Re: [PyMOL] (no subject)
For some reason, the people doing brew have decided to stop supporting compiling tcl-tk with X11 support. Not 100% sure, but I'm pretty certain pymol cannot use tcl-tk with aqua. If you already had pymol installed, this seems to eliminate the external gui. If you didn't, new installations of pymol will now crash randomly. Here's how I got to the old version that worked $ cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/ $ git checkout 46e1ef94247cd2fb9555b724c051e8907996 -- tcl-tk.rb $ cd ../../homebrew-science/ Edit the pymol.rb file so that it depends on "tcl-tk" instead of "homebrew/dupes/tcl-tk" $ brew remove tcl-tk python pymol $ brew install pymol $ brew pin tcl-tk Really, I uninstalled all my homebrew packages and then reinstalled everything because some of their changes over the last 6 months had made things oddly broken. If you want to do the same, you can try this: $ brew list > installed $ wrote: > Hi, > pymol external gui menus missing, I have compiled pymol in mac os by using > brew. > > Anyone can provide some suggestions? > > Jacky > > -- > Lei Zhao, Ph.D. & M.D. > Associate Professor > National Clinical Research Center for Normal Aging and Geriatric > National Engineering Research Center for Antibody Medicine > The Key Lab of Normal Aging and Geriatric > PLA General Hospital > Beijing 100853 > P.R.China > Tel:86-15210661966 > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > 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 > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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)
This worked! Thank you Leandro and Jed! From: jedg...@gmail.com [mailto:jedg...@gmail.com] On Behalf Of Jed Goldstone Sent: Tuesday, April 4, 2017 11:35 To: Vivien Schoonenberg <vivienschoonenb...@gmail.com> Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] (no subject) Try using remove not alt +A to remove alternative conformations. Jed On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg <vivienschoonenb...@gmail.com <mailto:vivienschoonenb...@gmail.com> > wrote: Hi there, I’m saving the sequences from each chain of the PDB via pymol with >>save something.fasta, chain A This is the same sequence that is shown in pymol and seems to correspond to the structure I am looking at. However, when I loaded new B-factors in my structure, I noticed something funny happened. The list which I made corresponding to the sequence I saved earlier was too short. I found out by iterating that some residues repeated themselves(>>iterate (chain A and n. CA), print resn). They carry the same residue number, and are not shown in the sequence. However, when I load my B-factors my list shifts because of these repeats, making it too short for the complete chain and loading the wrong value onto residues. Does anyone know why this happens and how I can fix this? Thank you, Vivien -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ 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 -- - Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS #32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI) -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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)
Try using remove not alt +A to remove alternative conformations. Jed On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg < vivienschoonenb...@gmail.com> wrote: > Hi there, > > > > I’m saving the sequences from each chain of the PDB via pymol with > > >>save something.fasta, chain A > > > > This is the same sequence that is shown in pymol and seems to correspond > to the structure I am looking at. > > However, when I loaded new B-factors in my structure, I noticed something > funny happened. The list which I made corresponding to the sequence I saved > earlier was too short. > > I found out by iterating that some residues repeated themselves(>>iterate > (chain A and n. CA), print resn). They carry the same residue number, and > are not shown in the sequence. However, when I load my B-factors my list > shifts because of these repeats, making it too short for the complete chain > and loading the wrong value onto residues. > > > > Does anyone know why this happens and how I can fix this? > > > > Thank you, > > Vivien > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > 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 > -- - Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS #32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI) -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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, You probably have a pdb file which has multiple possible conformations for some residues. You can check this by visual inspection of such residues. They have two side chains coming from the same CA. In the text file you can see the conformations marked as A and B in the residue name field, e.g. APHE BPHE. If that is the case, you have to choose one of them either manually or with some other molecular modeling software, e.g. gromacs. I hope it helps! Regards, Leandro On Mon, Apr 3, 2017 at 5:47 PM, Vivien Schoonenberg < vivienschoonenb...