Re: [ccp4bb] problems with molprobity in coot

2010-04-10 Thread Thomas Cleveland
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 P

Re: [ccp4bb] problems with molprobity in coot

2009-10-12 Thread Paul Emsley
Thomas Cleveland wrote: I just looked at the source code for "reduce." It seems there is a global variable that gets returned from main(), ReturnCodeGlobal, which is set to 0 by default. However, further down in the code is this (in the "processPDBfile" function): // adjust cliques s

Re: [ccp4bb] problems with molprobity in coot

2009-10-12 Thread Thomas Cleveland
Paul, I just looked at the source code for "reduce." It seems there is a global variable that gets returned from main(), ReturnCodeGlobal, which is set to 0 by default. However, further down in the code is this (in the "processPDBfile" function): // adjust cliques std::list< std::list

Re: [ccp4bb] problems with molprobity in coot

2009-10-12 Thread Thomas Cleveland
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

[ccp4bb] problems with molprobity in coot

2009-10-11 Thread Thomas Cleveland
Hi everyone, 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 . From the logs, it seems like reduce runs OK (it says that it "Added 6076 hy