.obj" and I was looking at the surface representation of a molecule, does the file contains only the external surface of the protein, or are the internal cavities also included? Thanks, F. -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ 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] Question about the .obj file saved by Pymol
Hello, If I use "save myscene.obj" and I was looking at the surface representation of a molecule, does the file contains only the external surface of the protein, or are the internal cavities also included? Thanks, F. -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ 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
