[PyMOL] install Pymol 1.5 on Linux Mint 13
Hi, I'm trying to install PyMOL-v1.5.0.4-Linux-x86_64 on Linux Mint 13. After successful unpacking, sh-ing and copying into /usr/local/bin/pymol I tried to execute Pymol from the terminal, but error came out: vitali@vs-Think ~/install/pymol $ pymol /home/vitali/install/pymol/pymol.exe: 1: /home/vitali/install/pymol/pymol.exe: Syntax error: ) unexpected What am I doing wrong? I tried to google, but nothing similar came up. Thanks, Vitali -- How ServiceNow helps IT people transform IT departments: 1. Consolidate legacy IT systems to a single system of record for IT 2. Standardize and globalize service processes across IT 3. Implement zero-touch automation to replace manual, redundant tasks http://pubads.g.doubleclick.net/gampad/clk?id=5127iu=/4140/ostg.clktrk___ 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] 1.5 version runs slow with large objects
Jason, I did install latest driver for a card (295.20) from nvidia site. The problem still exists. Any other suggestions? Thanks, Vitali On Wed, Feb 15, 2012 at 9:14 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Vitaly, Have you installed the latest graphics drivers for your card? Cheers, -- Jason On Tue, Feb 14, 2012 at 5:27 PM, Vitali Stanevich stanev...@wisc.edu wrote: Hi, I recently installed a new version of licensed pymol 1.5. It works ok with small molecules (25 kDa). But, unfortunately, I found that after I load relatively large molecules (60 kDa) everything really slows down, movements become somewhat abrupt and etc. At the same time, I can open this molecule with coot, generate bunch of symmetry mates, add maps, but everything runs really smooth. How can I make pymol run smooth again (version 1.2 worked well before)? Pymol: PyMOL-v1.5.0-Linux-x86_32-TclTk8.5 (I tried 64-bit with the same result) OS: Ubuntu 10.10 Video card: nVidia GeForce 7150M CPU: AMD Turion(tm) 64 X2 TL-62 (2100 MHz, 64 bits) Thanks, Vitali -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ 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] 1.5 version runs slow with large objects
Jason, I do not have .pymorc file. But when I set use_shaders to 0, then everything becomes fast and nice. I guess I just can turn on shaders only as the final step before ray_tracing. Thanks for help, Vitali On Thu, Feb 16, 2012 at 1:22 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Vitaly, It looks like the 7150M has only 57 megs of dedicated memory. Once you exhaust that your performance will decrease dramatically. I'l contact NVidia and see if they have any suggestions. Also, do you have a ~/.pymolrc file? If so, what's in it? For the new graphics to perform, you need the use_shaders setting turned on. Cheers, -- Jason On Thu, Feb 16, 2012 at 2:09 PM, Vitali Stanevich stanev...@wisc.edu wrote: Jason, I did install latest driver for a card (295.20) from nvidia site. The problem still exists. Any other suggestions? Thanks, Vitali On Wed, Feb 15, 2012 at 9:14 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Vitaly, Have you installed the latest graphics drivers for your card? Cheers, -- Jason On Tue, Feb 14, 2012 at 5:27 PM, Vitali Stanevich stanev...@wisc.edu wrote: Hi, I recently installed a new version of licensed pymol 1.5. It works ok with small molecules (25 kDa). But, unfortunately, I found that after I load relatively large molecules (60 kDa) everything really slows down, movements become somewhat abrupt and etc. At the same time, I can open this molecule with coot, generate bunch of symmetry mates, add maps, but everything runs really smooth. How can I make pymol run smooth again (version 1.2 worked well before)? Pymol: PyMOL-v1.5.0-Linux-x86_32-TclTk8.5 (I tried 64-bit with the same result) OS: Ubuntu 10.10 Video card: nVidia GeForce 7150M CPU: AMD Turion(tm) 64 X2 TL-62 (2100 MHz, 64 bits) Thanks, Vitali -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ 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] 1.5 version runs slow with large objects
Hi, I recently installed a new version of licensed pymol 1.5. It works ok with small molecules (25 kDa). But, unfortunately, I found that after I load relatively large molecules (60 kDa) everything really slows down, movements become somewhat abrupt and etc. At the same time, I can open this molecule with coot, generate bunch of symmetry mates, add maps, but everything runs really smooth. How can I make pymol run smooth again (version 1.2 worked well before)? Pymol: PyMOL-v1.5.0-Linux-x86_32-TclTk8.5 (I tried 64-bit with the same result) OS: Ubuntu 10.10 Video card: nVidia GeForce 7150M CPU: AMD Turion(tm) 64 X2 TL-62 (2100 MHz, 64 bits) Thanks, Vitali -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d___ 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] query
