Re: [PyMOL] Database with protein experimental pKa values, with possibility to search for Cysteines and .pdb structure.
Hi Troels, about 8 month again I used their dataset: PINT: Protein-protein Interactions Thermodynamic Database. Kumar MD, Gromiha MM. Department of Biochemical Engineering and Science, Kyushu Institute of Technology Iizuka 820-8502, Fukuoka, Japan. sh...@bse.kyutech.ac.jp http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347380/?tool=pubmed Unfortunately their website seems to be down right now, but maybe dropping an email does the magic. HTH, Thomas 2011/8/24 Troels Emtekær Linnet tlin...@gmail.com: Hi pymolers. I simple don't know where else so post this question. So I hope that some of you guys can help me. I need a Database with protein experimental pKa values, with possibility to search for Cysteines and .pdb structure Because, I have made a pymol script that predicts the pKa value for a cysteine very precise. The model is described in: Predicting Reactivities of Protein Surface Cysteines as Part of a Strategy for Selective Multiple Labeling Maik H. Jacob, Dan Amir, Vladimir Ratner, Eugene Gussakowsky, and Elisha Haas* Biochemistry 2005, 44, 13664-13672 With help from Maik, we got it to work very good. I got a pearson correlation coefficient of 0.90 and have batched up against propka, which gets 0.70 So, it looks like this script can be superior, at least for cysteine predictions. But to make the method more reliable, I need to find a database where experimental pKa values for cysteines is reported, and a related .pdb structure. Then I will predict the pKa with propka and this script and compare. I am aware of: http://www.ddg-pharmfac.net/ppd/PPD/pKasearch.htm But I could need a larger database. If any have read some articles with cysteine pKa values, I would be happy to hear about it. Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev ___ 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 -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev ___ 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] (no subject)
Hi Chris, the emails are only sent to you because you subscribed to the pymol-users list. If you don't want them anymore you need to unsubscribe. Click on Show details at the top of this email. Click then on: unsubscribe Unsubscribe from this mailing-list That will do the magic. On Fri, May 28, 2010 at 10:42, Christian De Ford cdefo...@gmail.com wrote: Please stop sending me daily emails its very annoying, i would appreciate if you erase me from the list Thank you! -- ___ 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-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] CEalign - PyMOL Build
+3 from me and people to busy writing grant applications. Built-in CE would be awesome! Thomas On Tue, Feb 2, 2010 at 12:19, Thomas Stout tst...@exelixis.com wrote: I thought that I had +1'd to this last week, but I don't see that note... If legal, I'm also +1-ing for 5 additional people here that do not subscribe to the mailing list... (or should that be +5-ing?) -Tom -Original Message- From: Sean Law [mailto:magic...@hotmail.com] Sent: Thursday, January 28, 2010 12:47 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] CEalign - PyMOL Build Jason, I would LOVE to see CEalign built along with PyMOL. +1 Sean Windows Live Messenger makes it easier to stay in touch - learn how! http://go.microsoft.com/?linkid=9706113 This email (including any attachments) may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. Exelixis, Inc. reserves the right, to the extent and under circumstances permitted by applicable law, to retain, monitor and intercept e-mail messages to and from its systems. -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ 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 -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ 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 Needed
Dear Kousik, Sue Jones PROTORP server should do the trick: http://bioinformatics.sussex.ac.uk/protorp Cheers, Thomas On Wed, Dec 9, 2009 at 14:57, Kousik Kundu kou...@informatik.uni-freiburg.de wrote: Dear Sir, I, Kousik Kundu, am a Ph.D student at university of Freiburg, Germany. I am using Pymol for my recent work. I need to to the amino acids involve in an interaction. For example 1BM2 (PDB id) is a complex of a SH2 domain and a small peptide. Here i want to know which amino acids (in both SH2 domain and peptide) are involved in the interaction. e.g. position 97 (SH2) interacting with position 11,14 (peptides) I need it little urgently. If you help me, I would be really grateful to you. Thank you in advanced .. Best Regards, Kousik Kundu ** Kousik Kundu Bioinformatics Group Institute of Computer Science Albert-Ludwigs-University Freiburg Georges-Köhler-Allee 106 79110 Freiburg Germany Tel: +49 761 203 7465 Fax: +49 761 203 7464 -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ 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 -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ 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] Fwd: Warren L Delano Memorial Award
