[PyMOL] Problem Compiling Pymol 1.2.x
I had successfully compiled Plymol from the Subversion repository in OpenSuSE v103. Linux. I say successfully, because I have just upgraded my linux computer to OpenSuSE v11.2. Unfortunaltely, I have a bit of a problem compiling the source code in the new linux OS in that I can compile the PyMol Viewer but notthe Pcl/Tck GUI. Obviously there is something missing in the new compiler installation, but I don't have the faintest idea as to what it could be. I was wonderig if anyone else has encountered this problem and/or might have a possible solution? Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate http://www.FoundationForChemistry.com -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] make morph with rigimol
I want to make movie showing conformational changes of one helix (including a couple of side chains) between two structures of the same protein. Could anybody teach me how to make morph using pymol version 1.2r2? Many Thanks. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Problem Compiling Pymol 1.2.x
Hey Stephen, make sure you have Tkinter and freeglut-devel installed. These are the dependencies that make trouble in RHEL. Andreas Stephen P. Molnar wrote: I had successfully compiled Plymol from the Subversion repository in OpenSuSE v103. Linux. I say successfully, because I have just upgraded my linux computer to OpenSuSE v11.2. Unfortunaltely, I have a bit of a problem compiling the source code in the new linux OS in that I can compile the PyMol Viewer but notthe Pcl/Tck GUI. Obviously there is something missing in the new compiler installation, but I don't have the faintest idea as to what it could be. I was wonderig if anyone else has encountered this problem and/or might have a possible solution? Thanks in advance. -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Problem Compiling Pymol 1.2.x
On 13:38 Fri 20 Nov , Stephen P. Molnar wrote: I had successfully compiled Plymol from the Subversion repository in OpenSuSE v103. Linux. I say successfully, because I have just upgraded my linux computer to OpenSuSE v11.2. Unfortunaltely, I have a bit of a problem compiling the source code in the new linux OS in that I can compile the PyMol Viewer but notthe Pcl/Tck GUI. Obviously there is something missing in the new compiler installation, but I don't have the faintest idea as to what it could be. I was wonderig if anyone else has encountered this problem and/or might have a possible solution? Dear Stephen, Could you supply the complete error message you encountered, along with the final line of compilation? It's very difficult to make any suggestions without seeing exactly what happened. If it's unclear to you what to send, just upload the whole build log somewhere and post a link to it here. -- Thanks, Donnie Donald S. Berkholz, Postdoctoral research fellow James R. Thompson lab, Physiology Biomedical Engineering Grazia Isaya lab, Pediatric Adolescent Medicine Mayo Clinic College of Medicine 200 First Street SW Rochester, MN 55905 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] make morph with rigimol
Michael, Great advice. Also, I'd like to point out that the incentive build of PyMOL ships with the rigimol morphing module built in. Rigimol is only to be used for visualization, not for pathwway determination. If you only need to make a movie and don't necessarily care about a perfect pathway it's as easy as: from pymol import rigimol load str1.pdb, str1# load two structures load str2.pdb, str2 align str1, str2# align them create m_in, str1, 1, 1 # create the input for rigimol create m_in, str2, 1, 2 rigimol.morph( m_in, m_out, refinement=5, async=1) This creates the m_out object as a multistate object. Save the output to a mutli-state PDB with: save myConf.pdb, m_out, 0 then use that in your movies. HTH, -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 2:08 PM, Michael Zimmermann micha...@iastate.edu wrote: one option would be to make intermediates based on linear interpolation and then make a movie of the morph. Gerstein's group has done some work at this. http://www2.molmovdb.org/wiki/info/index.php/Morph_Server If you just want to visualize them together my suggestion would be to: show one of the structures without the helix make an object for the helix in each structure and another object with both helices show cartoons of each helix show a transparent surface of the object with both helices color each helix differently so that the cartoons and surfaces represent conformational changes. play with clipping planes applied to the transparent surface. you could do this type of image for the morph too to emphasize the helix. On Fri, Nov 20, 2009 at 12:45 PM, Huang, Xin h...@amgen.com wrote: I want to make movie showing conformational changes of one helix (including a couple of side chains) between two structures of the same protein. Could anybody teach me how to make morph using pymol version 1.2r2? Many Thanks. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Problem Compiling Pymol 1.2.x
On 11/20/2009 02:16 PM, Donnie Berkholz wrote: On 13:38 Fri 20 Nov , Stephen P. Molnar wrote: I had successfully compiled Plymol from the Subversion repository in OpenSuSE v103. Linux. I say successfully, because I have just upgraded my linux computer to OpenSuSE v11.2. Unfortunaltely, I have a bit of a problem compiling the source code in the new linux OS in that I can compile the PyMol Viewer but notthe Pcl/Tck GUI. Obviously there is something missing in the new compiler installation, but I don't have the faintest idea as to what it could be. I was wonderig if anyone else has encountered this problem and/or might have a possible solution? Dear Stephen, Could you supply the complete error message you encountered, along with the final line of compilation? It's very difficult to make any suggestions without seeing exactly what happened. If it's unclear to you what to send, just upload the whole build log somewhere and post a link to it here. Here's teh end of the log file that I recorded. I really don't have anyplace to which to upload the entire 125 kb log file. running install running install_lib copying build/lib.linux-x86_64-2.6/pymol/_cmd.so - /usr/local/lib64/python2.6/site-packages/pymol copying build/lib.linux-x86_64-2.6/pymol/opengl/glu/_glu_num.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/glu copying build/lib.linux-x86_64-2.6/pymol/opengl/glu/_glu.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/glu copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/openglutil_num.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/gl copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/_opengl.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/gl copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/_opengl_num.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/gl copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/openglutil.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/gl copying build/lib.linux-x86_64-2.6/pymol/opengl/glut/_glut.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/glut copying build/lib.linux-x86_64-2.6/chempy/champ/_champ.so - /usr/local/lib64/python2.6/site-packages/chempy/champ running install_egg_info Removing /usr/local/lib64/python2.6/site-packages/pymol-1.2.0-py2.6.egg-info Writing /usr/local/lib64/python2.6/site-packages/pymol-1.2.0-py2.6.egg-info After running: python setup.py install Please run, to complete the installation: python setup2.py install To uninstall PyMOL, run: python setup2.py uninstall [1m[31mabnormal:/sda1/src/pymol # (B[mpython setup2.py install Installing into /usr/local/lib64/python2.6/site-packages ... Created ./pymol which can be used to launch PyMOL. You may wish to copy this file into a standard location such as /usr/bin or /usr/local/bin. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Problem Compiling Pymol 1.2.x
Stephen P. Molnar wrote: Here's teh end of the log file that I recorded. I really don't have anyplace to which to upload the entire 125 kb log file. Hi Stephen, as Donnie already mentioned, we cannot help if we could not see the _complete_ build.log. From the part you past, it looks succesfull. So please try to provide us the log, in worst case compress it and attach it to your mail. What exactly is the output if you start it in a shell? Justin -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institute for structural biochemistry Research Centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 signature.asc Description: OpenPGP digital signature -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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] Problem Compiling Pymol 1.2.x
Stephen, openSuse Linux does not come with Pmw installed by default. Please re-download and install Pmw. Let me know if it's something else. -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 4:54 PM, Justin Lecher j.lec...@fz-juelich.de wrote: Stephen P. Molnar wrote: Here's teh end of the log file that I recorded. I really don't have anyplace to which to upload the entire 125 kb log file. Hi Stephen, as Donnie already mentioned, we cannot help if we could not see the _complete_ build.log. From the part you past, it looks succesfull. So please try to provide us the log, in worst case compress it and attach it to your mail. What exactly is the output if you start it in a shell? Justin -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institute for structural biochemistry Research Centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] make morph with rigimol
I realized I made a mistake. The proper import statement is: from epymol import rigimol This is shipped in the incentive build of 1.1r2. -- Jaso Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 2:50 PM, Huang, Xin h...@amgen.com wrote: Thanks Jason. Does the latest version (1.2r2) of pymol comes with rigimol as warren indicates on the website? I cannot seem to import rigimol. (I typed import rigimol but have this import error no module named rigimol). Any suggestions? Many Thanks. -Original Message- From: Jason Vertrees [mailto:jason.vertr...@gmail.com] Sent: Friday, November 20, 2009 2:38 PM To: Michael Zimmermann Cc: Huang, Xin; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] make morph with rigimol Michael, Great advice. Also, I'd like to point out that the incentive build of PyMOL ships with the rigimol morphing module built in. Rigimol is only to be used for visualization, not for pathwway determination. If you only need to make a movie and don't necessarily care about a perfect pathway it's as easy as: from pymol import rigimol load str1.pdb, str1 # load two structures load str2.pdb, str2 align str1, str2 # align them create m_in, str1, 1, 1 # create the input for rigimol create m_in, str2, 1, 2 rigimol.morph( m_in, m_out, refinement=5, async=1) This creates the m_out object as a multistate object. Save the output to a mutli-state PDB with: save myConf.pdb, m_out, 0 then use that in your movies. HTH, -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 2:08 PM, Michael Zimmermann micha...@iastate.edu wrote: one option would be to make intermediates based on linear interpolation and then make a movie of the morph. Gerstein's group has done some work at this. http://www2.molmovdb.org/wiki/info/index.php/Morph_Server If you just want to visualize them together my suggestion would be to: show one of the structures without the helix make an object for the helix in each structure and another object with both helices show cartoons of each helix show a transparent surface of the object with both helices color each helix differently so that the cartoons and surfaces represent conformational changes. play with clipping planes applied to the transparent surface. you could do this type of image for the morph too to emphasize the helix. On Fri, Nov 20, 2009 at 12:45 PM, Huang, Xin h...@amgen.com wrote: I want to make movie showing conformational changes of one helix (including a couple of side chains) between two structures of the same protein. Could anybody teach me how to make morph using pymol version 1.2r2? Many Thanks. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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
