Re: [PyMOL] Pymol visualization problem
Hi Abida Is it possible that you have multiple states in your PDB file? Try clicking the arrow in the bottom right corner of PyMOL and see if you can display the other protein. If so, you probably need to delete the MODEL and END from your PDB file. Then all should appear at once. Martin On 08.01.13 06:12, Abida Siddiqa wrote: Hello, I have docked one protein named 'L1'( 450 amino acid) with another protein named 'E2'(68 amino acid, Chain A) and used pymol-v1.3r1-edu-Win32.msi to visualize the complex. my system is windows 7 , 64 bit. The problem is, i am unable to see the sequence of 'E2' protein and so as its structure. In order to confirm, if it is docking problem or visualization problem, i have used swiss pdb viewer. it has shown me sequence and structure of both proteins. i wonder why can not i see it in pymol. secondly, i docked L1 and E2 ( this time used chain A and B of it), and visualized the complex in pymol. i was only able to see L1, and chain A of E2 (both chain A and B are alike). Then in order to see if it is docking error or visualization error, i rendered the complex in swiss pdb viwer and saw the L1 and E2 (both chain A and B). Thirdly, i changed the docking software and generated a complex using another software, this time i still was unable to visualize complete complex in pymol. Any help will be much appreciated. Kind regards Abida -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ 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 -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512___ 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] DNA measurement help require by sculptor
Hi Briony, this sounds like a very cool project! Regarding question 1: If your PDB DNA model is long enough, you can use cafit_orientation from the psico module (a PyMOL extension) to draw the axis. It determines the axis by least-square linear fit on the backbone atoms. This requires a recent PyMOL version and numpy. If the helix is not long enough, cafit_orientation will most likely result in a slightly skewed axis, but I think you need a perfect axis, right? If you are interested, I could customize the script to take the bases orientations into account when interpolating the axis. Just let me know. http://www.pymolwiki.org/index.php/psico Cheers, Thomas Briony Marshall (Personal) wrote, On 01/07/13 17:43: Apologies - Slightly off topic request for collaboration from a sculptor, but it does relate to how Pymol works Dear all, I am a sculptor working on an ambitious bronze sculpture of DNA and I am looking to find out some more detailed measurements of ideal B-DNA which I am having difficulty getting from Pymol. You can see my previous work on my website: http://www.briony.com The sculpture I am making represents a single turn of ideal B-DNA at a scale of 500 million times life size, i.e. it will be 1m wide by 1.66m tall. Each atom is represented by a small human figure made of bronze, with the bonds between them represented by the arms and legs of the figures. (this is a much more complicated version of this sculpture I did previously based on the structure of diamond: http://www.briony.com/works/dream-II_1.html) I studied biochemistry at Oxford in the mid-90s and did a specialisation in DNA dynamics so I am not altogether wet behind the ears, but as I spend most of my time now with plaster and clay, my in depth DNA knowledge is a bit weak and I'm new to Pymol. I have been working from the ideal B-DNA PDB file for all my measurements. I am at the stage that I have made all 20 bases, and 20 sections of sugar phosphate backbone in bronze, and I am about to start constructing my double helix around a stainless steel central access. 1. I haven't worked out how to get the central axis of B-DNA to appear on Pymol. Is there a way to do this? If not, I would need a scale drawings of both base pairs with the central axis point (of B-DNA) marked. This would allow me to make various measurements to ensure I put the bases and sugar phospate sections together accurately. (In particular I need to know the distance between the central axis and the N of each base pair that attaches to the backbone, and the angle between these two lines within each base pair 'rung') 2. I was looking for advice on whether I can safely ignore the base pair axis inclination (as this is only 1.2° I think so) and the propelor twist of the base pairs (I was less sure about this). I think I can straightening up the base pairs but ensure that where they attach to the backbone stays in the same place. I'm hoping the only effect might be on the length and orientation of the hydrogen bonds. 3. Final question for now - is there a standard colour convention for representation of bases like there is for atoms? FYI, I had contemplated doing the patina (colouring) of the sculpture according to the atomic colour code, but with about 1000 atoms, this would be a very fiddly long job. I am now considering colouring each base a different colour and was wondering if there was a standard, such as Adenine is always represented blue, etc.. Many thanks in advance for any help you can give. Regards Briony Briony Marshall - Sculptor www.briony.com http://www.briony.com/ http://www.briony.com/join my mailing list: www.briony.com/subscribe.html http://www.briony.com/subscribe.html or like me on facebook: www.facebook.com/brionymarshallsculptor http://www.facebook.com/brionymarshallsculptor UK mobile: +44 (0)7956 107 893 Pangolin London Sculptor in Residence blog: www.a-n.co.uk/link/creative-year http://www.a-n.co.uk/link/creative-year -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ 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] Pymol visualization problem
