From: Keitaro Y. <yam...@ca...> - 2011-03-06 15:01:46
|
Dear all, Can PyMOL set different colors on each side of cartoon strand? I tried cartoon_discrete_colors but it was not for this purpose. (I mean the sides from which sidechains are protruded.) Thanks in advance, Keitaro |
From: Jason V. <jas...@sc...> - 2011-03-06 19:43:30
|
Hi Keitaro, Use the "cartoon_highlight_color" setting. For example: set cartoon_highlight_color, red Cheers, -- Jason On Sun, Mar 6, 2011 at 10:01 AM, Keitaro Yamashita <yam...@ca...> wrote: > Dear all, > > Can PyMOL set different colors on each side of cartoon strand? > > I tried cartoon_discrete_colors but it was not for this purpose. > (I mean the sides from which sidechains are protruded.) > > Thanks in advance, > > Keitaro > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Keitaro Y. <yam...@ca...> - 2011-03-07 00:32:52
Attachments:
long_strand.png
|
Dear all, Sorry for my unclear explanation. I made a picture explaining what I'd like to do. I want to color the front and back of sheets separately. Jason said it should be possible, could anyone tell me how to do it? Cheers, Keitaro 2011/3/7 Jason Vertrees <jas...@sc...>: > Hi Keitaro, > > Use the "cartoon_highlight_color" setting. For example: > > set cartoon_highlight_color, red > > Cheers, > > -- Jason > > On Sun, Mar 6, 2011 at 10:01 AM, Keitaro Yamashita > <yam...@ca...> wrote: >> Dear all, >> >> Can PyMOL set different colors on each side of cartoon strand? >> >> I tried cartoon_discrete_colors but it was not for this purpose. >> (I mean the sides from which sidechains are protruded.) >> >> Thanks in advance, >> >> Keitaro >> >> ------------------------------------------------------------------------------ >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > |
From: Schubert, C. [PRDUS] <CSC...@it...> - 2011-03-07 15:12:17
|
Not sure if this is possible but it would be a nice feature to have. Since it mimics the way helices are drawn, when cartoon_highlight_color is set. Cheers, Carsten > -----Original Message----- > From: Keitaro Yamashita [mailto:yam...@ca...] > Sent: Sunday, March 06, 2011 7:32 PM > To: pym...@li... > Subject: Re: [PyMOL] Different color on each side of strand > > Dear all, > > Sorry for my unclear explanation. > > I made a picture explaining what I'd like to do. > I want to color the front and back of sheets separately. > > Jason said it should be possible, could anyone tell me how to do it? > > Cheers, > > Keitaro > > > > 2011/3/7 Jason Vertrees <jas...@sc...>: > > Hi Keitaro, > > > > Use the "cartoon_highlight_color" setting. For example: > > > > set cartoon_highlight_color, red > > > > Cheers, > > > > -- Jason > > > > On Sun, Mar 6, 2011 at 10:01 AM, Keitaro Yamashita > > <yam...@ca...> wrote: > >> Dear all, > >> > >> Can PyMOL set different colors on each side of cartoon strand? > >> > >> I tried cartoon_discrete_colors but it was not for this purpose. > >> (I mean the sides from which sidechains are protruded.) > >> > >> Thanks in advance, > >> > >> Keitaro > >> > >> -------------------------------------------------------------------- > - > >> --------- 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 (PyM...@li...) > >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> Archives: > >> http://www.mail-archive.com/pym...@li... > >> > > > > > > > > -- > > Jason Vertrees, PhD > > PyMOL Product Manager > > Schrodinger, LLC > > > > (e) Jas...@sc... > > (o) +1 (603) 374-7120 > > |
From: Hongbo Z. <hon...@bi...> - 2011-03-07 15:48:21
|
how do you define "front" and "back" sides of sheets in general? On 03/07/2011 01:32 AM, Keitaro Yamashita wrote: > Dear all, > > Sorry for my unclear explanation. > > I made a picture explaining what I'd like to do. > I want to color the front and back of sheets separately. > > Jason said it should be possible, could anyone tell me how to do it? > > Cheers, > > Keitaro > > > > 2011/3/7 Jason Vertrees<jas...@sc...>: >> Hi Keitaro, >> >> Use the "cartoon_highlight_color" setting. For example: >> >> set cartoon_highlight_color, red >> >> Cheers, >> >> -- Jason >> >> On Sun, Mar 6, 2011 at 10:01 AM, Keitaro Yamashita >> <yam...@ca...> wrote: >>> Dear all, >>> >>> Can PyMOL set different colors on each side of cartoon strand? >>> >>> I tried cartoon_discrete_colors but it was not for this purpose. >>> (I mean the sides from which sidechains are protruded.) >>> >>> Thanks in advance, >>> >>> Keitaro >>> >>> ------------------------------------------------------------------------------ >>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 >> >> >> >> ------------------------------------------------------------------------------ >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... -- 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 |
From: Keitaro Y. <yam...@ca...> - 2011-03-08 02:12:01
|
