Re: [PyMOL] [PyMol] How to visualize surface within a given radius
Greetings, Please also investigate the following settings: # needs a real atom selection surface_carve_selection # distance from the above selection to cull surfaces surface_carve_cutoff I looked at your data and there is a small problem. You have a few points where one atom is mapped to multiple surface points. Thus, when you show it as surface two pocket fragments show up. When you hide it they both hide. Also of interest is PyMOL's ability to render pockets and cavities on its own (Settings > Surface > Cavities & Pockets). Cheers, -- Jason On Mon, Mar 4, 2013 at 2:15 PM, Sampson, Jared wrote: > Hi Yarrow - > > If you add "br. " to the show surface command, you will get more > continuous surfaces, as the selection will be made by residue instead of by > atom. > > show surface, br. protein within 0.5 of pocket_selection > > > If you don't want to show the surface from a particular residue (e.g. if > it's masking something else you want to show), you can hide surface for a > selection. > > hide surface, resi 225+347 > > > Cheers, > Jared > > -- > Jared Sampson > Xiangpeng Kong Lab > NYU Langone Medical Center > Old Public Health Building, Room 610 > 341 East 25th Street > New York, NY 10016 > 212-263-7898 > http://kong.med.nyu.edu/ > > > > > On Mar 4, 2013, at 2:37 PM, Yarrow Madrona wrote: > > Thank you for your help Thomas, > > Using your settings I get a lot of "partial surfaces" > > Showing the surface around the Pocket selection like this: > > show surface, protein within 0.5 of pocket_selection > > worked well but I still see a piece of surface that I really don't want to > show up. I guess I can take it out in photoshop but that just seems wrong. > I have attached it. > > -Yarrow > > > > Hi Yarrow, > should be as simple as: > PyMOL> hide surface > PyMOL> show surface, (organic around 8.0) > PyMOL> set transparency, 0.3 > PyMOL> set two_sided_lighting > See also: > http://pymolwiki.org/index.php/Selection_Algebra > Hope that helps. > Cheers, > Thomas > Yarrow Madrona wrote, On 03/03/13 18:34: > > Hello, > Does anyone know how to visualize a surface within a given radius from > > a > > ligand binding site? In chimera you can limit the display surface > > within > > 0-X angstrom of a ligand. This allows you to see the surface > > surrounding > > the ligand without the rest of the protein. > I guess you could create a new selection of residues around a ligand > > and > > show this surface but I wondered if there are any other ways of doing > > this. > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > > -- > > Everyone hates slow websites. So do we. > > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > ___ > 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 > > > -- > Yarrow Madrona > > Graduate Student > Molecular Biology and Biochemistry Dept. > University of California, Irvine > Natural Sciences I, Rm 2403 > Irvine, CA 92697 > > > -- > > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > > http://p.sf.net/sfu/appdyn_d2d_feb___ > 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 > > > > > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > ___ > 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 Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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 install
Hi Yeping, Check out http://www.pymolwiki.org/index.php/Linux_Install#Compile_and_install. Cheers, -- Jason On Mon, Mar 4, 2013 at 8:17 PM, yp sun wrote: > Dear pymol users, > > I try to install pymol in Linux system as following > > (1) download pymol-v1.5.0.1.tar.bz2 and decompress it to /opt directory. > (2) go into /opt/pymol/setup directiry and enter the command "setup.sh" > > Then I see the install success information: > > > Creating "./pymol" startup script with > PYMOL_PATH=/opt/pymol/setup > > If you need to move PyMOL in the future, > re-run "./setup.sh" afterwards. > > You may now want to copy or link: > "/opt/pymol/setup/pymol" > to something like "/usr/local/bin/pymol" > > Enjoy! > > However, when I type "pymol" command, I get the error information: > > ./pymol: line 14: /opt/pymol/setup/ext/bin/python: No such file or > directory > ./pymol: line 14: exec: /opt/pymol/setup/ext/bin/python: cannot execute: > No such file or directory > > Could you tell me why? > > Thanks! > > Yeping Sun > CAS Key Laboratory of Pathogenic Microbiology & Immunology > INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES > NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china > > > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > ___ > 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 Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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] pymol install
Dear pymol users, I try to install pymol in Linux system as following (1) download pymol-v1.5.0.1.tar.bz2 and decompress it to /opt directory. (2) go into /opt/pymol/setup directiry and enter the command "setup.sh" Then I see the install success information: Creating "./pymol" startup script with PYMOL_PATH=/opt/pymol/setup If you need to move PyMOL in the future, re-run "./setup.sh" afterwards. You may now want to copy or link: "/opt/pymol/setup/pymol" to something like "/usr/local/bin/pymol" Enjoy! However, when I type "pymol" command, I get the error information: ./pymol: line 14: /opt/pymol/setup/ext/bin/python: No such file or directory ./pymol: line 14: exec: /opt/pymol/setup/ext/bin/python: cannot execute: No such file or directory Could you tell me why? Thanks! Yeping Sun CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china-- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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] How to visualize surface within a given radius
