Re: [PyMOL] set transparency for selected elements of secondary structure
Hi James and Ali, Are you using PyMOL 2.3 yet? "As of PyMOL version 2.3, cartoon transparency is now an atom-level setting." https://pymolwiki.org/index.php/Cartoon_transparency Cheers, Thomas > On Jun 26, 2019, at 10:26 AM, Ali Kusay wrote: > > Hi James, > > I am not sure what the exact cause of your issue is but I think if you make a > selection first then apply the transparency to the selection that should > work, i.e.: > > sele ss H+S > set cartoon_transparency, 0.5, sele > > Something to do with selection based transparency settings not enabling newer > ones to be made > > Cheers, > > Ali > > On 26/6/19, 6:18 pm, "James Starlight" wrote: > >Dear pymol users! > >I am trying to set transparency based on the secondary structure using >pymol selection algebra > ># set transparency to all helix and sheets but not loops >set cartoon_transparency, 0.5, ss H+S > >which produce the following output >PyMOL>set cartoon_transparency, 0.5, ss H+S > Setting: cartoon_transparency set for 144 atoms in object > "0190_before_minim". > >but actually do nothing in terms of visualization. > >Could you suggest me how it would be possible to fix it? > >Thanks in advance! > > >___ >PyMOL-users mailing list >Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] set transparency for selected elements of secondary structure
Hi James, I am not sure what the exact cause of your issue is but I think if you make a selection first then apply the transparency to the selection that should work, i.e.: sele ss H+S set cartoon_transparency, 0.5, sele Something to do with selection based transparency settings not enabling newer ones to be made Cheers, Ali On 26/6/19, 6:18 pm, "James Starlight" wrote: Dear pymol users! I am trying to set transparency based on the secondary structure using pymol selection algebra # set transparency to all helix and sheets but not loops set cartoon_transparency, 0.5, ss H+S which produce the following output PyMOL>set cartoon_transparency, 0.5, ss H+S Setting: cartoon_transparency set for 144 atoms in object "0190_before_minim". but actually do nothing in terms of visualization. Could you suggest me how it would be possible to fix it? Thanks in advance! ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] set transparency for selected elements of secondary structure
Dear pymol users! I am trying to set transparency based on the secondary structure using pymol selection algebra # set transparency to all helix and sheets but not loops set cartoon_transparency, 0.5, ss H+S which produce the following output PyMOL>set cartoon_transparency, 0.5, ss H+S Setting: cartoon_transparency set for 144 atoms in object "0190_before_minim". but actually do nothing in terms of visualization. Could you suggest me how it would be possible to fix it? Thanks in advance! ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
