Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)
Dear Thomas, Thanks for good pointing for the weird problem, which I couldn't notice at all. You do compile with -D_FORTIFY_SOURCE=2, could you remove that? I'm afraid, I know not related PyMOL itself, but I wish to know how to do that. Searching 'setup.py', 'setup2.py' or some 'Makefile*' with the string 'D_FORTIFY_SOURCE' or 'gcc' returned no matches. And Zhijian and Andreas, Thank you for advices through your experiences, I will pursue at first as Thomas advised. Regards, Masataka 2011/12/5 Andreas Förster docandr...@gmail.com: Dear Masataka, a few months ago, I upgraded most of our computers from RHEL 5.x to 6.1. If version 6 of CentOS (free RHEL clone) is out, I would highly recommend, no I would urge you, to upgrade as well. RHEL and CentOS are rock-solid operating systems, but their libraries and dependencies show their age. Andreas On 05/12/2011 1:50, grantaka36 wrote: Hi, Marius, Troels and David, I appreciate very much for guiding, tried in three ways but no success currently. - I also think some difference on distributions (CentOS 5 here,) trapped at function 'IsosurfGetRange' Does anyone have information to workaround? - Do you think if any dependency on Python version (2.4.3 here)? Attached '20111205_script_and_error.zip' is for information sharing: - 'install_pymol.sh' : followed by below, some package name modified for CentOS http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support - 'install_pymol_sh_error.txt' layer0/Isosurf.c:2197:1: error: unterminated argument list invoking macro fprintf layer0/Isosurf.c: In function 'IsosurfGetRange': - 'install_pymol_gcc45.sh' - aiming to use default installed gcc4.5 instead of 4.4 - 'install_pymol_gcc45_sh_error.txt' layer0/Isosurf.c: In function 'IsosurfGetRange': layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro fprintf - 'compile_pymol.sh' : again by initial trying http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source - 'compile_pymol_sh_error.txt' layer0/Isosurf.c: In function 'IsosurfGetRange': layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro fprintf Regards, Masataka -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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] mmView - a tool for mmCIF exploration
Hi Troels, mmView is intended as a web-based viewer (and nothing more) of the textual mmCIF format, which i used by the PDB database as its archival format. mmCIF offers, with its flexible syntax, much better solution for storing biomolecular structures than the PDB format. However, mmCIF format is primarily intended for automatic processing, and is thus, in contrary to PDB format, much less readable by human. The data in the mmCIF format are stored as database tables (called categories), and our tool tries to facilitate the work with mmCIF files. All data shown by mmView are taken from the mmCIF file with the only exception, which is the abstract of the structure citation that is downloaded automatically from Pubmed database. Sure there is overlap with Proteopedia, however Proteopedia's aim is apparently to provide as much information about the given structure as possible (and there is much much more information in Proteopedia than in mmView, and certainly some information in Proteopedia is obtained from the mmCIF or PDB file). The aim of mmView is to present mmCIF categories in more readable form, and in addition some information about the structure we regard as interesting is aggregated from more categorie and presented in a summary form. We use mmView in the classes of structural biology and structural bioinformatics, and our experience shows that students grasp much easily basic principles of the mmCIF format if it is presented this way. More information about mmView you can find in the BMC Rasearch Notes journal: http://www.biomedcentral.com/content/pdf/1756-0500-4-121.pdf. Regards Daniel 2011/12/6 Troels Emtekær Linnet tlin...@gmail.com: That reminds me of: http://www.proteopedia.org/wiki/index.php/4ins What is the difference between the two web pages? Best Troels 2011/12/6 Daniel Svozil daniel.svo...@vscht.czmailto:daniel.svo...@vscht.cz Dear colleagues, We would like to announce the availability of mmView - the web-based application which allows to comfortably explore the structural data of biomacromolecules stored in the mmCIF (macromolecular Crystallographic Information File) format. The mmView software system is primarily intended for educational purposes but it can also serve as an auxiliary tool for working with biomolecular structures. The mmView application is offered in two flavors: as a publicly available web server http://ich.vscht.cz/projects/mmview/, and as an open-source stand-alone application (available from http://sourceforge.net/projects/mmview) that can be installed on the user’s computer. Petr Cech and Daniel Svozil -- Daniel Svozil, PhD Head of Laboratory of Informatics and Chemistry Institute of Chemical Technology Czech Republic phone: +420 220 444 391tel:%2B420%20220%20444%20391 http://ich.vscht.cz/~svozil -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 -- Daniel Svozil, PhD Head of Laboratory of Informatics and Chemistry Institute of Chemical Technology Czech Republic phone: +420 220 444 391 http://ich.vscht.cz/~svozil -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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] Electron Density
