Dear CCP4 users,
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 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.
So, is my syntax correct ?
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 dictionnaire… is that correct ?
Any clues will be more than welcome !
Have a nice day,
Laurent
Laurent Maveyraud
Prof. University of Toulouse
www.ipbs.fr | cribligand.ipbs.fr
IPBS-Toulouse | CNRS-Université Toulouse III-Paul Sabatier
205 Route de Narbonne, BP 64182, 31077 Toulouse Cedex 4
+33 5 61 17 54 35 | +33 6 46 04 21 11
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