@gmail.com> wrote: > Hi there, > > > > I’m saving the sequences from each chain of the PDB via pymol with > > >>save something.fasta, chain A > > > > This is the same sequence that is shown in pymol and seems to correspond > to the structure I am looking at. > > However, when I loaded new B-factors in my structure, I noticed something > funny happened. The list which I made corresponding to the sequence I saved > earlier was too short. > > I found out by iterating that some residues repeated themselves(>>iterate > (chain A and n. CA), print resn). They carry the same residue number, and > are not shown in the sequence. However, when I load my B-factors my list > shifts because of these repeats, making it too short for the complete chain > and loading the wrong value onto residues. > > > > Does anyone know why this happens and how I can fix this? > > > > Thank you, > > Vivien > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > 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 > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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)
On 04/19/2015 02:08 AM, leila karami wrote: Dear Marcelo Thanks for your quick answer. Unfortunately, I can't open the link (https://www.pymol.org/citing) you suggested me. perhaps your firewall or browser is blocking the https: connection or rejecting the certificate? Try http: instead- they seem to reach the same content. Just don't give your taxpayer ID number or bank password! Thanks in advance. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ 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 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ 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 Leila, No problem, here is the content of the site. If you need the reference manager files (BibTex or EndNote files), I am happy to email them to you as well. Cheers, Marcelo Citation Format Please cite PyMOL, AxPyMOL and JyMOL as shown below. Be sure to edit the version number in accordance with your usage. If you use BibTex or EndNote, download the handy citation files below. PyMOL The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC. JyMOL The JyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC. AxPyMOL The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.7.4 Schrödinger, LLC. BibTex Files PyMOL BibTex Entries [.bib] http://pymol.org/sites/default/files/pymol.bib For help with BibTex see: http://en.wikipedia.org/wiki/BibTeX http://en.wikipedia.org/wiki/BibTeX http://www.bibtex.org/Using/ http://www.bibtex.org/Using/ EndNote Files PyMOL EndNote Entries [.xml] http://pymol.org/sites/default/files/pymol_0.xml (right-click and save this file to your computer; most browsers dont' render XML nicely) On Apr 19, 2015, at 12:08 AM, leila karami karami.lei...@gmail.com wrote: Dear Marcelo Thanks for your quick answer. Unfortunately, I can't open the link (https://www.pymol.org/citing https://www.pymol.org/citing) you suggested me. Thanks in advance. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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)
PyMOL The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC. JyMOL The JyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC. AxPyMOL The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.7.4 Schrödinger, LLC. On Apr 18, 2015, at 11:08 PM, leila karami karami.lei...@gmail.com wrote: Dear Marcelo Thanks for your quick answer. Unfortunately, I can't open the link (https://www.pymol.org/citing https://www.pymol.org/citing) you suggested me. Thanks in advance. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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 Leila, Take a look at the link below: https://www.pymol.org/citing https://www.pymol.org/citing Cheers, Marcelo On Apr 18, 2015, at 11:55 PM, leila karami karami.lei...@gmail.com wrote: Dear all How to cite pymol in my paper? Thanks. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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 Aliya, yes, likely there is a clash. But that's hard to tell without seeing your data. Cheers, Thomas On 01 Jul 2014, at 11:34, Aliya Holland holland_al...@wheatoncollege.edu wrote: Hello, I just created an animation of a conformational change of a specific domain on a molecule. During the animation the domain rotates just as it should, however other parts of the molecule moves with the conformation change. I was wondering if that was part of the PyMOL programming or if there was a clash between the end domain and the rotating section. Why would there be movement in the entire molecule when only one section of it is morphing. Thank you A -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ 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)
Auto vyzdobena http://www.domarn.se/capcutgrahampatterson/?vhotmailID=gfesuzgz -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-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 Nina Marie, I haven't tested that thoroughly, but for me Incentive PyMOL 1.5.0.5 runs fine on Windows 8. Cheers, Thomas Wolf, Nina Marie wrote, On 03/19/13 21:11: Hi, I recently upgraded my computer to windows 8. Since then, pymol will not open. Is the latest version of pymol incompatible with windows 8? Or is there something I can do to get it working on my computer? -- 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_mar ___ 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 Mary, Just a hint for any future lists you might be on: most modern email lists, including pymol-users, have footers with links to subscription options. You simply click that to get to a subscription page where you can unsubscribe. In this case, I removed you from the list to save you the hassle. Cheers, -- Jason On Mon, Nov 26, 2012 at 5:30 PM, Mary Hall mh...@potomacschool.org wrote: How do I remove myself from the PyMOL users list? I'd like to stop receiving emails. Thank you. M. Hall -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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 Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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 Noloofar and Lina, I would like to calculate partial charges of my pdb. Is it possible to do it In pymol: Action- compute - partial charge sum this doesn't calculate partial charges, sorry. This does: Action - generate - vacuum electrostatics But better would be to use pdb2pqr: http://www.poissonboltzmann.org/pdb2pqr I have another question too, when aligning two structure in Pymol, there is a RMSD for the total structure, is there any command to calculate the RMSD for a specific region of the alignment. If the two structures have the same sequence (same atom identifiers) and you don't need an alignment, you can use rms_cur. http://pymolwiki.org/index.php/Rms_Cur Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ 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] (no subject)
On Fri, May 28, 2010 at 10:49 AM, Thomas Juettemann juettem...@gmail.comwrote: 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. Or click on the link at the bottom of *every email sent to the list*: Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users -- ___ 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, I think that it probably is possible to do this from within pymol, and probably quite convenient for single molecules. However, there are two other possible approaches, which would be helpful for multiple molecules. Firstly, there is a program called 'dang' made by the Richardson group: http://kinemage.biochem.duke.edu/software/dang.php and secondly, might I humbly submit that I have a program I call 'Tailor' that is intended for measuring and analysing (to a limited extent) selected parts of proteins: http://tailor.sourceforge.net/docs/index.html gilleain On Tue, Mar 24, 2009 at 7:06 AM, Rotem Sertchook rotem.sertch...@weizmann.ac.il wrote: Hi, I'm looking for a way to calculate set of torsion angels from selected residues (for example Chi1 dihedral of all His residues). Is it possible to write PyMOL script for such task ? Any hints to write such script will be appreciated! Thank you Rotem -- Rotem Sertchook, Ph.D. Bioinformatics Unit, Biological Services Weizmann Institute of Science, Rehovot 76100, Israel. -- -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] (no subject)
Rotem, Try starting with the script below. It will produce output like: PRO A 1Chi-1: 20.6 GLN A 2Chi-1: -178.8 LEU A 5Chi-1: -64.6 TRP A 6Chi-1: -55.6 GLN A 7Chi-1: -59.6 ARG A 8Chi-1: -83.1 PRO A 9Chi-1: 34.9 LEU A 10 Chi-1: -53.5 ... Cheers, Warren --- load $TUT/1hpv.pdb select chi1, polymer (br. */N) (br. */CA) (br. */CB) (br. */CG) N = cmd.index(chi1 */N ) CA = cmd.index(chi1 */CA) CB = cmd.index(chi1 */CB) CG = cmd.index(chi1 */CG) LABEL = [] iterate chi1 */CA, LABEL.append(resn+ +chain+ +resi) I = range(len(LABEL)) CHI1 = [0] * len(I) for i in I: CHI1[i] = cmd.get_dihedral(N[i],CA[i],CB[i],CG[i]) for i in I: print %-10s Chi-1: %6.1f % (LABEL[i],CHI1[i]) From: Rotem Sertchook [mailto:rotem.sertch...@weizmann.ac.il] Sent: Tuesday, March 24, 2009 12:11 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] (no subject) Hi, I'm looking for a way to calculate set of torsion angels from selected residues (for example Chi1 dihedral of all His residues). Is it possible to write PyMOL script for such task ? Any hints to write such script will be appreciated! Thank you Rotem -- Rotem Sertchook, Ph.D. Bioinformatics Unit, Biological Services Weizmann Institute of Science, Rehovot 76100, Israel. --
Re: [PyMOL] (no subject)
