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
