From: Nir Q. <nir...@gm...> - 2010-05-07 03:58:09
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Hi, Is there is a way to add a small molecule to a protein after loading a pdb file of the protein from the database? We are trying to make a figure of a protein and a small molecule that we know that is interacting with the protein. In the database there is the structure of the protein only. What will be the best way to add the small molecule to the protein for a schematic figure? thanks for your help, Nir Nir Qvit, Ph.D. Postdoctoral Fellow |
From: Jason V. <jas...@sc...> - 2010-05-07 06:32:37
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Paul, PyMOL is pretty good at this kind of thing and you can automate it at various levels (eg. bash/shell script level, inside PyMOL using Python commands, etc). Let's say you have 100 poses in your ouput directory; to do what you've asked, I'd try: python import glob inFiles = glob.glob("output/*.pdb") for f in inFiles: cmd.load(f, "current") cmd.zoom("org") cmd.zoom() cmd.show_as("surface", "poly") cmd.show_as("sticks", "org") cmd.png( f + ".png", f, ray=1, height=800, width=600) cmd.delete("current") python end This will write out 100 png files each just named with ".png" appended to the PDB name, ray traced, and at 800x600 image size. A couple other hints: (1) If it's the same protein over and over again, you can setup the best view by hand, just once, and then do get_view() and restore that view in all other proteins (2) PyMOL has a preset view for ligand binding sites; A > Preset > Ligand Sites > Transparent (better) is a good one. Good luck, -- Jason On Thu, May 6, 2010 at 1:00 AM, Paul Rigor (uci-ics) <pr...@ic...> wrote: > Hi, > > Is there anyway to access the rendering engine of pymol through a > command line script? > > I'd like to take a snapshot of a ligand-bound protein, but automate > the view such that > 1) The protein is shown as a surface > 2) The view centers around the binding area > 3) The view zooms out enough to present the entire protein > 4) Produce a png or a brief video. > > Thanks in advance! > Paul > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Paul R. (uci-ics) <pr...@ic...> - 2010-05-07 09:16:49
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Great! Looks like a good start. The session log is a good resource too. Thanks again, Paul On Thu, May 6, 2010 at 11:32 PM, Jason Vertrees <jas...@sc...> wrote: > Paul, > > PyMOL is pretty good at this kind of thing and you can automate it at > various levels (eg. bash/shell script level, inside PyMOL using Python > commands, etc). Let's say you have 100 poses in your ouput directory; > to do what you've asked, I'd try: > > python > import glob > inFiles = glob.glob("output/*.pdb") > for f in inFiles: > cmd.load(f, "current") > cmd.zoom("org") > cmd.zoom() > cmd.show_as("surface", "poly") > cmd.show_as("sticks", "org") > cmd.png( f + ".png", f, ray=1, height=800, width=600) > cmd.delete("current") > python end > > This will write out 100 png files each just named with ".png" appended > to the PDB name, ray traced, and at 800x600 image size. > > A couple other hints: > (1) If it's the same protein over and over again, you can setup the > best view by hand, just once, and then do > get_view() > and restore that view in all other proteins > (2) PyMOL has a preset view for ligand binding sites; A > Preset > > Ligand Sites > Transparent (better) is a good one. > > Good luck, > > -- Jason > > On Thu, May 6, 2010 at 1:00 AM, Paul Rigor (uci-ics) <pr...@ic...> wrote: >> Hi, >> >> Is there anyway to access the rendering engine of pymol through a >> command line script? >> >> I'd like to take a snapshot of a ligand-bound protein, but automate >> the view such that >> 1) The protein is shown as a surface >> 2) The view centers around the binding area >> 3) The view zooms out enough to present the entire protein >> 4) Produce a png or a brief video. >> >> Thanks in advance! >> Paul >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > -- Paul Rigor Pre-doctoral BIT Fellow and Graduate Student Institute for Genomics and Bioinformatics Donald Bren School of Information and Computer Sciences University of California, Irvine http://www.ics.uci.edu/~prigor |
From: Maia C. <ch...@ua...> - 2010-05-12 00:08:19
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Hi Jason, is it possible to print out a list of hydrogen bonds found by polar contacts. Maia |
From: Jason V. <jas...@sc...> - 2010-05-07 05:18:19
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Hi Nir, If you have the structure of the small molecule, why not try the following: load yourProtein.pdb load yourSmallMol.pdb create complex, * The new object called "complex" will now have the protein and small molecule. If you don't--and want something for illustration only--then you can convert it from SMILES to pdb using lots of different software. After this, you can throw it into a docking program and use the output for your image. Again, I stress "for illustration only." Cheers, -- Jason On Thu, May 6, 2010 at 11:57 PM, Nir Qvit <nir...@gm...> wrote: > Hi, > Is there is a way to add a small molecule to a protein after loading a > pdb file of the protein from the database? > We are trying to make a figure of a protein and a small molecule that we > know that is interacting with the protein. In the database there is the > structure of the protein only. > What will be the best way to add the small molecule to the protein for a > schematic figure? > thanks for your help, > Nir > > Nir Qvit, Ph.D. > Postdoctoral Fellow > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |