On 15/01/2019 20:49, Markus Heckmann wrote:
I have a structure where CYS is bound to OCA (octanoic acid). I
started with Jligand and created a CYS-OCA covalent link. It then
output a CIF file (verified looks OK). Add the LINK record to PDB
file:
LINK SG CYS A 161 C1 OCA A 902 CYS-OCA
Place OCA to the model using Coot. When I now use RealSpaceRefinement,
the OCA is placed on top of CYS itself. Coot does not recognise that
OCA-CYS link but why? therefore, I just place OCA at Place it in
*reasonable* position without any overlaps.
All files are located at
https://gist.github.com/ort163/e6b8411f45e5224f7d46fc36c3324e6f
Not all of them.
I tried to reproduce the problem and your dictionary worked OK for me. You will
need to make sure that the ligand is in the same chain as the protein to which
you
wish to link it (I see from above that that is the case here).
Now in REFMAC, input MTZ,PDB and the CIF file (from jligand). After
refinement, I find that the oxygen in the OCA is pointing wrongly. The
thioester bond is also NOT ideal distance (though density is good).
For me, refining to the wrong map (of course) the resulting bond length is 1.63
A.
Maybe if I had your files then I would see what you see.
Is there anything wrong with my procedure? *Shouldnt* the refinement
optimise everything in OCA-CYS link?
Yes, it should.
This, by the way, is not how I make links these days. More recently an Acedrg
interface
has been added to Coot: Extensions -> Modules -> CCP4 -> Acedrg -> Make a Link
You'll need to delete the O2 of course.
Paul.
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