[PyMOL] AutoDock plugin
Dear PyMol users! I've forced with the problem of the installation of AutoDock plugin pymoawiki.org/index.php/Autodock_plugin in recent pymol version. I've tried to install it manually from the downloaded py script but at the starting of pymol below error has bbeen appeared Unable to initialize plugin 'autodock' (pmg_tk.startup.autodock). Unable to initialize plugin 'autodock_plugin' (pmg_tk.startup.autodock_plugin). Also I've tried to search for the plugin in the pymol repositories but have not found it. How it could be solved ? James -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/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] AutoDock plugin
Hi James, is it recent version of PyMOL, or recent version of Windows which makes trouble? On Windows, the plugin tries to write to the PyMOL installation folder, which fails if you don't have write permissions there. This needs to be fixed, the plugin should write to the users folder also on Windows. Cheers, Thomas On 06 Dec 2013, at 08:47, James Starlight jmsstarli...@gmail.com wrote: Dear PyMol users! I've forced with the problem of the installation of AutoDock plugin pymoawiki.org/index.php/Autodock_plugin in recent pymol version. I've tried to install it manually from the downloaded py script but at the starting of pymol below error has bbeen appeared Unable to initialize plugin 'autodock' (pmg_tk.startup.autodock). Unable to initialize plugin 'autodock_plugin' (pmg_tk.startup.autodock_plugin). Also I've tried to search for the plugin in the pymol repositories but have not found it. How it could be solved ? James -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/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] AutoDock plugin
Thomas, Thanks for suggestions. 1)I have installed Numpy. 2) File /usr/lib/python2.7/dist-packages/pymol/parser.py, line 260, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1, in module File /usr/share/pyshared/pmg_tk/startup/autodock_plugin.py, line 62, in module from numpy import * File /usr/share/pyshared/numpy/__init__.py, line 137, in module import add_newdocs File /usr/share/pyshared/numpy/add_newdocs.py, line 9, in module from numpy.lib import add_newdoc File /usr/share/pyshared/numpy/lib/__init__.py, line 4, in module from type_check import * File /usr/share/pyshared/numpy/lib/type_check.py, line 8, in module import numpy.core.numeric as _nx File /usr/share/pyshared/numpy/core/__init__.py, line 5, in module import multiarray ImportError: No module named multiarray What package is needed which consist of multiarray module ? James 2013/12/6 Thomas Holder spel...@users.sourceforge.net Hi James, import pmg_tk.startup.autodock_plugin should tell you what's wrong. My next guess is that you don't have numpy installed. For the missing bonds in your example, PyMOL thinks those atoms are cations because of the symbol in the last column. By default, PyMOL doesn't make bonds to cations. But this will work: PyMOLunset pdb_unbond_cations, PyMOLload example.pdb Hope that helps. Cheers, Thomas On 06 Dec 2013, at 11:04, James Starlight jmsstarli...@gmail.com wrote: Thomas, I have this problem within the recent pymol 1.6.0.0 version installed on Linux Debian (all others plugins work correct. Also Autodock plugin is not seen in the repository) By the way in this Pymol version I've forced with some problems with the ligands representation. For example I've obtained typical docking output from the AutoDock consisted of 10 poses (in separate models) but some atoms of this ligands is visualized as a blank atoms. Below the atoms of the one model are provided as the example. HETATM1 CAG P0G R 1 -0.073 -2.031 12.923 1.00 0.00 .001 A HETATM2 CAH P0G R 1 -0.624 -2.630 11.797 1.00 0.00 .001 A HETATM3 CAI P0G R 1 0.713 -0.894 12.787 1.00 0.00 .007 A HETATM4 CAJ P0G R 1 -0.383 -2.091 10.540 1.00 0.00 .007 A HETATM5 CAW P0G R 1 -2.339 3.404 5.677 1.00 0.00 .008 A HETATM6 CAL P0G R 1 -1.712 3.845 4.518 1.00 0.00 .015 A HETATM7 CAK P0G R 1 -1.825 5.176 4.131 1.00 0.00 .039 A HETATM8 CAB P0G R 1 0.291 2.102 8.752 1.00 0.00 .046 C HETATM9 CAC P0G R 1 -1.618 0.656 9.433 1.00 0.00 .046 C HETATM 10 CAA P0G R 1 1.806 0.879 11.409 1.00 0.00 .049 C HETATM 11 CAV P0G R 1 0.396 -0.946 10.403 1.00 0.00 .050 A HETATM 12 CAT P0G R 1 0.950 -0.354 11.529 1.00 0.00 .056 A HETATM 13 NAP P0G R 1 -0.642 0.506 7.208 1.00 0.00 .064 N HETATM 14 CAO P0G R 1 0.652 -0.375 9.023 1.00 0.00 .077 C HETATM 15 CAU P0G R 1 -2.570 6.062 4.900 1.00 0.00 .095 A