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
