From: Baptiste L. <bap...@gm...> - 2011-08-16 15:54:39
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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 |
From: Thomas H. <sp...@us...> - 2011-08-16 16:54:23
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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 |
From: Baptiste L. <bap...@gm...> - 2011-08-16 17:57:02
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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 <sp...@us...> > 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 > |
From: Jason V. <jas...@sc...> - 2011-08-16 23:31:16
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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) Jas...@sc... (o) +1 (603) 374-7120 |
From: Tsjerk W. <ts...@gm...> - 2011-08-17 03:49:22
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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 <jas...@sc...> 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) Jas...@sc... > (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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands |
From: Baptiste L. <bap...@gm...> - 2011-08-17 07:13:09
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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 > <jas...@sc...> 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) Jas...@sc... >> (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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > |