[PyMOL] How to draw a cartoon representation on secondary structures containing beta-amino acids?
Dear all, I have a small helical pseudopeptide with mixed alpha and beta amino-acids. How can I make a cartoon representation of this helix with Pymol? For the moment, I have selected the peptide backbone atoms and tried the "alter" command to force pymol to recognize the helix but it do not work. Thanks. Best regards, Baptiste -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-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] How to draw a cartoon representation on secondary structures containing beta-amino acids?
Thanks Joseph and Thomas for your replies. When I use the "as cartoon" commands, all my molecule disappear. My *pdb file could be the problem as it is a *cif crystal structure file (converted with mercury) from the cambridge crystal data. Cheers, Baptiste 2011/8/16 Thomas Holder > Hi Baptiste, > > > I have a small helical pseudopeptide with mixed alpha and beta >> amino-acids. How can I make a cartoon representation of this helix with >> Pymol? For the moment, I have selected the peptide backbone atoms and tried >> the "alter" command to force pymol to recognize the helix but it do not >> work. >> > > are you sure? What happens if you try this: > > alter all, ss='H' > as cartoon > rebuild > > Cheers, > Thomas > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-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] How to draw a cartoon representation on secondary structures containing beta-amino acids?
Hi, The Tsjerk's solution works without modify the exotic *pdb file. :) set cartoon_trace_atoms select cacb, name c5+c6+c10+c12+c16+c19+c23+c25+c29+c32+c36+c38 alter cacb, ss='H' show cartoon, cacb Thanks all, Baptiste Le 17/08/2011 05:48, Tsjerk Wassenaar a écrit : > Hey, > > I noticed with coarse grained structures that cartoon_trace_atoms > really traces all atoms; you may need to restrict the selection: > > set cartoon_trace_atoms > show cartoon, n. ca+cb > > Hope it helps, > > Tsjerk > > On Wed, Aug 17, 2011 at 1:24 AM, Jason Vertrees > wrote: >> Hi Baptiste, >> >>> My pymol version is the 0.99rc6 on windows 7, the graphic card on my laptop >>> is an ATI Mobility Radeon HD 5650. I'm trying to reproduce the >>> representation on the page 7 of this article (in copy). >> I looked at the file you sent and even tried some tricks to force it >> to work. However, that converted PDB file is unusable--it's too >> non-standard. PyMOL's really confused on connectivity, geometry, and >> numbering. For example, there're 146 atoms but only one residue. Can >> you please try fixing the file and try again? To give you an example >> of how badly arrange the file is try, >> >> set cartoon_trace_atoms >> >> show cartoon >> >> The atom trace is all over the place. >> >> I'm happy to revisit this if you can improve the file. >> >> Cheers, >> >> -- Jason >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) jason.vertr...@schrodinger.com >> (o) +1 (603) 374-7120 >> >> -- >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> user administration capabilities and model configuration. Take >> the hassle out of deploying and managing Subversion and the >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> ___ >> 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 >> > > -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ 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] Chi torsion angles measurements on multiple structures
Dear all, I wounder to know about possible ways to measure chi1, chi2 dihedral angles on a set of structures. For example, I opened 10 pdb files and the phi_psi command allows us to easily obtain the phi and psi values: Ex: To obtain the phi and psi values of the residue 288 of the chain A in the 10 structures, >phi_psi ///A/288 PHE-288: ( -63.4, -25.1 ) PHE-288: ( -60.1, -35.9 ) PHE-288: ( -65.0, -28.1 ) PHE-288: ( -59.4, -31.0 ) PHE-288: ( -62.6, -34.7 ) PHE-288: ( -80.5, -36.4 ) PHE-288: ( -63.5, -24.7 ) PHE-288: ( -60.5, -31.7 ) PHE-288: ( -63.3, -38.5 ) PHE-288: ( -62.5, -35.2 ) Then, I tried to get the chi1 and chi2 values for the Phe288. It works for a single structure but not for the entire set (e.g. chi1), >get_dihedral ///A/288/N, ///A/288/CA, ///A/288/CB, ///A/288/CG PyMOL>get_dihedral ///A/288/N, ///A/288/CA, ///A/288/CB, ///A/288/CG GetDihedral-Error: Selection 1 doesn't contain a single atom/vertex. GetDihedral-Error: Selection 2 doesn't contain a single atom/vertex. GetDihedral-Error: Selection 3 doesn't contain a single atom/vertex. GetDihedral-Error: Selection 4 doesn't contain a single atom/vertex. cmd.get_dihedral: -1.000 degrees. Is there a simple way to obtain the same results than for phi and psi, may be tuning the phi_psi command... Thanks for your help, Best, Baptiste -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking
