Dear Tsjerk and Hongbo, Thank you very much for giving me ideas.
As mentioned by Honbo, I think shifting strand can work in only case of very planar strand. I'll try painting strands with GIMP -- thank you for your kindness! Keitaro 2011/3/10 Hongbo Zhu <[email protected]>: > I was also thinking along that line :) But that is pretty trick for a > structure like beta-barrel, since you have to actually shrink the barrel > toward the center. > > here is another hack that might work: > > 1. render only the black outline of the cartoon representation of your > protein: > set ray_trace_mode,2 # see http://www.pymolwiki.org/index.php/Ray > > 2. fill the cartoon, especially the beta strands using different colors > using some image manipulation program (a great example is GIMP). This is > fairly easy as most of such programs provide a "Fill Tool" (in GIMP it > is the bucket button). Using such a tool you have the picture in a few > clicks. I have actually made an example of a beta barrel (1opfA): > > http://www.biotec.tu-dresden.de/~hongboz/pymol_example/1opfA.html > > (In this quick example, I have oriented the protein such that both sides > of some strands can be seen.) > > hongbo > > > On 03/09/2011 04:03 PM, Tsjerk Wassenaar wrote: >> 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 >> <[email protected]> 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<[email protected]>: >>>> 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 >>>> <[email protected]> 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 [email protected]: >>>>>>> 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<[email protected]>: >>>>>>>>> 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 ([email protected]) >>>>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>>>>> Archives: http://www.mail-archive.com/[email protected] >>>>>>> >>>>>>> -- >>>>>>> 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 ([email protected]) >>>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>>>> Archives: http://www.mail-archive.com/[email protected] >>>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> 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 ([email protected]) >>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>>> Archives: http://www.mail-archive.com/[email protected] >>>>> >>>>> -- >>>>> 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 ([email protected]) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: http://www.mail-archive.com/[email protected] >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 ([email protected]) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/[email protected] >>> >>> ------------------------------------------------------------------------------ >>> 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 ([email protected]) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/[email protected] >> >> >> > > -- > 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 > > ------------------------------------------------------------------------------ > 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 ([email protected]) > Info Page: 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