Hi Keitaro, You can try to create a copy from the piece containing the sheet, colour it differently, and change the coordinates slightly. It's a bit tricky maybe, especially if you've got quite a bit of curvature.
Hope it helps, Tsjerk On Wed, Mar 9, 211 at 3:22 PM, Keitaro Yamashita <yamash...@castor.sci.hokudai.ac.jp> wrote: > Hi, > > Yes, there're definitely a few (?) exceptional cases. > But maybe people don't use this feature in such case. > > Anyway, this feature is not included in current PyMOL, right? > Then, is it hard to implement this feature (many changes in code required)? > > Keitaro > > 2011/3/8 gilleain torrance <gilleain.torra...@gmail.com>: >> Hi, >> >> Although most of the time the strands in a sheet have clear 'sides', >> this won't always be true. Keitaro already mentioned the possibility >> of twisted strands, but you can also get two sheets that share the >> 'same' long strand - well, depending on the SSE assignment algorithm, >> I suppose. >> >> Jellyrolls (http://www.cathdb.info/cathnode/2.60.120) are an example >> of this, I seem to remember, as they have long strands that cross from >> one sheet to another. As the sheets are in a sandwich, the strand will >> change side halfway through. >> >> This coloring scheme still sounds like it would be useful, but there >> might be some odd visual effects, or an algorithm to take care of >> corner cases. >> >> gilleain >> >> On Tue, Mar 8, 2011 at 10:12 AM, Hongbo Zhu >> <hongbo....@biotec.tu-dresden.de> wrote: >>> I like the idea about coloring tim-barrels. >>> >>> At the moment the secondary structures can be selected in PyMOL using >>> selector "ss". I wonder whether it makes sense to label each strand with >>> an index so we can select each strand individually, e.g. >>> >>> select ss s5 # select the 5th strand from the N-term >>> >>> and then one can flip the colors of the two "sides" of the strand in >>> case it is not colored properly according to the user. >>> >>> hongbo >>> >>> On 03/08/2011 10:16 AM, Keitaro Yamashita wrote: >>>> Dear Hongbo, >>>> >>>>>> For example, user can put something like light source and "front" is >>>>>> defined as the side light hits. >>>>>> (though it would be undefined If sheet plane is placed parallel to the >>>>>> ray..) >>>>> and even the same strand can have half of it facing the light source and >>>>> the other half turned opposite to the source. >>>> >>>> I think this definition is useful when color e.g. beta-barrel, but >>>> definitely includes ambiguity. >>>> Then, how about defining front side as the C-beta direction of >>>> starting residue of sheet? >>>> >>>> >>>> Cheers, >>>> >>>> Keitaro >>>> >>>> 2011年3月8日火曜日 Hongbo Zhu hongbo....@biotec.tu-dresden.de: >>>>> Hi, Keitaro, >>>>> >>>>> On 03/08/2011 03:11 AM, Keitaro Yamashita wrote: >>>>>> Dear Hongbo, >>>>>> >>>>>> For example, user can put something like light source and "front" is >>>>>> defined as the side light hits. >>>>>> (though it would be undefined If sheet plane is placed parallel to the >>>>>> ray..) >>>>> and even the same strand can have half of it facing the light source and >>>>> the other half turned opposite to the source. >>>>>> >>>>>> But I think any definition is ok if front and back could be alternated >>>>>> easily by user operation. >>>>> sounds like an interesting operation, though. >>>>>> >>>>>> >>>>>> Cheers, >>>>>> >>>>>> Keitaro >>>>>> >>>>>> 2011/3/8 Hongbo Zhu<hongbo....@biotec.tu-dresden.de>: >>>>>>> how do you define "front" and "back" sides of sheets in general? >>>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> What You Don't Know About Data Connectivity CAN Hurt You >>>>>> This paper provides an overview of data connectivity, details >>>>>> its effect on application quality, and explores various alternative >>>>>> solutions. http://p.sf.net/sfu/progress-d2d >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> -- >>>>> Hongbo ZHU >>>>> Postdoctoral Researcher >>>>> Structural Bioinformatics >>>>> >>>>> Technische Universität Dresden >>>>> Biotechnology Center >>>>> Tatzberg 47/49 >>>>> 01307 Dresden, Germany >>>>> >>>>> Tel: +49 (0) 351 463-40083 >>>>> Fax: +49 (0) 351 463-40087 >>>>> E-Mail: hongbo.zhu at biotec >>>>> Webpage: www.biotec.tu-dresden.de >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> What You Don't Know About Data Connectivity CAN Hurt You >>>>> This paper provides an overview of data connectivity, details >>>>> its effect on application quality, and explores various alternative >>>>> solutions. http://p.sf.net/sfu/progress-d2d >>>>> _______________________________________________ >>>>> 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 >>>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> What You Don't Know About Data Connectivity CAN Hurt You >>>> This paper provides an overview of data connectivity, details >>>> its effect on application quality, and explores various alternative >>>> solutions. http://p.sf.net/sfu/progress-d2d >>>> _______________________________________________ >>>> 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 >>> >>> -- >>> Hongbo ZHU >>> Postdoctoral Researcher >>> Structural Bioinformatics >>> >>> Technische Universität Dresden >>> Biotechnology Center >>> Tatzberg 47/49 >>> 01307 Dresden, Germany >>> >>> Tel: +49 (0) 351 463-40083 >>> Fax: +49 (0) 351 463-40087 >>> E-Mail: hongbo.zhu at biotec >>> Webpage: www.biotec.tu-dresden.de >>> >>> ------------------------------------------------------------------------------ >>> What You Don't Know About Data Connectivity CAN Hurt You >>> This paper provides an overview of data connectivity, details >>> its effect on application quality, and explores various alternative >>> solutions. http://p.sf.net/sfu/progress-d2d >>> _______________________________________________ >>> 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 >> >> ------------------------------------------------------------------------------ >> What You Don't Know About Data Connectivity CAN Hurt You >> This paper provides an overview of data connectivity, details >> its effect on application quality, and explores various alternative >> solutions. http://p.sf.net/sfu/progress-d2d >> _______________________________________________ >> 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 > > ------------------------------------------------------------------------------ > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit > for your organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ > 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 -- 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 ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ 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
