[buster-discuss] Coot not displaying disulfide bonds after buster refinement

[vonrhein at globalphasing.com]

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)