Re: [PyMOL] Cylindrical helices don't show up
Hi HJ, this should help: PyMOL> set cylinder_shader_ff_workaround Cheers, Thomas On 26 Dec 2013, at 04:11, HJ Lee wrote: > For some reasons, PyMOL (1.6.0.0, windows 64 bits) doesn't show the > cylindrical helices in cartoon presentation. It just presents helices as an > empty space when the cylindrical helices option is ON . Regular helix > representation works well. > > That would be really great if anyone could give me a clue how to fix it. > > Many thanks > > HJ -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/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
[PyMOL] Cylindrical helices don't show up
For some reasons, PyMOL (1.6.0.0, windows 64 bits) doesn't show the cylindrical helices in cartoon presentation. It just presents helices as an empty space when the cylindrical helices option is ON . Regular helix representation works well. That would be really great if anyone could give me a clue how to fix it. Many thanks HJ -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/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] cylindrical helices
Andreas, That's an interesting find. PyMOL is clearly being fooled by the secondary structure assignment. I don't think it's PyMOL's responsibility to address egregious cases like this—rare and non-standard. You can run 'dss' to update the secondary structure to something more reasonable or you can use the 'alter' command to update the secondary structure assignments. That should improve the result. Cheers, -- Jason On Fri, Nov 1, 2013 at 7:33 AM, Andreas Förster wrote: > Dear all, > > I've just been baffled for a while with a pdb that showed a strange > behavior upon changing the representation from cylindrical cartoon > helices to normal cartoon helices. It seemed to me that helices were > disappearing. > > A picture of the effect is here: > http://www.msf.bio.ic.ac.uk/images/helices.png > > The arrows show pairs of normal helices merged into single short > cylindrical helices. > > At some point, I realized the problem was the definition of pairs of > helices as one continuous secondary-structure element (encircled). > Running dss on the file fixed everything. > > I'm left wondering whether PyMOL should realize it's being fooled by the > secondary structure predictions in egregious cases like this. I looked > hard at the structure with cylindrical helices and started to interpret > differences to a homologous structure, which seemed to have additional > helices, and in perpendicular orientations. > > Best regards. > > > Andreas > > > > > -- >Andreas Förster > Crystallization and Xray Facility Manager > Centre for Structural Biology >Imperial College London > > > -- > Android is increasing in popularity, but the open development platform that > developers love is also attractive to malware creators. Download this white > paper to learn more about secure code signing practices that can help keep > Android apps secure. > http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/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 > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/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
[PyMOL] cylindrical helices
Dear all, I've just been baffled for a while with a pdb that showed a strange behavior upon changing the representation from cylindrical cartoon helices to normal cartoon helices. It seemed to me that helices were disappearing. A picture of the effect is here: http://www.msf.bio.ic.ac.uk/images/helices.png The arrows show pairs of normal helices merged into single short cylindrical helices. At some point, I realized the problem was the definition of pairs of helices as one continuous secondary-structure element (encircled). Running dss on the file fixed everything. I'm left wondering whether PyMOL should realize it's being fooled by the secondary structure predictions in egregious cases like this. I looked hard at the structure with cylindrical helices and started to interpret differences to a homologous structure, which seemed to have additional helices, and in perpendicular orientations. Best regards. Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/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] cylindrical helices
Hi Thomas, Thanks for input - the 'bug' was because the misbehaving PDB had ACs for residues in the helices that were not being drawn correctly. Stripping out the alternative conformations fixed problem, and dss forces cylinder to match dssp header, so I'm good. Mark >Hi Mark, > >cylindrical helices just connect start and end of continous helix >annotations. Could it be that those "misplaced" helices just have a >strong bend to one or both ends, pulling the cylinder from the major >axis of the helix? Same with the fused helices, are you sure there is at >least one none-helix residue between them? > >Does it look better if you type "dss" into the PyMOL command line? This >will reassign secondary structure more strict than dssp does. > >http://pymolwiki.org/index.php/Dss > >Cheers, >Thomas > >On 05/14/2012 05:39 PM, nih\mayerm wrote: >> I've run into a problem not encountered before: drawing a cartoon >> with cylindrical helices does not accurately follow secondary >> structure (a couple of helices are badly misplace and another 2 >> helices fused into 1) even though pdb has secondary structure >> defined by dssp in header. >> >> A cartoon with the same coords, but drawn as round or fancy helices >> is accurate. >> >> Are their settings I can use to control how the cylindrical helices >> are drawn? My backup plan at this point is to go back to >> molscript/raster3d, if I can remember how !!! >> >> Thanks >> >> Mark Mayer > >-- >Thomas Holder >MPI for Developmental Biology >Spemannstr. 35 >D-72076 Tübingen -- +++ Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://snb.nichd.nih.gov/index.htm Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] cylindrical helices
Hi Mark, cylindrical helices just connect start and end of continous helix annotations. Could it be that those "misplaced" helices just have a strong bend to one or both ends, pulling the cylinder from the major axis of the helix? Same with the fused helices, are you sure there is at least one none-helix residue between them? Does it look better if you type "dss" into the PyMOL command line? This will reassign secondary structure more strict than dssp does. http://pymolwiki.org/index.php/Dss Cheers, Thomas On 05/14/2012 05:39 PM, nih\mayerm wrote: > I've run into a problem not encountered before: drawing a cartoon > with cylindrical helices does not accurately follow secondary > structure (a couple of helices are badly misplace and another 2 > helices fused into 1) even though pdb has secondary structure > defined by dssp in header. > > A cartoon with the same coords, but drawn as round or fancy helices > is accurate. > > Are their settings I can use to control how the cylindrical helices > are drawn? My backup plan at this point is to go back to > molscript/raster3d, if I can remember how !!! > > Thanks > > Mark Mayer -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] cylindrical helices
I've run into a problem not encountered before: drawing a cartoon with cylindrical helices does not accurately follow secondary structure (a couple of helices are badly misplace and another 2 helices fused into 1) even though pdb has secondary structure defined by dssp in header. A cartoon with the same coords, but drawn as round or fancy helices is accurate. Are their settings I can use to control how the cylindrical helices are drawn? My backup plan at this point is to go back to molscript/raster3d, if I can remember how !!! Thanks Mark Mayer -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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