Dear friends and colleagues: It's now been over a week since Warren has passed away. We are trying to move toward a permanent way to honor Warren's memory and what he stood for: Open Source Computational Biosciences and molecular visualization. To do this, Jim Wells and I put together a mission statement with the approval of Warren's family: The Warren L. DeLano Memorial Award for Computational Biosciences This award shall be given to a top computational bioscientist in recognition of the contributions made by Warren L. DeLano to creating powerful visualization tools for three dimensional structures and making them freely accessible. The award, accompanying lecture, and honorium will be given annually in the context of a national bioscience meeting or a Bay Area gathering of computational bioscientists at Stanford, UCSF or UC Berkeley. For the award special emphasis will be given for Open Source developments and service to the bioscience community. The award selection committee, consisting of experts in the computational and biological sciences, will accept nominations from anyone.. To make something like this happen in perpetuity would take about ~100K for the endowment. For donations, Warren's family has set up a tax deductible fund: Silicon Valley Community Foundation memo: Warren L. DeLano Memorial Fund 2440 West El Camino Real, Suite 300 Mountain View, CA 94040 tel: 650.450.5400 We hope that you'll consider making a contribution (not matter how small) in Warren's honor. Also, please forward this message to anybody who might be able be willing to contribute. Best regards, Axel Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor of Molecular and Cellular Physiology Stanford University Web: http://atbweb.stanford.edu/http://atbweb.stanford.edu Email: mailto:brun...@stanford.edubrun...@stanford.edu Phone: +1 650-736-1031 Fax: +1 650-745-1463 ___ Compbio mailing list comp...@lists.soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/compbio -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] save sequence
Dear all, apologies for the stupid question, but I was wondering if it is possible to save the sequence (one letter AA codes) of the structure(s) open in PyMol? Many thanks, Thomas
Re: [PyMOL] Sequence alignment and Structure alignment
You can save the alignment object resulting from an align command to an aln file: align sele1, sele2, object=aln_obj save alignment.aln, aln_obj Cheers. Thomas On Sun, Sep 28, 2008 at 21:14, Praveen Madala p.mad...@imb.uq.edu.au wrote: Hi, Can I able to save sequence alignment got .. after performing the structural alignment of two proteins. Regards, Praveen K Madala Group - Fairlie Institute For Molecular Biosciences The University of Queensland,Brisbane QLD-4120, AUSTRALIA Ph: +61-7-33462987 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] APBS error
Dear all, when trying to use the APBS plugin I experience the following problem The first time I tried to run it it the error message was simply ObjectMapLoadDXFile-Error: Unable to open file! Now the second time it pops up an error log: Error: 1 WindowsError Exception in Tk callback Function: bound method PmwFileDialog.okbutton of pmg_tk.startup.apbs_tools.PmwFileDialog instance at 0x05961A30 (type: type 'instancemethod') Args: () Traceback (innermost last): File d:\Program Files\DeLano Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py, line 1747, in __call__ return apply(self.func, args) File d:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py, line 1711, in okbutton self.setfilename(fn) File d:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py, line 1745, in setfilename self.configure(directory=dir,filename=value) File d:\Program Files\DeLano Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py, line 729, in configureapbs.exe func() File d:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py, line 1769, in newdir self.fillit() File d:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py, line 1836, in fillit fl=os.listdir(dir) WindowsError: [Errno 123] The filename, directory name, or volume label syntax is incorrect: 'd:APBS-0.5.1\\bin\\d:APBS-0.5.1\\bin/*.*' Both pymol (1.0edu1) and apbs (0.5.1)are fresh and clean installations. APBS is installed in D:\APBS-0.5.1 I experienced similiar problems on another Windows machine and a Mac, but both without the error log above. I was realizing that when choosing the location of APBS binary pymol writes: d:APBS-0.5.1 where it should be d:\APBS-0.5.1 I tried to put the correct path manually d:\APBS-0.5.1\bin\apbs.exe, but did not help. Any suggestions? Many thanks, Thomas
