Re: [PyMOL] Dashed/Dotted Lines for Ribbon Representation
I see. It would be nice to have the cartoon_flat_sheets effect on the loop and tube variants, too. I like the looks of it. Maybe in a future version :-) Thanks, Yang On Thu, Apr 19, 2018 at 4:30 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Yang, > > That's an interesting observation, I wasn't aware that cartoon dash and > loop may be traced differently. Apparently the "cartoon_flat_sheets" > setting only applies to dash, not loop. Turning it off will make them > follow the same path: > > set cartoon_flat_sheets, 0 > > Cheers, > Thomas > > > On Apr 19, 2018, at 4:15 PM, Yang Su wrote: > > > > Also, 'cartoon dash' and 'cartoon loop' render beta-strands differently, > so I can't combine the two and get a consistent look and feel. The use case > is to show regions of the structure as dashed line to indicate 'not covered > in study'. I can't use different colors for this purpose because color > coding is already used to represent other properties. > > > > Best, > > Yang > > > > On Thu, Apr 19, 2018 at 3:56 PM, Yang Su wrote: > > Thanks for the tip, Thomas. 'cartoon dash' works with cartoon > representation, but doesn't seem to affect the ribbon representation. For > some use cases I like the 'cornered' ribbon representation better than the > smooth cartoon representation, but cartoon is still a good alternative if > it is not possible to show ribbon as dashed/dotted lines. > > > > Thanks, > > Yang > > > > > > On Thu, Apr 19, 2018 at 1:54 PM, Thomas Holder < > thomas.hol...@schrodinger.com> wrote: > > Hi Yang, > > > > Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.: > > > > fetch 1ubq, async=0 > > as cartoon > > cartoon dash > > > > See also: > > https://pymolwiki.org/index.php/Cartoon#USAGE > > > > Cheers, > > Thomas > > > > > On Apr 19, 2018, at 12:54 PM, Yang Su wrote: > > > > > > Hi, > > > > > > Is there an option to show the ribbon as dashed or dotted lines in > pymol? > > > > > > Thanks, > > > > > > Yang > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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
Re: [PyMOL] Dashed/Dotted Lines for Ribbon Representation
Hi Yang, That's an interesting observation, I wasn't aware that cartoon dash and loop may be traced differently. Apparently the "cartoon_flat_sheets" setting only applies to dash, not loop. Turning it off will make them follow the same path: set cartoon_flat_sheets, 0 Cheers, Thomas > On Apr 19, 2018, at 4:15 PM, Yang Su wrote: > > Also, 'cartoon dash' and 'cartoon loop' render beta-strands differently, so I > can't combine the two and get a consistent look and feel. The use case is to > show regions of the structure as dashed line to indicate 'not covered in > study'. I can't use different colors for this purpose because color coding is > already used to represent other properties. > > Best, > Yang > > On Thu, Apr 19, 2018 at 3:56 PM, Yang Su wrote: > Thanks for the tip, Thomas. 'cartoon dash' works with cartoon representation, > but doesn't seem to affect the ribbon representation. For some use cases I > like the 'cornered' ribbon representation better than the smooth cartoon > representation, but cartoon is still a good alternative if it is not possible > to show ribbon as dashed/dotted lines. > > Thanks, > Yang > > > On Thu, Apr 19, 2018 at 1:54 PM, Thomas Holder > wrote: > Hi Yang, > > Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.: > > fetch 1ubq, async=0 > as cartoon > cartoon dash > > See also: > https://pymolwiki.org/index.php/Cartoon#USAGE > > Cheers, > Thomas > > > On Apr 19, 2018, at 12:54 PM, Yang Su wrote: > > > > Hi, > > > > Is there an option to show the ribbon as dashed or dotted lines in pymol? > > > > Thanks, > > > > Yang -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ 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
Re: [PyMOL] Dashed/Dotted Lines for Ribbon Representation
Also, 'cartoon dash' and 'cartoon loop' render beta-strands differently, so I can't combine the two and get a consistent look and feel. The use case is to show regions of the structure as dashed line to indicate 'not covered in study'. I can't use different colors for this purpose because color coding is already used to represent other properties. Best, Yang On Thu, Apr 19, 2018 at 3:56 PM, Yang Su wrote: > Thanks for the tip, Thomas. 'cartoon dash' works with cartoon > representation, but doesn't seem to affect the ribbon representation. For > some use cases I like the 'cornered' ribbon representation better than the > smooth cartoon representation, but cartoon is still a good alternative if > it is not possible to show ribbon as dashed/dotted lines. > > Thanks, > Yang > > > On Thu, Apr 19, 2018 at 1:54 PM, Thomas Holder < > thomas.hol...@schrodinger.com> wrote: > >> Hi Yang, >> >> Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.: >> >> fetch 1ubq, async=0 >> as cartoon >> cartoon dash >> >> See also: >> https://pymolwiki.org/index.php/Cartoon#USAGE >> >> Cheers, >> Thomas >> >> > On Apr 19, 2018, at 12:54 PM, Yang Su wrote: >> > >> > Hi, >> > >> > Is there an option to show the ribbon as dashed or dotted lines in >> pymol? >> > >> > Thanks, >> > >> > Yang >> >> -- >> Thomas Holder >> PyMOL Principal Developer >> Schrödinger, Inc. >> >> > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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
Re: [PyMOL] Dashed/Dotted Lines for Ribbon Representation
Thanks for the tip, Thomas. 'cartoon dash' works with cartoon representation, but doesn't seem to affect the ribbon representation. For some use cases I like the 'cornered' ribbon representation better than the smooth cartoon representation, but cartoon is still a good alternative if it is not possible to show ribbon as dashed/dotted lines. Thanks, Yang On Thu, Apr 19, 2018 at 1:54 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Yang, > > Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.: > > fetch 1ubq, async=0 > as cartoon > cartoon dash > > See also: > https://pymolwiki.org/index.php/Cartoon#USAGE > > Cheers, > Thomas > > > On Apr 19, 2018, at 12:54 PM, Yang Su wrote: > > > > Hi, > > > > Is there an option to show the ribbon as dashed or dotted lines in pymol? > > > > Thanks, > > > > Yang > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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
[PyMOL] Multiple PyMOL Instances in Python Script
Hi, Is it possible to start multiple independent pymol backend processes in a python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol' and call a pymol.cmd function to start a backend process, but this is kind of 'global'. I'm looking for a way to manage multiple PyMOL sessions in parallel, each manipulating its own structures. Thanks, Yang -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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
Re: [PyMOL] Dashed/Dotted Lines for Ribbon Representation
Hi Yang, Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.: fetch 1ubq, async=0 as cartoon cartoon dash See also: https://pymolwiki.org/index.php/Cartoon#USAGE Cheers, Thomas > On Apr 19, 2018, at 12:54 PM, Yang Su wrote: > > Hi, > > Is there an option to show the ribbon as dashed or dotted lines in pymol? > > Thanks, > > Yang -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ 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
[PyMOL] Dashed/Dotted Lines for Ribbon Representation
Hi, Is there an option to show the ribbon as dashed or dotted lines in pymol? Thanks, Yang -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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
[PyMOL] interior color always white
Hi, I have found that with this settings the rendering keeps always white the interior color. fetch 1c0k, async=0 as spheres, clip near , -50 set ray_interior_color, pink set direct,off set spec_direct,1 set light_count, 1 ray If you change the light_count to 2 or try to shut down spec_direct, the problem disappears. Is this normal? -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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