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