Justin, Sorry about that... svn update and rebuild. I believe the warning is gone now. It should only print if you specifically request certain stereo modes. Cheeers, Warren -Original Message- From: Justin Lecher [mailto:j.lec...@fz-juelich.de] Sent: Thursday, February 19, 2009 5:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] (no subject) Hello all especially Warren, What does Sorry, time-sequential stereo 3D not available mean. It is printed out when I start pymol. I am using current HEAD. Thanks justin -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385
Re: [PyMOL] (no subject)
Hi Warren, Thank you very much. Under the help of one of PyMol users, at last figure out the right configuration. It needs AllowDFPStereo on in LCD and XineramaStereoFlipping on in CRT. Following is the part I changed: == begin the partial xorg.conf # for CRT Section Device Identifier Videocard0 Driver nvidia VendorName Videocard vendor BoardName NVIDIA Quadro FX3400 BusID PCI:5:0:0 Option Stereo 3 Screen 0 Option UBB 1 Option NoPowerConnectorCheck Option XineramaStereoFlipping 1 EndSection # for LCD Section Device Identifier Videocard1 Driver nvidia VendorName Videocard vendor BoardName NVIDIA Quadro FX3400 BusID PCI:5:0:0 Screen 1 Option UBB 1 Option Stereo 3 Option NoPowerConnectorCheck Option AllowDFPStereo 1 EndSection == end Bests, -Donglu Donglue, My suspicion is that stereo and windows spanning multiple displays may be mutually exclusive, possibly because the displays aren't necessarily sync'd on the VBL, or because the LCD context may not be stereo-capable. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Donglu Xie Sent: Saturday, July 15, 2006 9:36 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] (no subject) Hi Dear Pymol-users, Sorry about this long message. I am struggling to configure X Windwo to enable stereo. Two monitors are connected with the NVIDIA GPU Quadro FX 3400 card. One monitor is ViewSonic VP2030b LCD, another is ViewSonic G225fb CRT. Try to configure X widnow to enable stereo with Xinerama on so that application can cross the screen boundaries. There is no any error or warning message in Xorg.0.log (xorg.conf is below). However, when tried to run stereo application, such as PyMol or Coot, it doesn't work. It came out with different error messages. In PyMol, error is following: X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 78 (X_CreateColormap) Value in failed request: 0x0 Serial number of failed request: 14 Current serial number in output stream: 16 PyMOL: abrupt program termination. In Coot, the error is Gdk-ERROR **: BadValue (integer parameter out of range for operation) serial 390 error_code 2 request_code 78 minor_code 0 Googling doesn't get much useful information. I also tried to use Twinview. The stereo works well. However, the application interface cannot move cross the screen boundaries. The Xinerama enabled setting works perfect with systems connected with a CRT and a LCD monitors (2.4.20-6smp #1 SMP Thu Feb 27 09:36:38 EST 2003 i686 athlon i386 GNU/Linux) (NVIDIA Quadro4 750 XGL). The system with stereo problem is 2.6.9-34.0.1.ELlargesmp #1 SMP Wed May 17 17:19:07 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux xorg.conf and partial of Xorg.0.log files is below. Any help or suggestion is appreciated. Best, -Donglu Xie xorg.conf is following = Section ServerLayout Identifier Dual Layout Option Xinerama true Screen 0 Screen0 Screen 1 Screen1 RightOf Screen0 InputDeviceMouse0 CorePointer InputDeviceKeyboard0 CoreKeyboard EndSection Section Files RgbPath /usr/X11R6/lib/X11/rgb FontPath unix/:7100 EndSection Section Module Load dbe Load extmod Load fbdevhw Load glx Load glx Load record Load freetype Load type1 # Load dri EndSection Section InputDevice Identifier Keyboard0 Driver kbd Option XkbModel pc105 Option XkbLayout us EndSection Section InputDevice Identifier Mouse0 Driver mouse Option Protocol IMPS/2 Option Device /dev/input/mice Option ZAxisMapping 4 5 Option Emulate3Buttons yes EndSection Section Monitor Identifier LCD VendorName Viewsonic ModelNameVP2030b HorizSync24.0 - 92.0 VertRefresh 50.0 - 85.0 Option dpms EndSection Section Monitor Identifier CRT VendorName Viewsonic ModelNameG225fb HorizSync30.0 - 130.0 VertRefresh 50.0 - 160.0 Option dpms Modeline 1600x1200_99.00 277.61 1600 1728 1904 2208 1200 1201 1204 1270 -HSync +Vsync EndSection Section Device Identifier Videocard0 Driver nvidia VendorName Videocard vendor BoardName NVIDIA Quadro FX3400
Re: [PyMOL] (no subject)
Hi, for this purpose I have used caver program. You can download it free of charge from here http://loschmidt.chemi.muni.cz/caver/download.php I hope this help Regards andrea 2006/3/27, srilath...@jubilantbiosys.com srilath...@jubilantbiosys.com: dear sir iam a pymol user, do we can find area volume of active site in pymol if we can, just tell me how to do it thanking you srilatha Thanks Regards srilatha potlapelly MSc Biotechnology --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmdlnkkid0944bid$1720dat1642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- La conoscenza libera il genere umano dalla superstizione J. Watson
Re: [PyMOL] (no subject)
Hi, I found out how to do ... something ... like this the other day.
