show sticks, (cys/ca+cb+sg) and byres (cys/sg and bound_to cys/sg)
the above command provides better quality to draw a SS bond by pyMOL, in the past, pyMOL users can only use “dist” command to make dash lines first, and changed the intervals of dash lines as “zero” to make a fake stick lines.
NOW, pyMOL users can use the new command to generate a very nice SS bond in stick.
Enjoy pyMOL ^_^
My software notes 
Thanks a bunch!%
Comment by Tim — July 1, 2007 @ 12:06 pm |
Hi, As you seems to be quite good in pymol modelling, I would like to ask to make a special bond in pymol. Actually in my protein I have a real covalent bond between an Asn and a Lys.. Obviously, Pymol doesn’t know how to draw it. Can you help me ?
Thanks.
thierry
Comment by Thierry — March 31, 2009 @ 7:30 am |
Hi,
I think I will just use the way I drew disulfide bond at here. You can try to dig pymol mailing list or pymolwiki.org, there should be some solutions for you. E.g. define covalent bond by users. I haven’t played real cases for years, just learn pymol for fun.
Comment by kpwu — March 31, 2009 @ 7:41 am |
Even better addition to only recolour the sidechains but leave the backbone the same colour:
show sticks, (cys/ca+cb+sg) and byres (cys/sg and bound_to cys/sg)
set stick_radius, 0.15
select disulphides, resn cys&sc.
colour yellow, disulphides
Comment by Thomas — May 1, 2018 @ 12:10 am |
Thank you for some other informative blog. The place else may I am getting that kind of info
written in such a perfect manner? I have a venture that I am just now working on, and I have been on the look out for such info.
Comment by hypnosis — January 2, 2020 @ 9:10 am |