Re: [PyMOL] pymolrc file on Windows7
I believe your problem is that you named your file pymolrc.py instead of pymolrc This causes pymol to read it as python rather than pymol commands. Rename the file and you should be fine. -David On Aug 23, 2011, at 8:44 AM, Tatyana Sysoeva tatyanasyso...@gmail.com wrote: Hi Tsjerk, I am attaching the file and the terminal text. This Executable Build integrates and extends Open-Source PyMOL 1.3. Traceback (most recent call last): File C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py, line 338, in parse parsing.run_file(path,self.pymol_names,self.pymol_names) File C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parsing.py, line 455, in run_file execfile(file,global_ns,local_ns) File C:\Users\Tanya\pymolrc.py, line 1 set ray_trace_mode, on ^ SyntaxError: invalid syntax + Thanks, Tanya On Tue, Aug 23, 2011 at 12:18 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Tanya, Does it say more than syntax error? Can you send the whole output? (copy crom the grey screen). In addition, can you send the pymolrc file as attachment? There might be something to do with line endings; so don't paste it in the mail, but attach the actual file that fails. Cheers, Tsjerk On Tue, Aug 23, 2011 at 2:03 AM, Tatyana Sysoeva tatyanasyso...@gmail.com wrote: Dear all, I have quite silly question but I could not find an answer so far. I am trying to use Pymol in a Power point presentation. For that I would like to change the default setting in Pymol - set security, off I have created a file pymolrc and put it in C:/Program Files/PyMol/PyMol/. When I am launching Pymol, it reads the file, but respond with syntax error. I checked and the same command is working properly if I type it directly into the Pymol prompt. I would appreciate any corrections or advices! Thank you very much, Tanya -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands pymolrc.py -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ 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 -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ 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] Compilation of PyMOL on Mac
Does the existing fink pymol not work for you? http://pdb.finkproject.org/pdb/package.php/pymol-py27 You can look at it's info file for guidance on building on Mac if you want your own build. -David On Aug 11, 2011, at 12:15 PM, Matthias Schmidt matthias.rene.schm...@gmail.com wrote: Hi, I downloaded PyMol from https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol and tried to compile it with /sw/bin/python2.7 setup.py build The compilation works fine, but when it comes to linking, I get an error related to undefined symbols in an OpenGL library wrapper. Do you have any advice on how to compile Pymol succesfully on a Mac (SnowLeopard, with XCode and Fink) or how to solve the linking error? I have installed Glew using fink and so I have the following files in sw/ ./include/GL/glew.h ./include/GL/wglew.h ./lib/libGLEW.1.6.0.dylib ./lib/libGLEW.1.dylib ./lib/libGLEW.a ./lib/libGLEW.dylib ./lib/pkgconfig/glew.pc I use /opt/local/bin/i686-apple-darwin10-g++-4.0.1 from ports as compiler. Nevertheless, I don't manage to get it compiled. Best, Matthias -- Structural Bioinformatics and Computational Biochemistry Unit Dept. of Biochemistry University of Oxford http://sbcb.bioch.ox.ac.uk/schmidt.php -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-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 -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-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] how to load two separate pdb files simultaneously
Are you referring to files on your computer? You should just be able to use File - Open to open one file, then do it again to open the next. -David On Jun 29, 2011, at 6:36 AM, leila karami karami.lei...@gmail.com wrote: Dear Hongbo very thanks for your attention. None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not help me. I need to load two separate pdb files simultaneously. -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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 -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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] PyMOL installation
Both fink and macports have pymol packages. -David On Jun 15, 2011, at 10:37 AM, Spyros Charonis s.charo...@gmail.com wrote: Dear PyMOL community, I'm trying to get started with PyMOL, and the compilation is going wrong. After running python steup.py install on the terminal (I'm using OS X Snow Leopard) it complains with: GLEW_OK’ undeclared (first use in this function) lipo: can't open input file: /var/folders/Bh/Bh0rlnl0EkaDSfgci7c2Tk+++TQ/-Tmp-//ccp9fTEl.out I downloaded GLEW library but the compilation is still unsuccessful. Is there another way to get PyMOL running? Thanks in advance! Spyros -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-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 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-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] Pymol 1.4.1 does not load PDBs from command line anymore