HETATM 16 CAX P0G R 1 -3.197 5.612 6.048 1.00 0.00 .102 A HETATM 17 CAY P0G R 1 -3.084 4.294 6.426 1.00 0.00 .107 A HETATM 18 CBA P0G R 1 -0.335 0.720 8.612 1.00 0.00 .122 C HETATM 19 HAQ P0G R 1 -3.677 7.418 6.890 1.00 0.00 .169 H HETATM 20 CAZ P0G R 1 -2.233 1.990 6.093 1.00 0.00 .179 C HETATM 21 HAF P0G R 1 -2.600 0.245 5.251 1.00 0.00 .210 H HETATM 22 HAE P0G R 1 -2.798 7.416 3.572 1.00 0.00 .217 H HETATM 23 CAS P0G R 1 -4.971 5.977 7.513 1.00 0.00 .246 C HETATM 24 CAN P0G R 1 -0.768 1.610 6.272 1.00 0.00 .269 C HETATM 25 OAD P0G R 1 -5.901 6.691 7.854 1.00 0.00 .271 O HETATM 26 CAM P0G R 1 -4.980 4.505 7.870 1.00 0.00 .278 C HETATM 27 2HAP P0G R 1 -1.522 0.012 7.182 1.00 0.00 .278 H HETATM 28 3HAP P0G R 1 0.062 -0.118 6.840 1.00 0.00 .278 H HETATM 29 NAQ P0G R 1 -3.925 6.442 6.827 1.00 0.00 .321 N HETATM 30 OAR P0G R 1 -3.718 3.912 7.572 1.00 0.00 .339 O HETATM 31 OAE P0G R 1 -2.682 7.366 4.523 1.00 0.00 .358 O HETATM 32 OAF P0G R 1 -2.799 1.167 5.067 1.00 0.00 .389 O 2013/12/6 Thomas Holder spel...@users.sourceforge.net Hi James, is it recent version of PyMOL, or recent version of Windows which makes trouble? On Windows, the plugin tries to write to the PyMOL installation folder, which fails if you don't have write permissions there. This needs to be fixed, the plugin should write to the users folder also on Windows. Cheers, Thomas On 06 Dec 2013, at 08:47, James Starlight jmsstarli...@gmail.com wrote: Dear
[PyMOL] Capture PyMOL Output When Launched From Python
Is it possible to capture the output stream from PyMOL when it is launched from a Python script with... import os, __main__ os.environ['PYMOL_PATH'] = C:\Python27\PyMOL __main__.pymol_argv=[pymol, -qx] import pymol pymol.finish_launching() I see that an IDE can do this. Is there a way for me to capture the output to eliminate the command prompt window that appears? -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/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] Working with the pdb ensemble
Hi James - If I understand you correctly, you just need to give a selection argument to the save command. save ligand1.pdb, sele1 save ligand2.pdb, sele2 etc... See http://pymolwiki.org/index.php/Save for more info. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Dec 6, 2013, at 12:03 PM, James Starlight jmsstarli...@gmail.commailto:jmsstarli...@gmail.com wrote: Dear PyMol users! I'd be thankfull if you provide me with the easliest way how I could save selection to the separate pdbs. For example I've loaded 10 pdbs of the receptor and selected from in each 10 ligands. This selection is defined in one object (extracted or coppied from sele). How I could save it as 10 pdbs? Also I have a question about addtion of the hyrogens to each ligand in ensemble. How I could add hydrogens in accordance to the specified protonation states of the ligands (manually providing total charge)? Thanks for help, James -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/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 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/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] Working with the pdb ensemble
Hi Jared, The issue is that the all ligands are copied in one sele (and than extracted to one object). Consequently I'd like to split it to separate objects as the lig1.pdb lig2.pdb etc James 2013/12/7 Sampson, Jared jared.samp...@nyumc.org Hi James - If I understand you correctly, you just need to give a selection argument to the save command. save ligand1.pdb, sele1 save ligand2.pdb, sele2 etc... See http://pymolwiki.org/index.php/Save for more info. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Dec 6, 2013, at 12:03 PM, James Starlight jmsstarli...@gmail.com wrote: Dear PyMol users! I'd be thankfull if you provide me with the easliest way how I could save selection to the separate pdbs. For example I've loaded 10 pdbs of the receptor and selected from in each 10 ligands. This selection is defined in one object (extracted or coppied from sele). How I could save it as 10 pdbs? Also I have a question about addtion of the hyrogens to each ligand in ensemble. How I could add hydrogens in accordance to the specified protonation states of the ligands (manually providing total charge)? Thanks for help, James -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/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 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/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