Dear all, I tried to calculate a rmsd value between ligands from a crystal structure and after docking. The two molecules share similar nomenclatures and are really well superimposed. I think that the RMSD should be < 1 A. I used the following lines: alter all,segi="" alter all,chain ="" rms /ligand_crystal*, /ligand_docking* It works but I obtained an abnormal high RMSD value of 6.146 A. When I use the pair_fit function, pymol completely return one molecule and also write "ExecutiveRMS: RMS = 6.146 (51 to 51 atoms)". I should have missed something... thanks for the help, All the Best. Baptiste -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking
Thanks for your answers. The molecule is the rifampicin. Please find attached the pdb from the crystal structure and the pdbqt from autodock vina. May be the format of one or both files is not correct. Best, Baptiste Le 25/07/2018 à 18:57, Markus Heller a écrit : Not knowing what your molecule looks like, could it be automorphism? -Original Message- From: Baptiste Legrand Sent: Wednesday, July 25, 2018 9:17 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking Dear all, I tried to calculate a rmsd value between ligands from a crystal structure and after docking. The two molecules share similar nomenclatures and are really well superimposed. I think that the RMSD should be < 1 A. I used the following lines: alter all,segi="" alter all,chain ="" rms /ligand_crystal*, /ligand_docking* It works but I obtained an abnormal high RMSD value of 6.146 A. When I use the pair_fit function, pymol completely return one molecule and also write "ExecutiveRMS: RMS = 6.146 (51 to 51 atoms)". I should have missed something... thanks for the help, All the Best. Baptiste -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net REMARK Accelrys Discovery Studio PDB file REMARK Created: 2018-07-19T10:09:11Z CRYST1 91.537 91.537 85.504 90.00 90.00 90.00 P43212 HETATM1 C1 RFP A 1 14.806 77.125 -1.210 1.00 64.23 C HETATM2 C2 RFP A 1 14.953 76.751 -2.593 1.00 63.55 C HETATM3 C3 RFP A 1 14.241 77.375 -3.647 1.00 64.11 C HETATM4 C4 RFP A 1 13.348 78.432 -3.331 1.00 64.98 C HETATM5 C5 RFP A 1 12.215 79.956 -1.564 1.00 63.37 C HETATM6 C6 RFP A 1 12.088 80.304 -0.164 1.00 63.57 C HETATM7 C7 RFP A 1 12.755 79.735 0.904 1.00 62.43 C HETATM8 C8 RFP A 1 13.698 78.640 0.582 1.00 64.25 C HETATM9 C9 RFP A 1 13.888 78.210 -0.877 1.00 64.46 C HETATM 10 C10 RFP A 1 13.141 78.861 -1.979 1.00 64.85 C HETATM 11 C11 RFP A 1 11.347 80.802 -2.276 1.00 64.54 C HETATM 12 C12 RFP A 1 10.646 81.703 -1.287 1.00 64.67 C HETATM 13 C13 RFP A 1 10.916 83.176 -1.558 1.00 63.87 C HETATM 14 C14 RFP A 1 12.568 80.168 2.350 1.00 61.65 C HETATM 15 C15 RFP A 1 17.147 75.583 -2.766 1.00 66.95 C HETATM 16 C16 RFP A 1 17.640 74.255 -3.335 1.00 66.71 C HETATM 17 C17 RFP A 1 16.893 73.092 -3.337 1.00 66.67 C HETATM 18 C18 RFP A 1 15.523 72.841 -2.824 1.00 65.93 C HETATM 19 C19 RFP A 1 14.731 71.908 -3.315 1.00 64.44 C HETATM 20 C20 RFP A 1 13.238 71.937 -3.652 1.00 62.92 C HETATM 21 C21 RFP A 1 12.289 72.616 -2.635 1.00 59.36 C HETATM 22 C22 RFP A 1 10.769 72.547 -2.987 1.00 59.90 C HETATM 23 C23 RFP A 1 9.808 73.234 -1.990 1.00 58.88 C HETATM 24 C24 RFP A 1 9.459 74.694 -2.336 1.00 56.87 C HETATM 25 C25 RFP A 1 8.704 75.392 -1.187 1.00 58.02 C HETATM 26 C26 RFP A 1 9.142 76.908 -1.039 1.00 57.95 C HETATM 27 C27 RFP A 1 8.120 77.890 -0.389 1.00 59.54 C HETATM 28 C28 RFP A 1 8.622 79.330 -0.286 1.00 59.95 C HETATM 29 C29 RFP A 1 8.694 80.124 -1.346 1.00 61.62 C HETATM 30 C30 RFP A 1 19.036 74.327 -3.914 1.00 64.93 C HETATM 31 C31 RFP A 1 13.119 72.542 -5.082 1.00 61.29 C HETATM 32 C32 RFP A 1 10.278 71.093 -3.201 1.00 56.29 C HETATM 33 C33 RFP A 1 8.690 74.802 -3.666 1.00 56.59 C HETATM 34 C34 RFP A 1 10.469 76.870 -0.274 1.00 57.65 C HETATM 35 C35 RFP A 1 6.399 74.521 -0.626 1.00 60.22 C HETATM 36 C36 RFP A 1 5.021 74.498 -1.088 1.00 57.98 C HETATM 37 C37 RFP A 1 6.396 77.619 1.303 1.00 58.74 C HETATM 38 C43 RFP A 1 14.380 76.997 -5.048 1.00 62.89 C HETATM 39 N1 RFP A 1 15.815 75.705 -2.950 1.00 64.57 N HETATM
Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking
Thanks Marko and Thomas, It works removing the lines at the end as indicated by Marko. I also tried for other ligands. Indeed, I have the v1.5.0.5 version. Thanks a lot. Cheers, Baptiste Le 26/07/2018 à 10:32, Marko Hyvonen a écrit : Hi Thomas Perhaps this is a Pymol version issue? I just tried this (with the second command of yours) with the original coords and get the same as Baptiste. I tried this on v. 1.8.2 open source Pymol in Win10 laptop. With the fixed coords I just sent back, the result is the correct 0.032 A. cheers, Marko On 26/07/2018 09:26, Thomas Holder wrote: Hi Baptiste, These files look good to me, I get: PyMOL>rms Crystal_Rfp, Vina_Rfp Executive: RMSD =0.032 (51 to 51 atoms) Is it possible that you tried with a multi-model (multiple poses) pdbqt file before? If that's the case, specify "mobile_state" and/or "target_state": PyMOL>rms Crystal_Rfp, Vina_Rfp, mobile_state=1, target_state=1 Executive: RMSD =0.032 (51 to 51 atoms) See also "Notes" section here:https://pymolwiki.org/index.php/Align#Notes Cheers, Thomas On Jul 26, 2018, at 9:42 AM, Baptiste Legrand wrote: Thanks for your answers. The molecule is the rifampicin. Please find attached the pdb from the crystal structure and the pdbqt from autodock vina. May be the format of one or both files is not correct. Best, Baptiste Le 25/07/2018 à 18:57, Markus Heller a écrit : Not knowing what your molecule looks like, could it be automorphism? -Original Message- From: Baptiste Legrand Sent: Wednesday, July 25, 2018 9:17 AM To:pymol-users@lists.sourceforge.net Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking Dear all, I tried to calculate a rmsd value between ligands from a crystal structure and after docking. The two molecules share similar nomenclatures and are really well superimposed. I think that the RMSD should be < 1 A. I used the following lines: alter all,segi="" alter all,chain ="" rms /ligand_crystal*, /ligand_docking* It works but I obtained an abnormal high RMSD value of 6.146 A. When I use the pair_fit function, pymol completely return one molecule and also write "ExecutiveRMS: RMS =6.146 (51 to 51 atoms)". I should have missed something... thanks for the help, All the Best. Baptiste -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org!http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page:https://lists.sourceforge.net/lists/listinfo/pymol-users Archives:http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Marko Hyvonen Department of Biochemistry, University of Cambridge mh...@cam.ac.uk +44 (0)1223 766 044 @HyvonenGroup http://hyvonen.bioc.cam.ac.uk -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] MD analysis (distance, dihedral etc)
Hi all, Is it possible to monitor distances, dihedrals etc. in a protein trajectory? to finally plot distances or something else versus time. (as VMD or others) Thanks. Best, Baptiste ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] MD analysis (distance, dihedral etc)
Thanks Tamas, I will have a look on this. Best, Baptiste Le 04/09/2020 à 15:55, Tamas Hegedus a écrit : It is. -- Pseudo code: sel1 = u.select_atoms... sel2 = u.select_atoms... # it is important to make the selection out of the loop for t in u.trajectory: d = numpy.norm(sel1.center_of_geometry - sel2...) -- dihedral is somwhat more complex: SEL = "resid %i and name %s" C0 = SEL % (RESI-1, 'C') N1 = SEL % (RESI, 'N') CA = SEL % (RESI, "CA") C1 = SEL % (RESI, "C") N2 = SEL % (RESI+1, "N") phiL = [] psiL = [] u = MDA.Universe(GRO, TRJ) phi = sum([u.select_atoms(atom) for atom in [C0, N1, CA, C1]]).dihedral psi = sum([u.select_atoms(atom) for atom in [N1, CA, C1, N2]]).dihedral for f in u.trajectory: phiL.append(phi.value()) psiL.append(psi.value()) On 9/4/20 9:02 AM, Baptiste Legrand wrote: Hi all, Is it possible to monitor distances, dihedrals etc. in a protein trajectory? to finally plot distances or something else versus time. (as VMD or others) Thanks. Best, Baptiste ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