Works for me. -David On May 11, 2011, at 5:56 PM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: Hi Alvin, thanks for the reply. Sorry, but I was not clear in describing the problem. What I meant was that loading pdb files as arguments to pymol does not seem to work anymore, i.e. 'shell_prompt # pymol x.pdb y.pdb' does not load x.pdb and y.pdb on startup. At least in 1.3 that mechanism worked. Cheers, Carsten -Original Message- From: Alvin Oga [mailto:pymol.l...@mail.linux-1u.net] Sent: Wednesday, May 11, 2011 5:49 PM To: Schubert, Carsten [PRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore hi carsten on freebsd, command line works for me ( pymol load pept.pdb ), works as in the molecule changes to the new loaded one i downloaded pymol-1.4.1 from svn and compiled the sources on freebsd- 7.4, 8.2, 6.4 --- downloading/compiling pymol-1.4.1 on debian-sid has problems tho and it doesn't execute properly ( probably because i tend to change pesky/unreasonable system default files ) i can try to download/compile/test on other linux's .. i have centos-5.4, 5.5, 5.6, fedora-core14, opensuse-11.3, 11.4, slackware-12.3 ) centos/fedora supposed to be identical to redhat which linux versions do you have ?? have fun alvin http://Linux-1U.net/BioChem The latest PyMol (1.4.1, 32bit Linux version) does not load PDB files from the command line anymore. Does anybody have the same problem? What am I missing? -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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 -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ 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] PyMOL Project Updates Open Source PyMOL v1.4b1
I found the ce_types.h problem happens with autotools, but not with setup.py method. -David On Apr 6, 2011, at 5:59 PM, Paul Rigor paul.ri...@uci.edu wrote: Hi all, So I tried compiling the 1.4b today and came across a couple of issues. 1) The layer3/Executive.c is attempting to include ce_types.h locally but the header file is actually under 'modules/cealign/src' 2) With a quick hack, I was able to compile. However, when attempting to run the binary, I get the following error: ImportError: /lv_disk00/preserve/tmp/pymol/modules/pymol/_cmd.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE However, it seems that there is no missing library dependency (quick check with ldd). Has anyone run into any of these issues. I'm running python 2.6 on a CentOS 5.5 distro on a 64-bit machine. Thanks, paul -- Paul Rigor http://www.ics.uci.edu/~prigor On Mon, Apr 4, 2011 at 6:07 AM, Tru Huynh t...@pasteur.fr wrote: Hi Jason, On Mon, Apr 04, 2011 at 08:19:17AM -0400, Jason Vertrees wrote: As you have discovered, and I forgot to mention, Python 2.5 or later is now required. This is due to 64-bit types using Py_ssize_t. If the patch is the only thing needed to support Py_ssize_t for python 2.4 please consider adding it for backport. Cheers, Tru -- Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/ mailto:t...@pasteur.fr | tel/fax +33 1 45 68 87 37/19 Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ 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 -- 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
Re: [PyMOL] How to get pymol 1.4
a) you're mistaken, Warren's incentive builds had extra features. Also, Warren had announced pretty clear plans of adding more features to the incentive builds and not releasing them open source for several years b) if you've been following the list, Jason has stated that many of the 1.4 features are on their way to the open source repository. Sure, I am of the type that wishes all features were open source and that Jason did all development directly against a repository we could all see, but I think he's done a good job communicating the way development is happening to the list and schrodinger's model for the incentive builds seems to be hardly different from what Warren had started doing. -David On Mar 23, 2011, at 6:33 AM, Abhinav Verma abhinav1...@gmail.com wrote: And why would that be? I thought that pymol is open source and till Warren was there all updates were available in the open source domain and incentive builds were limited to windows executable and involving support!! On Wed, Mar 23, 2011 at 11:15 AM, Mark J van Raaij mjvanra...@cnb.csic.es wrote: Is the 1.4 version restricted to incentive downloads only?? Yes Thanks, -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ 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 -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ 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 -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ 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] pisa
Why do you expect PISA to agree with author assigned biological units? Read the paper and see if there's a reason the authors made the assignment. If you really don't understand why things might be different, read the intro to the ProtCID paper. -David On Mar 3, 2011, at 6:37 AM, kanika sharma ksharma...@gmail.com wrote: protein 1b8e says its a dimer by its pdb file info as: BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 REMARK 350 BIOMT2 1 0.00 1.00 0.000.0 REMARK 350 BIOMT3 1 0.00 0.00 1.000.0 REMARK 350 BIOMT1 2 -1.00 0.00 0.000.0 REMARK 350 BIOMT2 2 0.00 1.00 0.000.0 REMARK 350 BIOMT3 2 0.00 0.00 -1.00 33.43000 when i feed the same into pisa..it says no assemblies are possible... i can't make out...can ny1 help.. Regards, Kanika -- 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