Is there a difference in the sigma values assigned by pymol and coot I am able to see the density at 8 sigma in coot for the Fo-Fc map but can go to maximum at 4.5 sigma in pymol after which it disappears On Mon, Dec 5, 2011 at 11:33 PM, Roger Rowlett rrowl...@colgate.edu wrote: I think the isomesh command will let you set whatever contour level you wish, e.g.: isomesh map, mymap.map, X.X, maparea Where map is the name of the mesh object, mymap.map is the map file name, X.X is the desired contour level, and maparea, is the selection about which you would like to see the electron density mesh. I haven't tested the contour limits, but it's larger than 10. ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 12/5/2011 12:49 PM, Manas Sule wrote: I have tried that...but i can see the density in coot at even 8 sigma.. however the maximum i can go to in pymol is 4.5 simga on a F0-Fc map Can u suggest any method to see the same density at 6 sigma Manas On Mon, Dec 5, 2011 at 11:14 PM, Pete Meyer pame...@mcw.edu wrote: isomesh [mesh name], [map name], 6.0 -- 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 -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/___ 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] Electron Density
Hi Manas, have you tried turning the normalize_* setting off? set normalize_ccp4_maps, off set normalize_o_maps, off set normalize_grd_maps, off http://pymolwiki.org/index.php/Normalize_ccp4_maps http://pymolwiki.org/index.php/Display_CCP4_Maps#User_Notes Cheers, Thomas On 12/06/2011 03:12 PM, Manas Sule wrote: Is there a difference in the sigma values assigned by pymol and coot I am able to see the density at 8 sigma in coot for the Fo-Fc map but can go to maximum at 4.5 sigma in pymol after which it disappears -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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] Electron Density
Hi Manas Sule, this is a bit more complicated: For PyMOL, you usually calculate an electron density map covering your molecule. As far as I understand PyMOL, the sigma is taken directly from your input map. For Coot, this is completely different. Coot tries to reconstruct from your input map the complete map for the unit cell taking the crystallographic symmetry into account (using it for displaying an infinite map), and calculates the sigma from the unit cell map. This already might be different to the sigma within the box that you used to cover your molecule. However, if the reconstruction fails, either because the symmetry of your map is wrong (i.e., P1), or the input box is too small to allow reconstruction of the whole unit cell, the rest of the unit cell is filled with 0, resulting in much smaller sigma values! If this happens, you have to display the input map at a much higher sigma level in Coot to get the same absolute electron density value and thus appearance. Apparently, this is the case for your map. To get the sigma value right, you should calculate a map covering either the asymmetric unit with the right symmetry or covering the whole unit cell. Then, run a peak search program, like CCP4 peakmax, or play visually with the sigma value using that map - it should be same in PyMOL and in Coot, then. Best regards, Dirk. Am 06.12.11 15:12, schrieb Manas Sule: Is there a difference in the sigma values assigned by pymol and coot I am able to see the density at 8 sigma in coot for the Fo-Fc map but can go to maximum at 4.5 sigma in pymol after which it disappears On Mon, Dec 5, 2011 at 11:33 PM, Roger Rowlett rrowl...@colgate.edu mailto:rrowl...@colgate.edu wrote: I think the isomesh command will let you set whatever contour level you wish, e.g.: isomesh map, mymap.map, X.X, maparea Where map is the name of the mesh object, mymap.map is the map file name, X.X is the desired contour level, and maparea, is the selection about which you would like to see the electron density mesh. I haven't tested the contour limits, but it's larger than 10. ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu mailto:rrowl...@colgate.edu On 12/5/2011 12:49 PM, Manas Sule wrote: I have tried that...but i can see the density in coot at even 8 sigma.. however the maximum i can go to in pymol is 4.5 simga on a F0-Fc map Can u suggest any method to see the same density at 6 sigma Manas On Mon, Dec 5, 2011 at 11:14 PM, Pete Meyer pame...@mcw.edu mailto:pame...@mcw.edu wrote: isomesh [mesh name], [map name], 6.0 -- 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 mailto: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 mailto: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 -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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] H-bonds representation
