Re: [PyMOL] option pdb_conect_nodup unavailable in OpenSource version 1.7
Hi, Thomas, thanks for checking that and responding quickly. I also found out the meaning of the option myself. At the moment, I write some post-processing scripts to cope with that issue. best, Hongbo On Tue, Aug 19, 2014 at 4:05 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Hongbo, you are right that the website and the implementation don't match, thanks for pointing that out. This was a feature request from a paying PyMOL sponsor, which often means that we put the feature only (or first) in Incentive PyMOL. But thinking about it, this is a rather small change and probably not worth to keep as a distinguishing feature. I'll port it to open-source today. To clarify the issue with duplicated connect record. This is an unofficial PDB feature to store the bond order and is supported by several applications that read PDB files, but may break PDB file loading in other applications which don't support it. PyMOL always wrote duplicated connect records and the new setting allows you to switch that off. Cheers, Thomas On 18 Aug 2014, at 15:04, Hongbo Zhu 朱宏博 hongbo.zhu...@gmail.com wrote: Hi, I am using PyMOL 1.7 open source version in Ubuntu 14.04. I wanted to try a new setting pdb_conect_nodup in pymol 1.7. It is listed as new features available for both Open Source and Incentive at: http://pymol.org/features#v1.7 when I set it to on, I got: Setting-Warning: not supported in open-source version of PyMOL though the setting could be successfully set (get pdb_conect_nodup). After saving a test PDB files, I still see duplicate CONECT lines in the PDB file generated by PyMOL. So I guess the feature is indeed missing in open source version. Should the feature be made available to open source version users? cheers, Hongbo -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- ___ 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] Residue selection problem in PyMOL 1.6
Hi, I have downloaded PyMOL v1.6.0.0 from sourceforge and installed it on my Ubuntu 12.04. It works very well. Recently I noticed there is a problem when selecting residues from the sequence panel (Display - Sequence). If I select multiple residues using mouse in the sequence panel, only the first selected residue is highlighted in the corresponding structure. Then rest selected residues are not highlighted. But if I disable my selection and enable it again (e.g. by clicking on the selection name in the control panel), all the selected residues will be highlighted. This is different from PyMOL 1.5 or older version, and I don't think it is a feature (I read what's new for 1.6 :). There is no any warning or error message output on the terminal. Has anyone had similar problem? Hongbo -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/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] Residue selection problem in PyMOL 1.6
I found a previous report on the same issue and it is fixed in the svn: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11581.html I guess I will try the updated version. Hongbo -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/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] regarding the dssp plugins
I just ran dssp plugin for an NMR structure (randomly chosen, 2LE0). In my case, secondary structures are calculated for all the 10 states of 2LE0. The plugin can also update color and secondary structures for all the 10 states of the NMR structure. I did not have to choose one state and run, and the next state. I tested the plugin under both Ubuntu and Windows 7. Maybe I misunderstood your question? regards, hongbo On 16.09.2011 5:45, lina wrote: Hi, a quick question, how can update the ss for all states, not check one by one, and run dssp and update ... Thanks for any advice, -- Best Regards, lina -- BlackBerryreg; DevCon Americas, Oct. 18-20, San Francisco, CA http://p.sf.net/sfu/rim-devcon-copy2 ___ 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct___ 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 for surface coloring
I have a slightly different answer using (almost:) only PyMOL commands: # take 1acb as example fetch 1acb, async=0 import numpy # center is [x0,y0,z0] x0,y0,z0=[1,2,3] alldist = [] iterate_state 1, 1acb, alldist.append(numpy.sqrt(numpy.sum([(x-x0)**2,(y-y0)**2,(z-z0)**2]))) # assign dist to b-factors! di = iter(alldist) alter 1acb, b=di.next() spectrum b, rainbow, 1acb The distance computation line is awkward. I thought of using distance() command to replace it. It is also much faster to use distance(). But I failed to dig distance values out of the object generated by distance(). Anybody knows how to do that? cheers,hongbo On 28.07.2011 5:06, Thomas Holder wrote: Hi Robert, you can set the distance between each atom and the center as b-factor, and then use spectrum (or spectrumany [1]) for coloring. I wrote a small python script that will do that, see attachment. Example (in PyMOL command line): run distancecoloring.py centerdistance2b (all) spectrum b, blue_white_red, (all) Cheers, Thomas [1] http://pymolwiki.org/index.php/Spectrumany On 07/28/2011 04:29 PM, Muench, Robert wrote: Dear community, I was searching the internet for several days now to find out how to perform a distance dependent coloring in pymol. The idea is to color the surface of a viral (spherical) structure. I would like to define the xyz-coordinates of the center of the viral structure an color all residues with a gradient depending on the distance from these xyz coordinates. Can anyone please help me out? All the best Robert *Robert Münch*** - Dipl. Biologist / PhD-Student *Paul-Ehrlich-Institut* Federal Institute for Vaccines and Biomedicines Division of Medical Biotechnology Section 6/5 - Viral Gene Transfer Medicinal Products 63225 Langen, Germany Phone: +49-6103-77-4222 Fax: +49-6103-77-1255 -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ 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 -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey___ 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 load two separate pdb files simultaneously