Thomas and Martin I have tried both suggestions. Still it did not work out.RegardsAbida From: abida_sidd...@hotmail.com To: pymol-users@lists.sourceforge.net Subject: Pymol visualization problem Date: Tue, 8 Jan 2013 10:12:46 +0500 Hello, I have docked one protein named 'L1'( 450 amino acid) with another protein named 'E2'(68 amino acid, Chain A) and used pymol-v1.3r1-edu-Win32.msi to visualize the complex. my system is windows 7 , 64 bit. The problem is, i am unable to see the sequence of 'E2' protein and so as its structure. In order to confirm, if it is docking problem or visualization problem, i have used swiss pdb viewer. it has shown me sequence and structure of both proteins. i wonder why can not i see it in pymol. secondly, i docked L1 and E2 ( this time used chain A and B of it), and visualized the complex in pymol. i was only able to see L1, and chain A of E2 (both chain A and B are alike). Then in order to see if it is docking error or visualization error, i rendered the complex in swiss pdb viwer and saw the L1 and E2 (both chain A and B). Thirdly, i changed the docking software and generated a complex using another software, this time i still was unable to visualize complete complex in pymol. Any help will be much appreciated. Kind regards Abida -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512___ 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] Pymol visualization problem
Hi Abida, thanks for the PDB file that you sent me off-list. It is a naming conflict, you have more than one chain A which have overlapping residue numbers and even IDs. You can still load them like this: PyMOL set retain_order PyMOL load complex.1.pdb PyMOL as cartoon I also suggest to fix the chain identifier: PyMOL alter complex.1 and rank 3578-, chain=B PyMOL util.cbc And for the second file: PyMOL set retain_order PyMOL load complex.5.pdb PyMOL as cartoon PyMOL alter complex.5 and chain A and rank 1322-, chain=C PyMOL util.cbc Hope that helps. Cheers, Thomas Abida Siddiqa wrote, On 01/08/13 16:58: Thomas and Martin I have tried both suggestions. Still it did not work out. Regards Abida From: abida_sidd...@hotmail.com To: pymol-users@lists.sourceforge.net Subject: Pymol visualization problem Date: Tue, 8 Jan 2013 10:12:46 +0500 Hello, I have docked one protein named 'L1'( 450 amino acid) with another protein named 'E2'(68 amino acid, Chain A) and used pymol-v1.3r1-edu-Win32.msi to visualize the complex. my system is windows 7 , 64 bit. The problem is, i am unable to see the sequence of 'E2' protein and so as its structure. In order to confirm, if it is docking problem or visualization problem, i have used swiss pdb viewer. it has shown me sequence and structure of both proteins. i wonder why can not i see it in pymol. secondly, i docked L1 and E2 ( this time used chain A and B of it), and visualized the complex in pymol. i was only able to see L1, and chain A of E2 (both chain A and B are alike). Then in order to see if it is docking error or visualization error, i rendered the complex in swiss pdb viwer and saw the L1 and E2 (both chain A and B). Thirdly, i changed the docking software and generated a complex using another software, this time i still was unable to visualize complete complex in pymol. Any help will be much appreciated. Kind regards Abida -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ 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] Problem Opening Session File
I created a session file with Pymol Version 1.5.0.4 that I am unable to open up on my laptop which is running 1.2r5pre. I am able to see the first state but all of the other remaining states are lost. I haven't had opening session files with saved states in the past so I do not suspect it is a issue of compatibility between versions. The one difference that I think is causing the problem is that the session contains an electron density map that does not appear to save along with the session. Below is the message that I receive from when I go to the state containing the density map. Has anyone else had this issue and been able to resolve it? If so how? This Executable Build integrates and extends Open-Source PyMOL 1.2r3pre.Warning: This session was created with a newer version of PyMOL (15.04).Warning: Some content may not load completely.ExectiveSetSession-Error: after names.ExectiveSetSession-Warning: restore may be incomplete.ObjectMeshUpdate-Error: map 'Density' has been deleted. Thanks,Michael -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512___ 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] Problem Opening Session File
The handling of density maps changed with (I believe) version 1.5 - earlier versions would just load the map as given, later ones appear to try to do symmetry expansion (even if the map isn't covering the ASU). I've seen this result in a similar error message when loading session files (with electron density, created in 1.4) with 1.5. My solution has been to stick with 1.4. However, I don't generally use multi-state session files, so I don't know if the electron density problem is related to the multi-state problem or not. Pete Mike Feldkamp wrote: I created a session file with Pymol Version 1.5.0.4 that I am unable to open up on my laptop which is running 1.2r5pre. I am able to see the first state but all of the other remaining states are lost. I haven't had opening session files with saved states in the past so I do not suspect it is a issue of compatibility between versions. The one difference that I think is causing the problem is that the session contains an electron density map that does not appear to save along with the session. Below is the message that I receive from when I go to the state containing the density map. Has anyone else had this issue and been able to resolve it? If so how? This Executable Build integrates and extends Open-Source PyMOL 1.2r3pre.Warning: This session was created with a newer version of PyMOL (15.04).Warning: Some content may not load completely.ExectiveSetSession-Error: after names.ExectiveSetSession-Warning: restore may be incomplete.ObjectMeshUpdate-Error: map 'Density' has been deleted. Thanks,Michael -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ 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 -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ 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] DNA ligand presentation in PyMOL
Hi, I have a model of DNA-Ligand, defualt both ligand and DNA are represented as sticks i make DNA as cartoon and ligand as stick, this is general presentation DNA molecule has internal HBONDS too.. how can i see the hbonds made between just ligand and DNA, ??? how can i show just interacting residues of DNA with ligand i am unable to create this presentation.. Thanku regards amna khan -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ 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
