[buster-discuss] Disulphide sphere refinement fails in COOT after BUSTER?

[Clemens Vonrhein]

Dear Martin,

On Thu, Mar 23, 2023 at 01:48:02PM +0000, Martin Moche wrote:
> After running my pdb-files in BUSTER I cannot use "R" for sphere
> refinement anymore in COOT?

That is odd: we haven't seen anything like that before.
 
> In PDB files that never seen BUSTER, sphere refinement in COOT work
> fine - see PDF attached

Even weirder: a PDB file is after all a defined format no matter what
program wrote it, right?

Just ran a "R" (sphere refinement, same Coot version as you used) and
I don't see any problems here: see attached screenshots. Nothing
explodes or breaks bonds here.

Are you on MacOS, Windows or Linux? Are you using Coot from CCP4
(8.0.008)? Maybe anything in your personal Coot settings/preferences
that could interfere?

> I noticed
>
> - BUSTER writes the order of atoms of each residue differently as
>   compared to my "original" PDB file used for refmac

That shouldn't matter at all (some programs write first all main-chain
then all side-chain atoms, some write N-terminal, then side-chain,
then C-terminal atoms).

> - SSBOND looks different in refmac compared to BUSTER, but changing
>   the BUSTER PDB with SSBOND lines as written in refmac does not
>   matter to COOT that still fail sphere refinement next to
>   disuphides.

SSBOND is also a defined format [1] and should look like this:

  SSBOND   1 CYS A  152    CYS A  181                          1555   1555  2.05

How does the Refmac lines differ? The only difference should be the
exact distance value (last item).

Is there anything else "interesting" close to those SSBONDs:
modified/non-standard amino-acids, metals, co-factors etc that could
interfere in some way and confuse Coot?

> Neither BUSTER PDB nor refmac PDB contain LINK/LINKR records.

BUSTER will never write LINKR records anyway, since these are
non-standard PDB.

> Thanks for outstanding BUSTER software!

And if we get your refinement results to work with your Coot setup it
would be even better ;-)

Cheers

Clemens

[1] http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
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