In one PyMOL instance you can load many structures. They can be load into different objects, or different states of the same object. If you mean using one command line to load multiple structures, since its grammar is very similar to python, I think you can always use semicolon to separate two commands: fetch 1A00; fetch 1A07 this command will load both 1A00 and 1A07, but one after the other, not simultaneously. On 06/29/2011 03:07 PM, leila karami wrote: Daer users I want to know how to load two separate pdb files simultaneously. any help will highly appreciated. -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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 load two separate pdb files simultaneously
this also works: fetch 1A00 or 1A07 or 1A08 but not: load 1A00 or 1A07 or 1A08 On 06/29/2011 03:07 PM, leila karami wrote: Daer users I want to know how to load two separate pdb files simultaneously. any help will highly appreciated. -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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 load two separate pdb files simultaneously
would python module multiprocessing meet your need? is that simultaneity the kind of simultaneity you want? On 06/29/2011 03:36 PM, leila karami wrote: Dear Hongbo very thanks for your attention. None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not help me. I need to load two separate pdb files simultaneously. -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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 load two separate pdb files simultaneously
for local files, apart from using load: load pdb1; load pdb2; load pdb3; load pdbN there is another shortcut: you put all the PDB files you need to load in the fetch_path of pymol. To find out the current fetch_path, use command: get fetch_path Then you can simply load all pdb at once using: fetch pdb1 pdb2 pdb3 pdb4 pdbN On 06/29/2011 03:56 PM, Hongbo Zhu wrote: would python module multiprocessing meet your need? is that simultaneity the kind of simultaneity you want? On 06/29/2011 03:36 PM, leila karami wrote: Dear Hongbo very thanks for your attention. None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not help me. I need to load two separate pdb files simultaneously. -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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] glycan surface
other people recently asked about the ligand surface, and Jason gave the following answer on 02 Apr. Hope it is also helpful to your glycan case. - Hi Peter, In order to do this you either need to extract the ligand to its own object or unset the ignore flag on rep surface. That is, # fetch the protein fetch 1rg7, async=0 # show surface show surface, resn MTX # do not ignore surfacing of ligands flag ignore, not rep surface # force PyMOL to rebuild the surface rebuild Cheers, -- Jason On 05.05.2011 9:22, Yamei Yu wrote: Hi all, I want to display the surface of my structure with pymol. The problem is that it automatically excludes all the glycans. Does anybody know the method to solve this problem? Thank you very much! yamei -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ 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 -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ 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] Get Protein Dimension
you can write your own loop in python to implement the function.
fh = open(pdbfilename)
coords =
numpy.array([[float(line[30:38]),float(line[38:46]),float(line[46:54])]
for line in fh.readlines() if line.startswith('ATOM ') or
line.startswith('HETATM')])
fh.close()
extent = (numpy.min(coords,axis=0), numpy.max(coords,axis=0))
or course the code needs to be tuned if you need only the first MODEL or
only the first alternate position etc.
cheers,hongbo
On 04/26/2011 01:40 PM, Martin Hediger wrote:
Dear all
I found that PyMOL offer the cmd.get_extent('protein') function, which
returns the dimensions of the selection.
Is it complicated to make this function available from within an
ordinary Pythonscript?
Thanks for hints.
Martin
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Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object
Hi, Harry, I am curious. How do you merge objects resulting from distance ? Do you mean to group them? If so, you can use ungroup command to, well, ungroup them. But if the merged object is generated using a CGO, I doubt you can unmerge the CGO object. But I don't know dash CGOs, either. (Unless you make dashes using small line fragments :) So do you have dashes or solid lines? Do you see a plus sign before the object in PyMOL? hongbo On 04/26/2011 11:47 AM, Harry Jubb wrote: Hi Everyone, I'd like to ask for some help with dash/distance objects. I have PyMOL session files which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually. I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution. Thanks, Harry -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ 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 -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ 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 color in a different way different helix types?
Hi, just for your information, the DSSP plugin for PyMOL has been updated to DSSP Stride plugin for PyMOL :-) The plugin generates a selection for each SSE type assigned by DSSP or Stride. Using the brilliant copy to object function of PyMOL, you can make two copies of protein fragments of the same SSE defined by DSSP and Stride respectively and compare them visually ! The plugin also accepts (correct) PyMOL selection expressions as input beside selection/object names. Thanks for Thomas Holder for the suggestion! Your feedback and suggestions are always welcome! cheers,hongbo On 04/12/2011 04:22 PM, Hongbo Zhu wrote: Hi, if anybody is still interested in the topic, I have made a DSSP plugin for running DSSP and coloring proteins according to the DSSP secondary structure assignment. Please have a look at: http://www.pymolwiki.org/index.php/DSSP This plugin invokes DSSP (presuming you already have DSSP binary on your hard drive) and reads the output using BioPython. It then makes several selections, each for a kind of secondary structure elements (SSE) if there is at least one residue in the input selection is assigned with the SSE. regards, hongbo On 04/06/2011 04:34 PM, H. Adam Steinberg wrote: Hi Ramiro, Like you, I would love to see secondary structure colored by helix type. Jmol however does not show this as a default. Do you know what steps you took to get Jmol to show secondary structure colored by helix type? I can't seem to find that setting in any of the menu options. style/scheme/cartoon color/structure/cartoon/By Scheme/Secondary Structure This shows all of the helices in the same color. Adam -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails ___ 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 color in a different way different helix types?
Hi, Jason and Thomas,
Thank you for your interest and suggestions!
The plugin has been updated s.t. it now also recognizes objects. The
support for single-word selectors ('polymer', 'all', etc) is also added.
Thanks again for the feedback!
best regards,
hongbo
On 04/12/2011 05:16 PM, Thomas Holder wrote:
Hi Hongbo,
very nice!
Your plugin only accepts named selections, predefined selections like
(all), (polymer) or object names do not work. Could you change this?
Cheers,
Thomas
On Tue, Apr 12, 2011 at 4:22 PM, Hongbo Zhu
hongbo@biotec.tu-dresden.de wrote:
Hi, if anybody is still interested in the topic, I have made a DSSP
plugin for running DSSP and coloring proteins according to the DSSP
secondary structure assignment. Please have a look at:
http://www.pymolwiki.org/index.php/DSSP
This plugin invokes DSSP (presuming you already have DSSP binary on your
hard drive) and reads the output using BioPython. It then makes several
selections, each for a kind of secondary structure elements (SSE) if
there is at least one residue in the input selection is assigned with
the SSE.
regards,
hongbo
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Re: [PyMOL] How to color in a different way different helix types?
Hi, if anybody is still interested in the topic, I have made a DSSP plugin for running DSSP and coloring proteins according to the DSSP secondary structure assignment. Please have a look at: http://www.pymolwiki.org/index.php/DSSP This plugin invokes DSSP (presuming you already have DSSP binary on your hard drive) and reads the output using BioPython. It then makes several selections, each for a kind of secondary structure elements (SSE) if there is at least one residue in the input selection is assigned with the SSE. regards, hongbo On 04/06/2011 04:34 PM, H. Adam Steinberg wrote: Hi Ramiro, Like you, I would love to see secondary structure colored by helix type. Jmol however does not show this as a default. Do you know what steps you took to get Jmol to show secondary structure colored by helix type? I can't seem to find that setting in any of the menu options. style/scheme/cartoon color/structure/cartoon/By Scheme/Secondary Structure This shows all of the helices in the same color. Adam On Apr 6, 2011, at 4:22 AM, Ramiro Téllez Sanz wrote: Hi and thanks for reading this. I have googled for a way to achieve what I want and have gone through the wiki, to no avail. I would like to color in a different way the different helix types: alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get distinct colors for each type by default. But if the same pdb file is open with PyMOL all helices are treated the same way. Can't PyMOL distinguish helix types? Thanks in advance, Ramiro Téllez Sanz Dept. Physical Chemistry University of Almeria Spain -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ 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 * *art*/for/*science* *H. Adam Steinberg* Artist, Scientist, Developmental Editor www.artforscience.com http://www.artforscience.com 7904 Bowman Rd Lodi, WI 53555 608/729-5944 * -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ 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 -- Forrester Wave Report - Recovery time is now measured in hours and minutes not days. Key insights are discussed in the 2010 Forrester Wave Report as part of an in-depth evaluation of disaster recovery service providers. Forrester found the best-in-class provider in terms of services and vision. Read this report now! http://p.sf.net/sfu/ibm-webcastpromo ___ 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] Display coordinate vectors
Hi, Martin, how about this: http://www.pymolwiki.org/index.php/Symmetry_Axis also check out the script drawing X, Y, and Z reference axes by Robert: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/axes_cyl.py hope it helps, hongbo On 04/08/2011 04:29 PM, Martin Hediger wrote: Dear all I'm sure this question was answered before, but I could not find anything related to it in neither the mail list nor on the Wiki. Is it possible to display something like coordinate vectors in PyMOL? I.e. arrows in the 3d view space pointing towards [1,0,0], [0,1,0] and [0,0,1]? I would like to illustrate the alignment of the principal axes of a protein with the coordinate system. Kind regards and thank you for answers. Martin Hediger -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ 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 -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ 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] symexp
Hi, Kanika, The source code can be found at function ExecutiveSymExp() in the file ./trunk/pymol/layer3/Executive.c Normally, a PDB is equivalent to an ASU (except for some cases like capsid). Symexp is used to reconstruct neighboring ASUs. ( http://pymolwiki.org/index.php/Symexp ) It seems REMARK 290 that contains crystallographic symmetry transformations is used for computing the positions of neighboring ASUs. But be careful with some of the capsid cases (e.g. 3p0s). The symexp will not generate any neighboring molecules as they are not related by crystallographic symmetry, but non-crystallographic symmetry. BTW, it seems symexp has a bug when running on 3p0s. It does not return after displaying the message: ExecutiveSymExp: Generating symmetry mates... regards, hongbo On 03/22/2011 06:44 AM, kanika sharma wrote: I used symexp command for 3QK9 using distance of 2.75 to generate ASU(asymmetric unit). Does symexp generate these symmetry mates from the remark290 of PDB file? I couldnot find the code for symexp in pymolwiki. Can anyone help out? Regards, Kanika -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ 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] CASTp plugin
Hi, Tomas, Usually, the Bad magic number is caused by wrong python version when running .pyc file (the .pyc must have been compiled using a different version of python than the one in PyMOL 1.3, which is python 2.5.4). Maybe you have also noticed on the first line of the CASTpyMOL webpage : To use CASTpyMOL version 2, you must be using PyMOL version 0.99 pymol 0.99 and pymol 1.3 uses different versions of python. Maybe you should contact the CASTpyMOL people to get a .py file so you can try them with your pymol 1.3, or ask them to compile a .pyc using python 2.5.4 for you. Or install pymol 0.99 in parallel to you pymol 1.3. good luck! hongbo On 03/22/2011 11:03 AM, Tomáš Kučera wrote: Hello pymol users, I try to install this castp plugin: http://sts.bioengr.uic.edu/castp/pymol.php - http://sts.bioengr.uic.edu/castp/infoPages/CASTpyMOL_v2.pyc I have pymol 1.3 (windows7 64bit) and I got: ImportError: Bad magic number in C:\Program Files (x86)\PyMOL\PyMOL/modules\pmg_tk\startup\CASTpyMOL_v2.pyc Error: unable to initialize plugin 'CASTpyMOL_v2'. Does anyone have any idea how to fix this issue? Thanks, Tomas -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ 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] symexp
You are right, Thomas! The information is redundant in REMARK 290. I just performed a small test which confirms your conclusion: remove CRYST1 will make symexp to complain ExecutiveSymExp-Error: No symmetry loaded! even if REMARK 290 is present, while removing REMARK 290 does not have any effect on symexp. don't know whether it make sense to monitor both cryst1 and remark 290... On 03/22/2011 10:19 AM, Thomas Holder wrote: It seems REMARK 290 that contains crystallographic symmetry transformations is used for computing the positions of neighboring ASUs. the CRYST1 record is sufficient for generating symmetry mates, so pymol most likely does not read REMARK 290. Cheers, Thomas -- Hongbo ZHU -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ 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] New plugin: MSMS plugin for PyMOL
Dear PyMOLers, As many of you might be aware of, MSMS is an excellent program developed by Michel Sanner for computing protein surface, especially solvent excluded surface (SES). (see http://mgltools.scripps.edu/packages/MSMS/ ). Due to its outstanding usability, Robert Campbell had already provided several very helpful PyMOL scripts about MSMS (see http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ ). I have also been using the MSMS program heavily in my work and developed a MSMS plugin for PyMOL with a graphical user interface (GUI). If you have interest, please take a look at the plugin at: --- http://www.pymolwiki.org/index.php/MSMS --- Features: MSMS can be configured and invoked in the GUI. The triangulated protein SES can be rendered as mesh or/and vertices plus normal vectors. The color of surface mesh or vertices can also be configured. Your feedback and suggestions are particularly welcome! Best regards, Hongbo -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ 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] plugin dependencies
Just another reminder: If the version of the external python and the python shipped with PyMOL are different enough on the user's computer, the package might still fail to work in PyMOL even if the user has installed the package using the external python and edited the PYTHONPATH. So, how about ship all the BioPython packages you need in your python code together with your plugin? Of course all dependencies should be included. On 03/10/2011 06:17 AM, rv...@libero.it wrote: Hello everyone, my plugin needs Biopython. I wish check the Biopython installation by try: from Bio import AlignIO # or similar except ImportError: .. prompt the user with a msg .. The problem is: what the msg to the user? Downloading and installing Biopython is not enough: If the user downloads and installs Biopython in the external python interpreter still Biopython continues to be unavailable for the internal python interpreter in pyMOL. Of course the user could edit the PYTHONPATH environment variable and so all the python interpreters can read Biopython but working with environment variables could be too difficult for a not experienced user. Is there a simpler way? Cheers, roberto -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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] Different color on each side of strand
I like the idea about coloring tim-barrels. At the moment the secondary structures can be selected in PyMOL using selector ss. I wonder whether it makes sense to label each strand with an index so we can select each strand individually, e.g. select ss s5 # select the 5th strand from the N-term and then one can flip the colors of the two sides of the strand in case it is not colored properly according to the user. hongbo On 03/08/2011 10:16 AM, Keitaro Yamashita wrote: Dear Hongbo, For example, user can put something like light source and front is defined as the side light hits. (though it would be undefined If sheet plane is placed parallel to the ray..) and even the same strand can have half of it facing the light source and the other half turned opposite to the source. I think this definition is useful when color e.g. beta-barrel, but definitely includes ambiguity. Then, how about defining front side as the C-beta direction of starting residue of sheet? Cheers, Keitaro 2011年3月8日火曜日 Hongbo Zhu hongbo@biotec.tu-dresden.de: Hi, Keitaro, On 03/08/2011 03:11 AM, Keitaro Yamashita wrote: Dear Hongbo, For example, user can put something like light source and front is defined as the side light hits. (though it would be undefined If sheet plane is placed parallel to the ray..) and even the same strand can have half of it facing the light source and the other half turned opposite to the source. But I think any definition is ok if front and back could be alternated easily by user operation. sounds like an interesting operation, though. Cheers, Keitaro 2011/3/8 Hongbo Zhuhongbo@biotec.tu-dresden.de: how do you define front and back sides of sheets in general? -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ 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 -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ 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] Different color on each side of strand
Hi, Keitaro, On 03/08/2011 03:11 AM, Keitaro Yamashita wrote: Dear Hongbo, For example, user can put something like light source and front is defined as the side light hits. (though it would be undefined If sheet plane is placed parallel to the ray..) and even the same strand can have half of it facing the light source and the other half turned opposite to the source. But I think any definition is ok if front and back could be alternated easily by user operation. sounds like an interesting operation, though. Cheers, Keitaro 2011/3/8 Hongbo Zhuhongbo@biotec.tu-dresden.de: how do you define front and back sides of sheets in general? -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ 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] Selecting ASP and GLU
I believe the confusion is caused by the simplified selection expression in PyMOL (and some other visualization tools as well). I remember that one of my colleagues once questioned strongly the reason of using OR instead of AND in such situation. The expression: select resn GLU or resn ASP actually means select (resn == GLU) or (resn == ASP) The reason of using Boolean operator *or* is very clean when the two operands are stated completely. But when the operands are simplified, our first reaction is to use *and* because it is very natural to say I want GLU *and* ASP if you want both GLU and ASP. And it is even more confusing in Jmol : select 110 or 112 (select resno==110 or resn==112) if want you really want is 110 *and* 112 :) hongbo On 03/01/2011 05:43 PM, Jason Vertrees wrote: Hi Martin, To select all ASPs and GLUs just type, select resn GLU+ASP or select resn GLU or resn ASP or, if you need parentheses, select ((resn GLU) or (resn ASP)) Maybe this will help: # fetch a test protein fetch 1rsy, async=0 # color all ASPs and GLUs red color tv_red, (resn ASP or resn GLU) While the boolean 'and' works, the following will fail to select and color any atoms: color tv_red, (resn ASP and resn GLU) because there will be no _single atom_ in both an ASP and a GLU. The boolean 'and' in (resn ASP and resn GLU) requests an atom that is in any ASP _and_ in any GLU--which is impossible. Cheers, -- Jason On Tue, Mar 1, 2011 at 7:44 AM, Martin Hedigerma@bluewin.ch wrote: Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh# remove water h_add # add hydrogens as surface color grey90 color slate, resn lys # lysines in light blue color paleyellow, resn cys # cysteines in light yellow color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red but, the selection kind of does not work for me (I'm assuming the operator for the logical AND is 'and'). What is it that I need to do differently? Kind regards Martin -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-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] Selecting ASP and GLU
On 03/02/2011 10:07 PM, Tsjerk Wassenaar wrote: Hey :) It's good to note that programs are written by programmers, using programmer's logic. First of all, I was not complaining about the logic of the PyMOL programmers. I tried to help find out the reason that might cause Martin's script to break based on the similar complains I had received. It is true that programs are written by programmers. But I guess many users actually hate that fact so much because they see again and again that some programmers just presume that all users will think the same way as they think. (Of course after these users become programmers they start to do the same ;) The confusion is not so much caused by the simplified expression, but by users with little background in mathematics/logic assessing 'and' and 'or' from a linguistic background.In computer science and mathematics OR := union, AND := intersection. It's covered quite well in http://www.pymolwiki.org/index.php/Selection_Algebra I disagree. I think it is caused by the simplified expression to the users who think intuitively instead of immediately mathematically when they try to write down the first line of selection script, no matter how much mathematics/logic they have (the colleague I mentioned is a computer scientist). After staring at the unexpected outcome for a while, they will try to think mathematically or google-ly ;). I can not think of a good way to address this small issue for new users. Maybe a more informative hint to the users is helpful rather than just print 0 atoms selected. For example, PyMOL can print the selection result of each operand, or print the complete selection expression translated from the the simplified selection expression. Cheers, Tsjerk On Wed, Mar 2, 2011 at 11:06 AM, Hongbo Zhu hongbo@biotec.tu-dresden.de wrote: I believe the confusion is caused by the simplified selection expression in PyMOL (and some other visualization tools as well). I remember that one of my colleagues once questioned strongly the reason of using OR instead of AND in such situation. The expression: select resn GLU or resn ASP actually means select (resn == GLU) or (resn == ASP) The reason of using Boolean operator *or* is very clean when the two operands are stated completely. But when the operands are simplified, our first reaction is to use *and* because it is very natural to say I want GLU *and* ASP if you want both GLU and ASP. And it is even more confusing in Jmol : select 110 or 112 (select resno==110 or resn==112) if want you really want is 110 *and* 112 :) hongbo On 03/01/2011 05:43 PM, Jason Vertrees wrote: Hi Martin, To select all ASPs and GLUs just type, select resn GLU+ASP or select resn GLU or resn ASP or, if you need parentheses, select ((resn GLU) or (resn ASP)) Maybe this will help: # fetch a test protein fetch 1rsy, async=0 # color all ASPs and GLUs red color tv_red, (resn ASP or resn GLU) While the boolean 'and' works, the following will fail to select and color any atoms: color tv_red, (resn ASP and resn GLU) because there will be no _single atom_ in both an ASP and a GLU. The boolean 'and' in (resn ASP and resn GLU) requests an atom that is in any ASP _and_ in any GLU--which is impossible. Cheers, -- Jason On Tue, Mar 1, 2011 at 7:44 AM, Martin Hedigerma@bluewin.chwrote: Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh# remove water h_add # add hydrogens as surface color grey90 color slate, resn lys # lysines in light blue color paleyellow, resn cys # cysteines in light yellow color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red but, the selection kind of does not work for me (I'm assuming the operator for the logical AND is 'and'). What is it that I need to do differently? Kind regards Martin -- Free Software Download: Index, SearchAnalyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu
Re: [PyMOL] installing_running vasco
