[buster-discuss] Coot not displaying disulfide bonds after buster refinement
vonrhein at globalphasing.com
vonrhein at globalphasing.com
Fri Oct 31 18:04:38 CET 2014
Dear Donald,
On Fri, Oct 31, 2014 at 10:59:12AM -0400, Donald Damian Raymond wrote:
> Hi all,
>
> I've been having this issues for some time now and cannot seem to
> figure it out. Whenever, I refine my structure in buster and
> visualize the result in COOT, the disulfide bonds are not
> displayed. However, if I refine the structure in refmac or phenix,
> the S--S show up just fine in COOT.
>
> Buster records for SSBOND below
>
> SSBOND 1 CYS A 43 CYS A 276 1555 1555 2.04
which follows the PDB format as described in
http://www.wwpdb.org/documentation/format33/sect6.html#SSBOND
and
http://www.wwpdb.org/documentation/format33/sect1.html#Field
Eg:
1 2 3 4 5 6 7
12345678901234567890123456789012345678901234567890123456789012345678901234567890
SSBOND 1 CYS A 43 CYS A 276 1555 1555 2.04
> SSBOND 2 CYS A 56 CYS A 68 1555 1555 2.03
> SSBOND 3 CYS A 91 CYS A 137 1555 1555 2.02
> SSBOND 4 CYS A 280 CYS A 304 1555 1555 2.04
[... snip ...]
> SSBOND 16 CYS L 135 CYS L 195 1555 1555 2.04
>
> Refmac records for SSBONDS below
>
> SSBOND 1 CYS A 43 CYS A 276
which doesn't exactly follow the documentated standard - although the
missing SymOP and Length fields might be ignored by Coot anyway.
> SSBOND 2 CYS A 56 CYS A 68
> SSBOND 3 CYS A 91 CYS A 137
> SSBOND 4 CYS A 137 CYS A 91
Why is the same SS-bond duplicated here? First as A91-A137 and then as
A137-A91?
> SSBOND 5 CYS A 276 CYS A 43
> SSBOND 6 CYS A 280 CYS A 304
[... snip ...]
> SSBOND 16 CYS D 135 CYS D 195
>
> Any help in this matter would be greatly appreciated.
Are you running the latest version of Coot? You might need to ask the
Coot developers for more details or help.
Cheers
Clemens, Claus & Gerard (for BUSTER developers)
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