here it is: http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts vitali On Mon, Nov 21, 2011 at 8:50 AM, rjayashree13-scie...@yahoo.co.in rjayashree13-scie...@yahoo.co.in wrote: Thank you. It works, but it does not bring out the type of interaction responsible for interface contact-hydrogen bonding or electrostatic interaction etc. I am using another tool called PSAP for analyzing inter-molecular interactions (iris.physics.iisc.ernet.in/psap) It gives me the residues involved in hydrogen bonding, now using Pymol I can label these residues, but is there any way to depict these hydrogen bonds also and the distances? Dr. Jayashree Ramana http://www.juit.ac.in/bio/jsr.php -- *From:* Vitali Stanevich stanev...@wisc.edu *To:* rjayashree13-scie...@yahoo.co.in rjayashree13-scie...@yahoo.co.in *Cc:* pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net *Sent:* Sunday, 20 November 2011 1:57 PM *Subject:* Re: [PyMOL] query check this out: http://www.pymolwiki.org/index.php/InterfaceResidues if you want faster and easier, but less reliable (in my opinion) way, you can analyze your .pdb with PISA: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html vitali On Sun, Nov 20, 2011 at 1:51 AM, rjayashree13-scie...@yahoo.co.in rjayashree13-scie...@yahoo.co.in wrote: I have a PDB file for a dimeric protein. Is it possible to depict the intersubunit contacts for any PDB file? Is Pymol alone sufficient for this purpose or will it only help visualization? Could you also tell me which commands in Pymol can I use for this purpose? I have tried a lot but could not get an answer to this. I will be very thankful for the favour. Dr. Jayashree Ramana http://www.juit.ac.in/bio/jsr.php -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, 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-novd2d ___ 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 the data continuously generated in your IT infrastructure contains a definitive record of customers, 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-novd2d___ 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] query
check this out: http://www.pymolwiki.org/index.php/InterfaceResidues if you want faster and easier, but less reliable (in my opinion) way, you can analyze your .pdb with PISA: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html vitali On Sun, Nov 20, 2011 at 1:51 AM, rjayashree13-scie...@yahoo.co.in rjayashree13-scie...@yahoo.co.in wrote: I have a PDB file for a dimeric protein. Is it possible to depict the intersubunit contacts for any PDB file? Is Pymol alone sufficient for this purpose or will it only help visualization? Could you also tell me which commands in Pymol can I use for this purpose? I have tried a lot but could not get an answer to this. I will be very thankful for the favour. Dr. Jayashree Ramana http://www.juit.ac.in/bio/jsr.php -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, 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-novd2d ___ 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 the data continuously generated in your IT infrastructure contains a definitive record of customers, 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-novd2d___ 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] Movie to export
have a look at this link: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera disregard morph part. you can modify script to contain frames instead of states. i installed ffmpeg from repositories on ubuntu and don't remember any issues with kodecs. vitali On Wed, Nov 9, 2011 at 8:14 AM, Tim Schulte tim.schu...@ki.se wrote: ** Hi, Quick time player 7 pro does a great job for me. Cheers Tim Am 11/8/11 9:54 PM, schrieb Troels Emtekær Linnet: Hi. I have made a nice little movie in Pymol. 1500 frames. So now I am wondering what is the best method to export? At the moment I do export to .png with ray tracing each image. set ray_trace_frames = 1 That takes a long time. And what program should I use to pack them together? The easy wasy? Can it be done faster with the MPEG method? Best Troels Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register nowhttp://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ 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] Movie to export
one more thing: ffmpeg script at that link didn't work for me so i had to modify it like that ffmpeg -f image2 -qscale 5 -r 24 -b 9600 -i image%d.png movie.mpg On Wed, Nov 9, 2011 at 11:22 PM, Vitali Stanevich stanev...@wisc.eduwrote: have a look at this link: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera disregard morph part. you can modify script to contain frames instead of states. i installed ffmpeg from repositories on ubuntu and don't remember any issues with kodecs. vitali On Wed, Nov 9, 2011 at 8:14 AM, Tim Schulte tim.schu...@ki.se wrote: ** Hi, Quick time player 7 pro does a great job for me. Cheers Tim Am 11/8/11 9:54 PM, schrieb Troels Emtekær Linnet: Hi. I have made a nice little movie in Pymol. 1500 frames. So now I am wondering what is the best method to export? At the moment I do export to .png with ray tracing each image. set ray_trace_frames = 1 That takes a long time. And what program should I use to pack them together? The easy wasy? Can it be done faster with the MPEG method? Best Troels Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register nowhttp://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ 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