Hi Yarrow - If you add "br. " to the show surface command, you will get more continuous surfaces, as the selection will be made by residue instead of by atom. show surface, br. protein within 0.5 of pocket_selection If you don't want to show the surface from a particular residue (e.g. if it's masking something else you want to show), you can hide surface for a selection. hide surface, resi 225+347 Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 4, 2013, at 2:37 PM, Yarrow Madrona mailto:amadr...@uci.edu>> wrote: Thank you for your help Thomas, Using your settings I get a lot of "partial surfaces" Showing the surface around the Pocket selection like this: show surface, protein within 0.5 of pocket_selection worked well but I still see a piece of surface that I really don't want to show up. I guess I can take it out in photoshop but that just seems wrong. I have attached it. -Yarrow Hi Yarrow, should be as simple as: PyMOL> hide surface PyMOL> show surface, (organic around 8.0) PyMOL> set transparency, 0.3 PyMOL> set two_sided_lighting See also: http://pymolwiki.org/index.php/Selection_Algebra Hope that helps. Cheers, Thomas Yarrow Madrona wrote, On 03/03/13 18:34: Hello, Does anyone know how to visualize a surface within a given radius from a ligand binding site? In chimera you can limit the display surface within 0-X angstrom of a ligand. This allows you to see the surface surrounding the ligand without the rest of the protein. I guess you could create a new selection of residues around a ligand and show this surface but I wondered if there are any other ways of doing this. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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] How to visualize surface within a given radius
Thank you for your help Thomas, Using your settings I get a lot of "partial surfaces" Showing the surface around the Pocket selection like this: show surface, protein within 0.5 of pocket_selection worked well but I still see a piece of surface that I really don't want to show up. I guess I can take it out in photoshop but that just seems wrong. I have attached it. -Yarrow > Hi Yarrow, > should be as simple as: > PyMOL> hide surface > PyMOL> show surface, (organic around 8.0) > PyMOL> set transparency, 0.3 > PyMOL> set two_sided_lighting > See also: > http://pymolwiki.org/index.php/Selection_Algebra > Hope that helps. > Cheers, > Thomas > Yarrow Madrona wrote, On 03/03/13 18:34: >> Hello, >> Does anyone know how to visualize a surface within a given radius from a >> ligand binding site? In chimera you can limit the display surface within >> 0-X angstrom of a ligand. This allows you to see the surface surrounding >> the ligand without the rest of the protein. >> I guess you could create a new selection of residues around a ligand and >> show this surface but I wondered if there are any other ways of doing this. > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > -- Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > ___ > 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 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 <>-- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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] Showing secondary structure of coarse grained protein
Hi Stephane, You don't have phi/psi angles, so determining secondary structure is a bit problematic. What you can do is draw a trace through the backbone beads and set the secondary structure representation explicitly. You'll have to make sure to exclude connections between chains. set cartoon_trace_atoms show cartoon, CG_protein and n. bb cartoon helix cartoon loop, i. 1-10 # and so on... Hope it helps, Tsjerk On Mon, Mar 4, 2013 at 4:03 PM, ABEL Stephane 175950 wrote: > Hello everybody, > > I have done several MD simulations with the Martini force field of systems > that contain a small protein and surfactant with GROMACS. It is possible to > show with pymol the secondary structure of the protein with a cartoon > representation and the detergent molecules with beads at the same time. I > know from you that I can use for the detergent molecules, the "connects" but > for protein i don't know how to do (with the alter command?). > > Can you help me? > > Thanks you in advance > > Stephane > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > ___ > 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 Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] Showing secondary structure of coarse grained protein
Hello everybody, I have done several MD simulations with the Martini force field of systems that contain a small protein and surfactant with GROMACS. It is possible to show with pymol the secondary structure of the protein with a cartoon representation and the detergent molecules with beads at the same time. I know from you that I can use for the detergent molecules, the "connects" but for protein i don't know how to do (with the alter command?). Can you help me? Thanks you in advance Stephane -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] Help to compile u3d converter - IDTF to U3D on linux 64
On 04/03/13 12:21, Troels Emtekær Linnet wrote: > Dear Pymolers. > > I am playing around with creating a pdf file with 3 D graphics. > I am saving in *idtf* format, which I convert to *u3d, *and then include > in pdf through latex. > > I can do this on windows, but I can't compile IDTFConverter *on linux 64.* > > I have made this progress > > http://pymolwiki.org/index.php/3d_pdf#Linux_install > > But when I compile, I get. Hi, try this one http://www2.iaas.msu.ru/tmp/u3d/u3d-1.4.3.tar.gz it only has problems with gcc-4.7 but I can provide a patch if needed. Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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] Help to compile u3d converter - IDTF to U3D on linux 64
Dear Pymolers. I am playing around with creating a pdf file with 3 D graphics. I am saving in *idtf* format, which I convert to *u3d, *and then include in pdf through latex. I can do this on windows, but I can't compile IDTFConverter *on linux 64.* I have made this progress http://pymolwiki.org/index.php/3d_pdf#Linux_install But when I compile, I get. ### ERROR ### Building Core Build started: Project: Base, Configuration: release Lin32 - In file included from IFXVectorHasher.cpp:32: IFXVectorHasher.h: In member function ‘BOOL IFXVectorHasherNodeIterator::Next()’: IFXVectorHasher.h:215: error: cast from ‘IFXVectorHasherVectorNode*’ to ‘BOOL’ loses precision IFXVectorHasher.h: In member function ‘BOOL IFXVectorHasherBinIterator::Next()’: IFXVectorHasher.h:279: error: cast from ‘IFXVectorHasherBinNode*’ to ‘BOOL’ loses precision make: *** [all] Error 1 Base - 2 error(s), 0 warning(s) *** BUILD Core ERROR * --- Build done --- Base - 2 error(s), 0 warning(s) : failed -- Entire build: 0 succeeded, 1 failed = ERROR, build process is not complete = # I think it it because that I try to compile 32 bit, with a gcc 64 bit version. *Does anyone know how-to compile this on a linux machine?* I would be happy if we could get IDTFConverter on out linux machines in the lab. Best Troels Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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
