Dear Martin,
On Fri, Mar 24, 2023 at 10:00:25AM +0000, Martin Moche wrote:
> Dear Clemens and colleagues,
>
> I spot the issue in COOT logfile - see COOT-BUSTER-issue-captured.PNG -
> however why does COOT connect Cys31 with Cys223?
The Coot log with BUSTER PDB (1 SSBOND record per chain in standard
PDB format) says:
Made 2 CHO-SS-and-other bond restraints
Made 4 CHO-SS-and-other angle restraints
while the REFMAC PDB file (1 SSBOND record per chain with truncated
format) has
Made 1 CHO-SS-and-other bond restraints
Made 2 CHO-SS-and-other angle restraints
So somewhere Coot seems to decide to add another SS bond restraint
(and additional angles) - even if the SSBOND record information is
identical between the two programs.
Is the difference in SSBOND record (BUSTER contains the full symmetry
and distance information) triggering a different path/logic in Coot
compared to REFMAC? But a difference that only hits your particular
model due to something else (occupancy? alt confs?).
Cheers
Clemens
>
> The disulphide is between Cys31 and Cys52 as indicated correctly in the
> right-hand side COOT logfile using Refmac PDB
>
> I share the headers of the buster PDB (buster6_header.pdb) and refmac
> (cutc-x31-1-header.pdb)
>
> Cheers,
> Martin
>
> Head of Macromolecular X-ray Crystallography | Protein Science Facility
> Medical Biochemistry and Biophysics
> 171 65 Solna | Solnavägen 9
> +46 8 524 868 43 | +46 73 322 93 27
> martin.mo...@ki.se | ki.se
> ______________________________________
> Karolinska Institutet – a medical university
>
> -----Original Message-----
> From: Clemens Vonrhein <vonrh...@globalphasing.com>
> Sent: den 24 mars 2023 10:26
> To: Martin Moche <martin.mo...@ki.se>
> Cc: COOT@jiscmail.ac.uk
> Subject: Re: Disulphide sphere refinement fails in COOT when PDB file comes
> from BUSTER?
>
> Dear all,
>
> just to avoid confusion: BUSTER version numbering is maybe a bit unusual and
> differs between academic and commercial users (for various historic reasons).
> The most relevant version information is the release data, ie 20230217
> currently [1].
>
> Another short note: we also don't see that sphere refinement issue for
> typical PDB entries (with standard SSBOND records) from BUSTER.
>
> Cheers
>
> Clemens
>
> [1]
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