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..) But I think any definition is ok if front and back could be alternated easily by user operation. Cheers, Keitaro 2011/3/8 Hongbo Zhu <hon...@bi...>: > how do you define "front" and "back" sides of sheets in general? > |
From: Hongbo Z. <hon...@bi...> - 2011-03-08 07:52:38
|
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<hon...@bi...>: >> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- 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 |
From: Keitaro Y. <yam...@ca...> - 2011-03-08 09:16:48
|
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 hon...@bi...: > 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<hon...@bi...>: >>> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > -- > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Hongbo Z. <hon...@bi...> - 2011-03-08 10:12:40
|
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 hon...@bi...: >> 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<hon...@bi...>: >>>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> -- >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- 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 |
From: gilleain t. <gil...@gm...> - 2011-03-08 10:51:05
|
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 <hon...@bi...> 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 hon...@bi...: >>> 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<hon...@bi...>: >>>>> 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 (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>> >>> -- >>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> ------------------------------------------------------------------------------ >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > -- > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Keitaro Y. <yam...@ca...> - 2011-03-09 14:23:13
|
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 <gil...@gm...>: > 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 > <hon...@bi...> 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 hon...@bi...: >>>> 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<hon...@bi...>: >>>>>> 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 (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: http://www.mail-archive.com/pym...@li... >>>> >>>> -- >>>> 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 (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>>> >>> >>> ------------------------------------------------------------------------------ >>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> -- >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Tsjerk W. <ts...@gm...> - 2011-03-09 15:03:45
|
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 <yam...@ca...> 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 <gil...@gm...>: >> 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 >> <hon...@bi...> 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 hon...@bi...: >>>>> 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<hon...@bi...>: >>>>>>> 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 (PyM...@li...) >>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>> >>>>> -- >>>>> 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 (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>> >>> -- >>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> ------------------------------------------------------------------------------ >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- 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 |
From: Maia C. <ch...@ua...> - 2011-03-13 06:06:49
|
Hello, I have an old saved session as a pse file. How can I save a script that produced that pse file. It may be easier just to get information about each object in that pse file. Maia |
From: Schubert, C. [PRDUS] <CSC...@it...> - 2011-03-13 10:02:11
|
Maia, as far as I know a .pse is just a dump of the internal data structure of Pymol. You can save the molecules contained in the session, but the graphical representation and any modifications would need to be recreated. Hopefully Jason proves me wrong ... Cheers, Carsten > -----Original Message----- > From: Maia Cherney [mailto:ch...@ua...] > Sent: Sunday, March 13, 2011 7:07 AM > To: Jason Vertrees > Cc: pym...@li... > Subject: Re: [PyMOL] write a script from pse file > > Hello, > > I have an old saved session as a pse file. How can I save a script that > produced that pse file. It may be easier just to get information about > each object in that pse file. > > Maia > > > ----------------------------------------------------------------------- > ------- > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Tsjerk W. <ts...@gm...> - 2011-03-13 10:36:19
|
Hi, Well, a .pse file indeed is a kind of dump. But it does contain the information, of which most can be extracted. To begin with, it is quite trivial to get a listing of the settings (get) and of the view (get_view). It is also possible to obtain the color per atom, for which code is somewhere in the archives and maybe on the wiki. The real problem is the representation. All in all, it is a bit cumbersome. So before attempting to script something... how necessary is it? What's the underlying problem to be solved? Cheers, Tsjerk On Mar 13, 2011 11:04 AM, "Schubert, Carsten [PRDUS]" <CSC...@it...> wrote: Maia, as far as I know a .pse is just a dump of the internal data structure of Pymol. You can save the molecules contained in the session, but the graphical representation and any modifications would need to be recreated. Hopefully Jason proves me wrong ... Cheers, Carsten > -----Original Message----- > From: Maia Cherney [mailto:ch...@ua...] > Sent: Sunday, March ... |
From: Maia C. <ch...@ua...> - 2011-03-13 16:35:11
|
Hi, My major problem is hydrogen bonds (hb). Under each hb1, or hb2, .. hb10 there are many hbs, (not just one individual hb). I want a list of them for each hb. Now how can I use "get " to see all hbs in hb1, etc? I need to make a table of all hydrogen bonds for this pse. Maia Tsjerk Wassenaar wrote: > > Hi, > > Well, a .pse file indeed is a kind of dump. But it does contain the > information, of which most can be extracted. To begin with, it is > quite trivial to get a listing of the settings (get) and of the view > (get_view). It is also possible to obtain the color per atom, for > which code is somewhere in the archives and maybe on the wiki. The > real problem is the representation. All in all, it is a bit > cumbersome. So before attempting to script something... how necessary > is it? What's the underlying problem to be solved? > > Cheers, > > Tsjerk > >> On Mar 13, 2011 11:04 AM, "Schubert, Carsten [PRDUS]" >> <CSC...@it... <mailto:CSC...@it...>> wrote: >> >> Maia, >> >> as far as I know a .pse is just a dump of the internal data structure of >> Pymol. You can save the molecules contained in the session, but the >> graphical representation and any modifications would need to be >> recreated. >> Hopefully Jason proves me wrong ... >> >> Cheers, >> >> Carsten >> >> > -----Original Message----- > From: Maia Cherney >> [mailto:ch...@ua... <mailto:ch...@ua...>] > Sent: Sunday, >> March ... >> |
From: Hongbo Z. <hon...@bi...> - 2011-03-09 15:52:35
|
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 > <yam...@ca...> 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<gil...@gm...>: >>> 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 >>> <hon...@bi...> 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 hon...@bi...: >>>>>> 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<hon...@bi...>: >>>>>>>> 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 (PyM...@li...) >>>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>>> >>>>>> -- >>>>>> 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 (PyM...@li...) >>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> 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 (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: http://www.mail-archive.com/pym...@li... >>>> >>>> -- >>>> 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 (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>> >>> ------------------------------------------------------------------------------ >>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> ------------------------------------------------------------------------------ >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > > -- 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 |
From: Keitaro Y. <yam...@ca...> - 2011-03-11 12:48:38
|
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 <hon...@bi...>: > 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 >> <yam...@ca...> 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<gil...@gm...>: >>>> 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 >>>> <hon...@bi...> 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 hon...@bi...: >>>>>>> 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<hon...@bi...>: >>>>>>>>> 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 (PyM...@li...) >>>>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>>>> >>>>>>> -- >>>>>>> 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 (PyM...@li...) >>>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> 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 (PyM...@li...) >>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>> >>>>> -- >>>>> 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 (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: http://www.mail-archive.com/pym...@li... >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>> >>> ------------------------------------------------------------------------------ >>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> >> > > -- > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |