Dear Paul,
a promising way to fix the problem is the program pdbset (or pdbcur), both
available with ccp4.
You can place the molecule into a P1 cell large enough to hold all
coordinates, e.g. from the command line
pdbset XYZIN yourbroken.pdb XYZOUT yourfixed.pdb << eof
SPACEGROUP P1
CELL 25 25 25 90 90 90
END
eof
the cell is arbitrary, just make it sufficiently big.
Kindly,
Tim
On Friday 31 March 2017 09:11:17 AM Johannes Cramer wrote:
> Hi,
>
> I had the same problem once. Some chemistry programs are not really good at
> exporting to pdb. Check the file format definition of pdb files, here:
> ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf
> Most interesting for you is probably pp. 174.
> Also make sure, there is an "END" at the end.
> It might help, if you send a link to the ligand file.
>
> Cheers,
> Johannes
>
> 2017-03-30 19:41 GMT+02:00 Paul Emsley <[log in to unmask]>:
> > On 30/03/17 14:59, chemocev marker wrote:
> >> Hi
> >
> > Hi.
> >
> > I have model of ligand molecule and it does not open in coot. Its not a
> >
> >> crystal structure. I can view it in the pymol or chimera but not in the
> >> coot. It gives error that it does not have any space group information.
> >> Is
> >> there is a way to open it in coot.
> >
> > If there is not a CRYST1 card in your pdb file, then Coot will warn you
> > that your molecule does not have symmetry. It is merely a warning, not an
> > error.
> >
> > If coot can't read the pdb file it's likely (it seems to me) that it's not
> > actually a (specifications-compliant) pdb file. Coot should give you an
> > error about any line that it particularly doesn't like.
> >
> >
> > Paul.
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