From: lina <lin...@gm...> - 2011-09-04 14:02:03
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On Sun, Sep 4, 2011 at 8:37 PM, niloofar niknam <nil...@ya...> wrote: > > > Deal list, > I would like to calculate partial charges of my pdb. Is it possible to do it In pymol: Action-> compute -> partial charge sum > by Pymol? If not, Is anyone know any server > or software to do it? > 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. > Any offer would be appreciated. > kind regards. > Niloofar > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Best Regards, lina |
From: Thomas H. <sp...@us...> - 2011-09-04 17:07:42
|
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 |
From: <gu...@im...> - 2011-10-29 19:29:22
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From: Suhaila H. M. H. <bel...@ho...> - 2012-04-04 03:31:55
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From: Mintu C. <mi...@gm...> - 2012-06-13 16:02:05
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I have downloaded the pymol linux version in my kubuntu 12.4 , but while > installing, it is asking for -Kubuntu 11.04 _Natty Narwhal_ - Release i386 > (20110427.1). Please suggest me what shoul i do??? |
From: Sheyore O. <omo...@ho...> - 2012-10-16 15:14:29
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From: Mary H. <mh...@po...> - 2012-11-27 00:01:46
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How do I remove myself from the PyMOL users list? I'd like to stop receiving emails. Thank you. M. Hall |
From: Jason V. <jas...@sc...> - 2012-11-27 01:29:31
|
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...@po...> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Wolf, N. M. <nin...@ui...> - 2013-03-19 20:11:27
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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? |
From: Thomas H. <tho...@sc...> - 2013-03-20 10:38:40
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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 |
From: Davi de M. F. <dav...@nt...> - 2013-04-26 20:23:54
|
My PyMOL 1.5.0.5 works fine in Windows 8 (64 bits). Try the following: - Press Windows Key + Q - This should open the search apps thingy, type pymol - It should show all PyMOL shortcuts, try the "PyMOL + Tcl-Tk GUI + Console" - Does PyMOL still refuses to open? Did you get any error message? On 20/03/2013 03:11, Thomas Holder wrote: > 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? |
From: Aliya H. <hol...@wh...> - 2014-07-01 16:00:31
|
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 |
From: Thomas H. <tho...@sc...> - 2014-07-02 17:02:59
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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 <hol...@wh...> 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. |
From: Pawe? G. <gni...@gm...> - 2014-09-02 04:13:57
|
Hi all, I wonder if it's possible to fill the space (like in the case of nucleotide's ring) between three arbitrary/selected atoms. I'm trying to render an object which is not a biomolecule so "cartoon_ring_mode" is no use for me. Cheers, pawel |
From: leila k. <kar...@gm...> - 2015-04-19 05:55:22
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Dear all How to cite pymol in my paper? Thanks. |
From: Marcelo M. <mm...@na...> - 2015-04-19 05:58:51
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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 <kar...@gm...> 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_15&utm_medium=email&utm_campaign=VA_SF_______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: leila k. <kar...@gm...> - 2015-04-19 06:08:17
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Dear Marcelo Thanks for your quick answer. Unfortunately, I can't open the link (https://www.pymol.org/citing) you suggested me. Thanks in advance. |
From: Jordan W. <jwi...@gm...> - 2015-04-19 06:11:43
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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 <kar...@gm...> 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_15&utm_medium=email&utm_campaign=VA_SF_______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Marcelo M. <mm...@na...> - 2015-04-19 06:13:18
|
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 <kar...@gm...> 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_15&utm_medium=email&utm_campaign=VA_SF_______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Edward A. B. <Be...@up...> - 2015-04-21 00:12:35
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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_15&utm_medium=email&utm_campaign=VA_SF > > > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Dak A. M. <da...@ya...> - 2015-08-04 16:34:07
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da...@ya... |
From: Raag S. <sal...@gm...> - 2015-10-09 08:02:56
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Hi! What is the command for superimposing a .gro file and a .pdb file in PyMOL? I tried opening the .gro file and then loading the .pdb file. Consequently, I could only see the latter and not the former. Thank you in advance! -- Regards, Raag |
From: Dan L. <dh...@ca...> - 2015-12-11 03:06:35
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Dear all: It appears that pymol only interpolates motions that include rotations by moving the object along an arc. I would like to make a movie that does not do this, but rather, moves the object along a straight line while rotating the object. Unfortunately, I'm absolutely at a loss about how I could do this. Would anybody have any suggestions about where to look for this information? Thanks, Dan |
From: Vivien S. <viv...@gm...> - 2017-04-03 15:47:54
|
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 |
From: Leandro B. <lea...@gm...> - 2017-04-04 12:36:51
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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 < viv...@gm...> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |