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 <pems...@mrc-lmb.cam.ac.uk>: > > 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. -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/104 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A
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