On 08/07/2020 12:39, Laurent wrote:
I am currently refinining an enzyme structure obtained in the presence
of a substrate analog : the catalytic serine is acylated and form an
ester bond with the ligand. I have added a LINK record in the PDB file
to specify the newly created covalent bond between OG atom of Serine
and C1 atom of the ligand. I would also like to restraint the ester
linkage in a plane (atom OG of Ser623 and atoms O1, C1 and CA or
residue 901, both in chain A) I am trying to use the external
restraint keyword in refmac (the documentation clearly indicates the
syntax in case of a dihedral external restraint and only says that if
can also be used for planar restraint).
external planar first chain A residue 623 atom OG next chain A residue
901 atom CA next chain A residue 901 atom C1 next chain A residue 901
atom O1 value 0 sigma 10
In the refmac logfile there are no error messages, but this specific
command line is not echoed, although all other are. However, it seems
to be red [sic] and checked by refmac, as introducing a wrong keyword
(eternal instead of external) generated an error message. However, the
ester linkage is not planar in the refined PDB when viewed with coot.
While one can refine a model this way, it is not typically the way to do
so - we use a dictionary for the link rather than external restraints.
So, is my syntax correct ?
I notice that you don't include a specifier for the insertion code.
Maybe that's related. Coot should give you an error message if it fails
to parse the external planar restraints line. If you are using Coot to
do so, what does it say?
Should I keep the value keyword (as it is likely not used I the case
of a plane restraint) ?
Sigma is set to 10… As far as I understood, this means that this
specific plane restraint will be 10 times weaker than the normal plane
restraint defined in the standard dictionnairy… is that correct ?
I don't think so. 10 means 10A, not 10 rmsd. Such a restraint will
practically be ignored in the minimization.
Any clues will be more than welcome !
Have a look at my blog for how to add a link between a ligand and a
protein residue:
https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html
In your case, only the bottom part is relevant - where Coot interacts
with Acedrg.
Paul
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