[PyMOL] how to count all the Polar contacts
Dear PyMol users! I'm analysing polar contacts by preset:technical. I got so many yellow bar measurements that I can't count the number. IS there any else way to count the number of all polar contacts ? Thanks for help, Merlin-- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/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] Bug in interpretation of SCALEn records
Hi Takanori, PyMOL uses SCALEn to transform into fractional coordinates, and then the unit cell parameters (CRYST1) to transform back into cartesian coordinates. The PDB spec says: The unit cell parameters are used to calculate SCALE. For 1VW3, CRYST1 defines a unit cube, so I assume SCALEn should be the identity matrix, but it's not. You can skip this back-and-forth transformation with a setting: PyMOL set pdb_insure_orthogonal, off I assume PyMOL is doing the right thing here. If we want to know more about the intended interplay of CRYST1, ORIGXn and SCALEn, we might want to crosspost the topic to the CCP4BB list. Cheers, Thomas Takanori Nakane wrote, On 05/24/14 03:48: Dear all, I noticed a strange behaviour in the handling of SCALEn records in PDB files. When I load 1VW3, all atomic coordinates are scaled down to one thousandth and therefore all atoms get connected. The fact that the coordinates are incorrectly transformed can be confirmed by saving the loaded model again. This is probably due to the presence of SCALEn records: SCALE1 0.001000 0.00 0.000.0 SCALE2 0.00 0.001000 0.000.0 SCALE3 0.00 0.00 0.0010000.0 When they are deleted, the model can be loaded correctly. According to the PDB format specification http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#SCALEn , SCALEn records should not affect real space (orthogonal) coordinates. Best regards, Takanori Nakane -- Thomas Holder PyMOL Schrödinger, Inc. -- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/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] how to count all the Polar contacts
Hi Merlin - Try limiting the distances shown to those between atoms in specific selections using the `distance` command. For example, to show H-bonds to solvent, disable the “my_obj_pol_conts” object created by the technical preset and use the command: distance my_dist, my_obj and not solvent, my_obj and solvent, cutoff=3.5 Make sure to specify a cutoff or you’ll get every pair of polar atoms between your selections. Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On May 27, 2014, at 3:33 AM, 天元 422294...@qq.commailto:422294...@qq.com wrote: Dear PyMol users! I'm analysing polar contacts by preset:technical. I got so many yellow bar measurements that I can't count the number. IS there any else way to count the number of all polar contacts ? Thanks for help, Merlin -- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/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. = -- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/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] align or pair_fit display problem
Hi I-Ji - You say the superimposed atoms are still there; that seems like normal behavior to me. If you disable one of the objects, can you see the other one, and vice versa? If the two structures are nearly identical, you may not be able to differentiate them visually after alignment. If that is the case, you may wish to use different representations and/or colors for the two objects. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On May 26, 2014, at 6:58 PM, I-Ji Jung u5205...@anu.edu.aumailto:u5205...@anu.edu.au wrote: Hi, I'm trying to superimpose a small structure to a residue of a protein. When I use align or pair_fit to do this, the superposition works, but for some weird reason I can't see my small structure anymore. Like it's whole structure disappears. The superimposed atoms are there - but then those are overlapped by the same atoms of the residue, so you can't see them anyway. I've tried pair_fit some while ago and I recall using it without a problem. Why am I suddenly having this problem? Can somebody help me? Thanks, I-Ji -- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/4140/ostg.clktrk___ 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 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. = -- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/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
[PyMOL] Winners of the Teach-Discover-Treat 2014 Challenge
The 2014 Teach-Discover-Treat Initiative (TDTi) competition resulted in many high quality computational chemistry tutorials submitted across the four challenges. The judging panel selected the top three winners based on the published criteria for scientific content, presentation and clarity, educational benefit, and reproducibility. The winners receive a TDTi Travel Award when presenting their work at the TDTi 2014 Challenge Award symposium at the ACS 2014 Fall meeting in San Francisco, August 10-14, 2014. Please visit: http://www.tdtproject.org/blog/strong-showing-in-tdts-2014-challenge for the full 2014 Challenge announcement. All tutorials will be made available for download on this website at the time of the Award symposium. Follow us on Twitter ( https://twitter.com/TeachDiscoTreat ) for updates on the time and location of the symposium and celebratory social event! Thank you! The TDT Steering Committee Hanneke Jansen, Rommie Amaro, Jane Tseng, Wendy Cornell, Patrick Walters and Emilio Xavier Esposito www.TDTproject.org twitter.com/TeachDiscoTreat -- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/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
[PyMOL] autodock plugin -- no subprocess.py
Hello, I've been working through different tabs of the AD plugin, trying to find out what works with PyMOL v.1.7.1.3. The radio buttons on the grid tab are not working, but the biggest hurdle I've come against to this point is on the receptor tab. The plugin will correctly import the receptor file I have loaded into pymol, but when I click on Generate Receptor, the following error message pops up: Error: 1 type 'exceptions.WindowsError' Exception in Tk callback Function: bound method Autodock.generate_receptor of pmg_tk.startup.autodock_plugin.Autodock instance at 0x0A4F42C8 (type: type 'instancemethod') Args: () Traceback (innermost last): File C:\Python27\lib\site-packages\Pmw\Pmw_1_3\lib\PmwBase.py, line 1747, in __call__ return apply(self.func, args) File C:/Python27/Lib/site-packages/pymol/pymol_path/Pymol-Scripts-Pymol-script-repo/plugins\autodock_plugin.py, line 1952, in generate_receptor result, output = getstatusoutput(command) File C:/Python27/Lib/site-packages/pymol/pymol_path/Pymol-Scripts-Pymol-script-repo/plugins\autodock_plugin.py, line 54, in getstatusoutput p = Popen(command.split(), stdout=PIPE, stderr=STDOUT, env=env) File C:\Python27\lib\subprocess.py, line 709, in __init__ errread, errwrite) File C:\Python27\lib\subprocess.py, line 957, in _execute_child startupinfo) type 'exceptions.WindowsError': [Error 2] The system cannot find the file specified I'm not a python expert, but as far as I can tell the error lies with the AD plugin not being able to find subprocess.py. I DO have subprocess.py in my python 2.7 directory, but there is a slight difference my path name -- the actual location is \Python27\Lib, whereas the AD plugin is looking for subprocess.py in \Python27\lib. I don't know where in the autodock_plugin.py script it specifies the path for locating subprocess.py, otherwise I would have fixed this by now. Any help would be greatly appreciated, as I'm not sure if Seeliger is actively maintaining the plugin anymore. Blake -- Time is money. Stop wasting it! Get your web API in 5 minutes. www.restlet.com/download http://p.sf.net/sfu/restlet___ 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
