My software notes

March 19, 2006

draw better disulfide bond

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

1pjw-ss-bond.png

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 ^_^

About these ads

3 Comments »

  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 ?
    Thanks.
    thierry

    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 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 | Reply


RSS feed for comments on this post. TrackBack URI

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

The Rubric Theme. Create a free website or blog at WordPress.com.

Follow

Get every new post delivered to your Inbox.

Join 31 other followers

%d bloggers like this: