Dear Jeorge,
It is worthwhile keeping the discussion on the ccp4bb, as others may
contribute and find a solution much better than the two of us alone.
(0,0,0) is also a valid coordinate, and since the position of the molecule in
the mmCIF file is arbitrary, I guess one atom is placed to the origin.
I guess the coordinates are anyhow not used by the refinement program. The
'bond' and 'angle' table is much more interesting: is the particular atom and
its binding partner(s) listed, and is it listed correctly?
Best,
Tim
On Thursday, June 09, 2016 07:16:48 PM jeorgemarley thomas wrote:
> Dear Tim
> The x,y,z values for the this atom (which is lost after refinement) in the
> cif file is assigned as 0, 0, 0 but rest atoms have the coordinate values.
> Now what could be done in such case, should I manually assign the x,y,z
> value from the pdb to the cif file for this particular atom ?
> Please suggest
> Thanks
>
> On Thu, Jun 9, 2016 at 7:01 PM, Tim Gruene <[log in to unmask]> wrote:
> > Dear Jeorge,
> >
> > the refmac logfile should tell you which cif-file it reads in for
> > restraints.
> > Can you compare the atom names in that cif-file with the atom names in
> > your
> > PDB-file? My first guess is that the respective atom is named differently,
> > or
> > that maybe the bond is not specified at all.
> >
> > Best,
> > Tim
> >
> > On Thursday, June 09, 2016 06:30:37 PM jeorgemarley thomas wrote:
> > > Dear all,
> > > I have been encountered a problem when the ligand in the active site is
> > > fitted (it is a modified form of glutamate). After refinement with
> > > refmac
> > > the one of the oxygen atom bonded with carbon is always getting lost and
> >
> > no
> >
> > > coordinate is being available afterwards for this bond only, although
> > > cif
> > > file of the ligand is used during the refinement. I have used sketcher
> > > (ccp4) to get the cif file of the ligand. please suggest what can be
> >
> > done.
> >
> > > I tried phenix also to generate the cif from elbow but did not work.
> > > Thanks in advance
> > > Jeorge
> >
> > --
> > --
> > Paul Scherrer Institut
> > Dr. Tim Gruene
> > - persoenlich -
> > OFLC/102
> > CH-5232 Villigen PSI
> > phone: +41 (0)56 310 5297
> >
> > GPG Key ID = A46BEE1A
--
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
GPG Key ID = A46BEE1A
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