Dear all :) I want to find Hbonds beetween different helices in the membrane receptor ( H bonds beetween sidechains only) I know possible way to do it wihin selection if I defined different helixes but is there any way to find almost all Hbonds between polar sidecains groups ? Could I use find- polar contact- sidechain only for this purpose ? James 2011/11/30 Jason Vertrees jason.vertr...@schrodinger.com James, It works quite well in case of not very compliated ligands ( e.g bonds beetween aa-tRNA and the aa-tRNA syntase were correct ) but in the sugar-bound enzyme there were some mistakes in representation of the H-bonds netween water/ligand/active center ( some water also partisipate in the ligand binding but in case where water and some residues of the active sites were positioned iclosely the bonds were incorect ). So a I understood I can fix this mistakes only manually ? Please ask the pymol-users about this. By the way, on what assumptions helix elements of my proteins were colored after representation of the ligand binding with the cartoons ? It's colored rainbow from start to end. Finally how I could represent ionic contacts in the ion-binding proteins ? E.g now I'm studing calmodulin wich has Ef-hand Ca-binding motifs. I've tried to represent bonds beetwen some polar residues of the active site with the ligand but failed :( Please ask the pymol-users about this. I'm gearing up for the PyMOL v1.5.0 release, so I won't have time right now to personally answer your questions. Please keep relying on the pymol-users list--they're very knowledgeable about PyMOL. Cheers, -- Jason 2011/11/29 Jason Vertrees jason.vertr...@schrodinger.com James, Is there any semi-avtomated way to find ligand binding pocket and do all such things ? For your given object, click A preset ligands sites cartoon. Try other options under that menu. Cheers, -- Jason 2011/11/28 Thomas Holder spel...@users.sourceforge.net Hi James, most trivial manner: as cartoon show sticks, resn LEU+ILE+VAL set cartoon_side_chain_helper and eventually something like this: show spheres, resn LEU+ILE+VAL and not name N+O+C set sphere_transparency, 0.5 Cheers, Thomas On 11/28/2011 02:58 PM, James Starlight wrote: Another question also linked with the non-covalent interaction. In particular I wounder to know how i Could represent all hydrophobic ( Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd like to represent the hydrophobic core of the proteins made from those residues. Thanks, James -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives:
Re: [PyMOL] Electrostatic calculations with ligand bound
Hi Andrew, The main limitation for problems like this is that you need to have parameters for the ligand. Making sure that you have good parameters is often an expert-level topic, and you're probably best served by the APBS or PDB2PQR listservs as well as the literature ... but, you can get a decent start on things with PDB2PQR itself. See http://www.poissonboltzmann.org/pdb2pqr/examples/ligand-parameterization for some good starting instructions. Once you have a PQR file that includes both the protein and the ligand, the PyMOL/APBS plugin should do everything that you need. If that doesn't solve your problem, please let me know. Cheers, -Michael On Tue, Nov 29, 2011 at 11:44 AM, Malaby, Andrew andrew.mal...@umassmed.edu wrote: Hey guys, I am trying to calculate electrostatics with a ligand bound to my molecule using ABPS. I am not having success. Everything I've read seems to say that this is a normal limitation with APBS, and I've tried other programs to no avail. I have not been able to rebuild my molecule in the correct format either. Any help here is greatly appreciated. Andrew UMass Med School, Worcester, MA -- 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 -- Michael Lerner Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095 -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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] Electrostatic calculations with ligand bound
Hi Andrew. I experienced something similar for the autodock_plugin. http://www.pymolwiki.org/index.php/Autodock_plugin During my trials, I notified two things for autodock. It did not like funny atom names or Alternative configuration Could this be a case for your protein / ligand? I don't know if is the same for the APBS plugin, but you could try? http://www.pymolwiki.org/index.php/Autodock_plugin#Example_1_-_Rename_of_funny_atom_names Some of the preparation scripts for both plugins are coming from the same research groups. I think they both use: pdb2pqr or something. Best Troels 2011/12/7 Michael Lerner mgler...@gmail.com Hi Andrew, The main limitation for problems like this is that you need to have parameters for the ligand. Making sure that you have good parameters is often an expert-level topic, and you're probably best served by the APBS or PDB2PQR listservs as well as the literature ... but, you can get a decent start on things with PDB2PQR itself. See http://www.poissonboltzmann.org/pdb2pqr/examples/ligand-parameterization for some good starting instructions. Once you have a PQR file that includes both the protein and the ligand, the PyMOL/APBS plugin should do everything that you need. If that doesn't solve your problem, please let me know. Cheers, -Michael On Tue, Nov 29, 2011 at 11:44 AM, Malaby, Andrew andrew.mal...@umassmed.edu wrote: Hey guys, I am trying to calculate electrostatics with a ligand bound to my molecule using ABPS. I am not having success. Everything I've read seems to say that this is a normal limitation with APBS, and I've tried other programs to no avail. I have not been able to rebuild my molecule in the correct format either. Any help here is greatly appreciated. Andrew UMass Med School, Worcester, MA -- 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 -- Michael Lerner Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095 -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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 -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/___ 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
