Hello Rongjin Guan,
your problem most likely comes from different pdb version formats. The
files which work are probably pre pdb v. 3.0. Although (Win)Coot is
mainly v. 3 compliant here we are not (really (*)). A fix (at least for
the files which are not working) may be to change two lines (198/199) in
the file 'generic_objects.py' (in YOURWINCOOTDIRECTORY\share\coot\python)
Change from:
198: # ["-build", mol_pdb_file],
199: ["-build", "-oldpdb",
mol_pdb_file],
to
198: ["-build", mol_pdb_file],
199: # ["-build", "-oldpdb",
mol_pdb_file],
Hope this helps,
B
(*) note to self (and Paul) we probably should have this as an optional
parameter and/or ideally automatically detected which pdb version we are
using and adjust the probe parameters accordingly?!
Rongjin Guan wrote:
> Hello,
> I just installed Wincoot 0.6.1 and reduce/probe as well, and tested
> with several
> PDB files for probe/clash validation.
> For some PDBs it worked perfectly; but for my own model, it did not
> work and I have
> the following message:
> .............................
> Found 0 hydrogens (0 hets)
> Standardized 0 hydrogens (0 hets)
> Added 3946 hydrogens (0 hets)
> Removed 0 hydrogens (0 hets)
> Adjusted 113 group(s)
> If you publish work which uses reduce, please cite:
> Word, et. al. (1999) J. Mol. Biol. 285, 1735-1747.
> For more information see http://kinemage.biochem.duke.edu
> BL WARNING:: reduce didnt run ok, so stop here!
> run_generic_script (probe, 0)
> My model was outputed from phenix refinement and I checked the format
> and can not
> see anything wrong. Can anyone give me some hints?
> Thanks
> Rongjin Guan
>
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