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

[Donald Damian Raymond]

Hi Buster developers,

Thanks for the reply. I’ve done some more investigations and it appears to be a bug in coot. 

Since I’m working with multiple chains I tend to set “color by chain” in coot. This causes a bug where SSBONDS are not drawn.

Thanks again,
Donald



> On Oct 31, 2014, at 1:04 PM, vonrhein at globalphasing.com wrote:
> 
> 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)