RE: [PyMOL] (no subject)
Hi Blanton You are probably looking for the symexp command. I don't remember the exact syntax, but there is a small help text. You can also try to search the mail archive. Best wishes Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net on behalf of Blanton Tolbert Sent: Sat 2006-03-04 15:01 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] (no subject) Hi pymol community I would like to recapitulate the crystal packing arrangement of a protein structure to look for neighbor interactions. Is it possible to do this in pymol? If so, please provide me some insight. Thanks, Blanton Tolbert Graduate Student University of Rochester Biophysics and Structural Biology 585-275-5189 blanton_tolb...@urmc.rochester.edu --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] (no subject)
Hi try align or fit regards andrea 2006/3/3, srilath...@jubilantbiosys.com srilath...@jubilantbiosys.com: dear all can we superimpose structures in pymol Thanks Regards srilatha potlapelly MSc Biotechnology Drug discovery, #450,4th D Main, 12th cross, Mahalakshmipuram - 560086 Bangalore Office: +9180-23495461-64 Extn.-1029 --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmdlnkkid0944bid$1720dat1642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- La conoscenza libera il genere umano dalla superstizione J. Watson
RE: [PyMOL] (no subject)
Yes, the create command provide you with this ability, though at the end of the process you end up with a new object. create new_object, old_object1 | old_object2 In some cases, new_object can be the same name as either old_object1 or old_object2: create old_object1, old_object1 | old_object2 Also note that the vertical bar (the or operator) is optional in recent betas, so create old_object1, old_object1 old_object2 becomes legal. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Joseph Fernandez Sent: Sunday, September 25, 2005 11:19 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] (no subject) There is a very useful functionality in Sybyl, whereby the user can merge a residue from one molecular area, into another molecular area. The residue then becomes a part of the latter moleculear area, without deleting it. I wonder whether there is such a functionality in PyMol. As an example, I have created a new object, consisting of several residues that I have extracted from the active site of a protein (using the create command). I then deleted these residues from the original object (active site of protein). I now want to merge an additional residue from the active site into the ligand object, and delete the residue from the active site, but without deleting the ligand object. Any assistance on this matter would be appreciated. Joe __ Yahoo! for Good Donate to the Hurricane Katrina relief effort. http://store.yahoo.com/redcross-donate3/ --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] (no subject)
Yi,
To stuff a bunch of identical object in one PDB file, you need to assign
a unique segment ID to each one. For example:
load $PYMOL_PATH/test/dat/1tii.pdb
symexp s,1tii,1tii,5
names=cmd.get_names()
for a in range(len(names)): cmd.alter(names[a],segi=+str(a))
save multi.pdb
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of yi zhang
Sent: Sunday, July 24, 2005 8:43 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)
Hi, everyone,
I used symexp command in pymol to generate symmetry-related
molecule, something like:
cmd.symexp('sym', 'obj', 'obj',10 )
of course, I can manually save each symmetry-related molecule
to *.pdb file by clicking save molecule button, but how can I
write a script to save all of them or part of them? the
symmetry-related objects are not appendable.
thanks!
yi
__
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection
around http://mail.yahoo.com
---
SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
from IBM. Find simple to follow Roadmaps, straightforward articles,
informative Webcasts and more! Get everything you need to get up to
speed, fast. http://ads.osdn.com/?ad_id=7477alloc_id=16492op=click
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] (no subject)
On Sunday 24 July 2005 05:42, yi zhang wrote:
cmd.symexp('sym', 'obj', 'obj',10 )
of course, I can manually save each symmetry-related
molecule to *.pdb file by clicking save molecule
button, but how can I write a script to save all of
them or part of them? the symmetry-related objects
are not appendable.