Hi, Yarrow, It says MSMS calculation error. *Possible reason* MSMS is a brilliant program for computing protein solvent excluded surfaces. It is a 3rd-party program (see http://mgltools.scripps.edu/downloads ) and its binary is included in VASCo. The version shipped with VASCo by default is for Linux (msms255i86Linux.5 and msms261x86_64Linux). Since you are using a mac (I suppose it is not running Linux), the binary MSMS will not execute successfully. *Possible solution* Solution 1. Try using VASCo on Linux (e.g. remove your mac OS X and install Linux on your mac :) Solution 2. replace the linux version of MSMS by the mac OsX version (again, see http://mgltools.scripps.edu/downloads). Then, you either have to look for where MSMS is invoked in the python source code of VASCo and replace all the names of the MSMS program, or, cheat VASCo by renaming the mac version of MSMS to the linux version MSMS (this is a easier way, but I do not have a mac at hand and can not tell you whether this trick will work). hope that helps, hongbo On 02/24/2011 05:18 PM, Yarrow Madrona wrote: Hello pymol users, I apologize if this posting is not appropriate for the pymol user list. If there is a better place to direct these questions please let me know. I have installed the vasco plugin into pymol on my mac by: python setup_vasco_x.py install in the Vasco modules directory. I have also installed the plugin into pymol. python VASCo.py -testrun 1. However instead of making a test_out directory it makes an input.ppix to use on the next run. 2. When I add my pdb and run I get an error message. Here is the log file: (Is this a problem with PDB format?) Write ./CIN4sfA.pdb_atoms.csv file (for HydroCalc) Write ./CIN4sfA.pdb_c2fmtx.csv file (for PatchCalc) Run MSMS... -no_header -probe_radius 1.4 -density 1 -all_components Delete Inner MSMS Surface files... MSMS Warnings: 0 ERROR: msms calculation error MSMS surface calculating error, try to skip file and continue run. CODE ;TIME SEC ;DATE;RUN_ID;STATUS ;REASON;PROPERTIES;CHAINS;UNITS ;ATOMS ;SURFPNT ; PATCHPNT CIN4sfA ;0.000 ;Wed Feb 23 20:57:24 2011;0 ;ERROR ;MSMS:ERROR: msms calculation error; ;1 ;1 ;3152 ; ; Finish: time:16 sec Thank you for your help. -Yarrow -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel.: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo@biotec.tu-dresden Webpage: www.biotec.tu-dresden.de -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-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] installing_running vasco
I forgot to mention that the msms shipped with your VASCo (v1.0.2) is installed at: VASCo_1.0.2/unix/VASCo-Modules-1.0.2/ppix_modules/cprogr/unix/msms cheers, hongbo On 02/24/2011 05:18 PM, Yarrow Madrona wrote: Hello pymol users, I apologize if this posting is not appropriate for the pymol user list. If there is a better place to direct these questions please let me know. I have installed the vasco plugin into pymol on my mac by: python setup_vasco_x.py install in the Vasco modules directory. I have also installed the plugin into pymol. python VASCo.py -testrun 1. However instead of making a test_out directory it makes an input.ppix to use on the next run. 2. When I add my pdb and run I get an error message. Here is the log file: (Is this a problem with PDB format?) Write ./CIN4sfA.pdb_atoms.csv file (for HydroCalc) Write ./CIN4sfA.pdb_c2fmtx.csv file (for PatchCalc) Run MSMS... -no_header -probe_radius 1.4 -density 1 -all_components Delete Inner MSMS Surface files... MSMS Warnings: 0 ERROR: msms calculation error MSMS surface calculating error, try to skip file and continue run. CODE ;TIME SEC ;DATE;RUN_ID;STATUS ;REASON;PROPERTIES;CHAINS;UNITS ;ATOMS ;SURFPNT ; PATCHPNT CIN4sfA ;0.000 ;Wed Feb 23 20:57:24 2011;0 ;ERROR ;MSMS:ERROR: msms calculation error; ;1 ;1 ;3152 ; ; Finish: time:16 sec Thank you for your help. -Yarrow -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel.: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo@biotec.tu-dresden Webpage: www.biotec.tu-dresden.de -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-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] rotation of protein
Hi, Kanika, are you looking for biological units of proteins when you say stable dimer? If this is the case, I recommend the page: http://pdbwiki.org/index.php/Biological_unit at the bottom of the page you can find four very useful servers for the determination of biological units of proteins (PQS is not updated anymore): The Protein Quaternary Structure Server (PQS) [2] or [3] The Macro-Molecular Structure Database (MSD) [4] or [5] The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6] Protein quaternary structure investigation (PiQSi) [7] As a matter of fact, the PDB also provides the biological assembly of each PDB entry for download. More information can be found at: http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html If your protein is not from the PDB, you can still try pisa ( http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts protein coordinate files uploaded by the users and determines the stable dimer or else-mer of your protein. hope these help! hongbo On 02/25/2011 01:46 PM, kanika sharma wrote: Hi, i am working to generate a dimer of my protein..I have made a duplicate of my proteinCan any one tell me how to rotate my molecule to get maximum stability..??? Regards.. Kanika -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel.: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo@biotec.tu-dresden Webpage: www.biotec.tu-dresden.de -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-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] msms_pymol.py
You can solve it by adding the following line in the msms_pymol.py you
downloaded from Robert's page to line 133, right before msms_cmd is defined.
