My software notes

March 19, 2006

draw better disulfide bond

Filed under: pymol/ molmol — kpwu @ 5:45 am


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 ^_^



  1. Thanks a bunch!%

    Comment by Tim — July 1, 2007 @ 12:06 pm | Reply

  2. 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 ?

    Comment by Thierry — March 31, 2009 @ 7:30 am | Reply

  3. Hi,

    I think I will just use the way I drew disulfide bond at here. You can try to dig pymol mailing list or, 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 | Reply

  4. 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 | Reply

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