Rongjin, It does look like you have the same problem I did. I was never totally able to figure it out completely. First of all, it was only a problem with some PDB files and not others. Modifying generic_objects.py (i.e., change the line "if (reduce_status):" to "if (True):" ) as suggested by Paul Emsley and Bernhard Lohkamp did seem to fix the problem for some PDB files, but for others, I would then encounter a second error that I couldn't get past. I don't remember the details of the second error, and I'm not on that computer, so I can't get any more details right now. I think that ultimately I reprocessed my data (for an unrelated reason) and the problem went away, but it was a few months ago and I can't remember all the details.
Sorry I could not be of more help! -Tom On Wed, Apr 7, 2010 at 11:06 PM, Rongjin Guan <rjg...@gmail.com> wrote: > Hi Thomas > > I have a similar problem and wonder if you can help. > > 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 works perfectly but for another two, 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) > > I saw you had this message before; did you figure out what happened? > > Thanks > > Rongjin Guan > > > = = = = = = = = On 2009-10-12 12:37:34 You wrote = = = = = = = = > > Bernhard, > I have tried this using several versions of coot. I tried it first in > the coot that came packaged with ccp4 (Coot 0.5.2). I then tried > WinCoot-0.6-pre-1-revision-2411, which is one of the later revisions > of 0.6-pre, just to see if a more recent version would work. As far > as I can tell, I am using the correct versions of probe and reduce. > I am attaching a file with the relevant portion of the output > (starting with when I run "probe clashes," up until it fails). > Thanks for your help! > -Tom > On Mon, Oct 12, 2009 at 3:21 AM, Bernhard C. Lohkamp > <bernh...@chem.gl.ac.uk> wrote: > > > > Thomas, > > > >> I am trying to use molprobity to check a structure in coot (platform is > >> 64-bit vista). I followed the instructions found here to set up > >> molprobity: > >> http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-faq.html<http://www.ysbl.york.ac.uk/%7Elohkamp/coot/wincoot-faq.html> > . From the > >> logs, > >> it seems like reduce runs OK (it says that it "Added 6076 hydrogens"). > > >> However, at the very end, I get the message "BL WARNING:: reduce didnt run > >> ok, so stop here!" It seems like probe never runs. > >> > >> Does anyone know how to solve this? > >> > > > > Maybe you can give me some more information. Which version of WinCoot are > > > you running and which versions of probe and reduce are you using? Make sure > > you use the right version of probe (2.12.something) and reduce > > > (3.13.something). Note to self: update the website with respect to versions. > > If have the 'right' versions please sent me the console output. Hopefully > > that will give more information. > > > > B > > > > > >