if msms_path.startswith('C:/'): msms_path = '\%s\' % (msms_path,)
Basically, your problem was caused by the whitespace in the path to the
MSMS executable file in Windows systems. By adding quotes to the full
path solves the problem.
regards,
hongbo
On 5/12/2010 1:00 PM, sujuan wang wrote:
Dear Robert,
I downloaded the msms 2.6.1 from
http://mgltools.scripps.edu/downloads#msms and installed into
C:\Program Files\MSMS. But there are still something wrong after
running the script:
There seems to be a problem with the msms output
Traceback (most recent call last):
File C:\Program Files\DeLano
Scientific\PyMOL/modules\pymol\parser.py, line 250, in parse
self.result=apply(layer.kw
http://layer.kw[0],layer.args,layer.kw_args)
File C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py, line
282, in calc_msms_area
volume,area_dict,tmp_msms_vert_file,tmp_msms_face_file =
calc_msms(object_name,probe,density,keep,debug)
File C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py, line
159, in calc_msms
sys.exit(1)
SystemExit: 1
My pymol version is 1.1r1 with python 2.4.2 (#67, Sep 28 2005,
12:41:11) [MSC v.1310 32 bit (Intel)]
As a beginner of pymol, thank you for your kindly help.
regards
Sujuan
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Re: [PyMOL] msms_pymol.py
Hi, sujuan, Robert provides a rich collection of pymol plugins. I myself benefit a lot from the collection. For using msms, you can have a try of my alternative to Robert's msms_pymol.py at: http://www.biotec.tu-dresden.de/~hongboz/pymol_script/msms_pymol.py It has a graphical user interface. You can install it from PyMOL menu Plugin--Manage Plugins--Install. You can use the plugin to invoke MSMS for either a pdb file or a selection in PyMOL. It has been tested on PyMOL 0.98 and 1.20. best regards, Hongbo Zhu Hi Sujuan, Given that this is my script, I'll answer. :) On Tue, 11 May 2010 14:38:52 +0800 sujuan wang wsjpy...@gmail.com wrote: Hi All, When i run the script download from http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/, I issue the commond: calc_msms_area 2mlt-melittin, there are always something wrong as follows: CmdLoad: D:/singapore-NTU/HU/modelling/2MLT-melittin.pdb loaded as 2MLT-melittin. PyMOLrun C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py PyMOLcalc_msms_area 2MLT-melittin Traceback (most recent call last): File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py, line 250, in parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py, line 281, in calc_msms_area volume,area_dict,tmp_msms_vert_file,tmp_msms_face_file = calc_msms(object_name,probe,density,keep,debug) File C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py, line 131, in calc_msms convert_pdb_to_xyzrn(tmp_pdb_file,tmp_xyzrn_file,atmnumbers_file) File C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py, line 21, in convert_pdb_to_xyzrn lines = open(numfile).readlines() IOError: [Errno 2] No such file or directory: '' who can give me an example of this command? or something needed to change the option of script? It appears that the program is unable to find the file containing the atom type numbers. This should be a file called atmtypenumbers that comes with the msms program -- they are all in the one .zip file. My script attempts to find this file wherever your msms.exe program is installed. If you need further assistance, let me know. Cheers, Rob -- ___ 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