I have used something like this in the past:
#--
# get symmetry mates
objs = [ n for n in cmd.get_names() if n[0:3]==sym ]
for obj in objs:
if cmd.get_type(obj)!=object:molecule:
print Something's wrong!
else:
cmd.save(obj+.pdb,obj)
#--
Hope this helps,
--
Lieven Buts
Ultrastructure Laboratory
Vrije Universiteit Brussel
Re: [PyMOL] (no subject)
Check out the post on High end graphics. This will solve the problem. Basically you can ray-trace your molecule at a resolution bigger tahn teh screen size and then cut it down afterwards effectively generating a high resolution graphic from a 72 dpi starting point Cheers J Kolli, Madhavi wrote: Hi, I’ve just started using PyMol for making some figures. I’m very happy that it is so easy to use. However the resolution of my pictures is very bad even after rendering them. When I print them they are very pixellated. I’m sure there is something I’m not doing right. Any help, suggestions will be appreciated. Thanks. Regards, Madhavi Kolli Graduate Student UMass Medical School Worcester -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034
RE: [PyMOL] (no subject)
Christian, This isn't implemented yet, but it is on the to do list. Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Christian Rummey Sent: Thursday, April 22, 2004 2:35 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] (no subject) hi ppl, is there a way to sort the list of objects/selections in the panel on the right side other than loading/selecting stuff in a specific order? simple example: I compare several ligands in a specific site, and save the data as pymol sessions; after adding new ligands//site conformations I'd like to sort the sites 1st, then the ligands. any hints? thanks a lot, christian -- NEU : GMX Internet.FreeDSL Ab sofort DSL-Tarif ohne Grundgeb|hr: http://www.gmx.net/dsl --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] (no subject)
Hi Blanton, Are you running the unstable tree, or have you just copied the pymol-0.90-2 package to stable, you either have to enable the unstable tree, or copy the numeric-py22 package from the unstable to stable, it can be found at '/sw/fink/dists/unstable/main/finkinfo/sci' see here; http://fink.sourceforge.net/faq/usage-fink.php#unstable Matt On Wednesday, Aug 20, 2003, at 12:01 Australia/Canberra, Tolbert, Blanton wrote: I was attempting to install pymol 0.9 using fink and got the following error message, Failed: Can't resolve dependency numeric-py22 for package pymol-0.90-2 (no matching packages/versions found) Can anyone advise me on what to do to get around this? Thanks in advance. Blanton --- This SF.net email is sponsored by Dice.com. Did you know that Dice has over 25,000 tech jobs available today? From careers in IT to Engineering to Tech Sales, Dice has tech jobs from the best hiring companies. http://www.dice.com/index.epl?rel_code=104 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] (no subject)
Hi Martin, Visit Robert Campbell's repository of PyMOL scripts (http://adelie.biochem.queensu.ca/~rlc/work/pymol/)...where you'll find Python scripts to import into PyMOL for drawing unit cell edges (draw_cell.py), symmetry axes (draw_symops.py), and lots of other stuff... Cameron mkienetz wrote: Dear All, How do I show the unit cell using pymol? Martin Martin Kienetz 429 MSB Department of Biochemistry University of Alberta Edmonton AB T6G 2H7 (780) 492-2422 --- This SF.net email is sponsored by: eBay Get office equipment for less on eBay! http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] (no subject)
Fei Xu wrote: HI! Dr. Delano: Would you like to tell me how I can control the size of the ball, if I pick an atom and show it like a ball? Dear Fei Xu: 1. You select an atom 2. You display it as a ball 3. You type: set sphere_scale = 2.0 Here, the number is the size proportional to an original size of 1.0. Unfortunately, settings for individual objects are not functional yet. Kristian
