[ccp4bb] problems with molprobity in coot

[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 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?

Thanks,
Thomas Cleveland
(graduate student, Johns Hopkins University)

Re: [ccp4bb] problems with molprobity in coot

[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, 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
 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 .  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
>
>
write_pdb_file (0, "coot-molprobity/for-reduce.pdb")
BL INFO:: run reduce as  C:\WinCoot\bin\reduce.exe coot-molprobity/for-reduce.pd
b > coot-molprobity/reduced.pdb
reduce: version 3.13 04/28/2008, Copyright 1997-2008, J. Michael Word
Processing file: "coot-molprobity/for-reduce.pdb"
Database of HETATM connections: "reduce_het_dict.txt"
Processing only 'A' conformations.
VDW dot density = 16/A^2
Orientation penalty scale = 1 (100%)
Eliminate contacts within 3 bonds.
Ignore atoms with |occupancy| <= 0.01 during adjustments.
Waters ignored if B-Factor >= 40 or |occupancy| < 0.66
Aromatic rings in amino acids accept hydrogen bonds.
Building His ring NH Hydrogens.
Flipping Asn, Gln and His groups.
For each flip state, bumps where gap is more than 0.4A are indicated with '!'.
Building or keeping OH & SH Hydrogens.
Rotating existing OH & SH Hydrogens
Rotating NH3 Hydrogens.
Processing Met methyls.
ERROR CTab(reduce_het_dict.txt): could not open
 Singles(size 270): A  25 THR OG1 : A  33 SER OG  : A  35 HIS : A  46 SER OG

  : A  53 GLN : A  60 TYR OH  : A  64 TYR OH  : A  68 SER OG  : A  70 HIS

  : A  72 GLN : A  73 THR OG1 : A  75 LYS NZ  : A  78 TYR OH  : A  79 LYS NZ

  : A  80 GLN : A  83 TYR OH  : A  84 THR OG1 : A  91 SER OG  : A  92 SER OG

  : A  93 HIS : A  94 TYR OH  : A  97 THR OG1 : A  99 LYS NZ  : A 102 ASN

  : A 103 ASN : A 111 TYR OH  : A 113 SER OG  : A 116 THR OG1 : A 119 HIS

  : A 120 THR OG1 : B  25 THR OG1 : B  33 SER OG  : B  35 HIS : B  46 SER OG

  : B  53 GLN : B  60 TYR OH  : B  64 TYR OH  : B  68 SER OG  : B  70 HIS

  : B  72 GLN : B  73 THR OG1 : B  75 LYS NZ  : B  78 TYR OH  : B  79 LYS NZ

  : B  83 TYR OH  : B  84 THR OG1 : B  91 SER OG  : B  92 SER OG  : B  93 HIS

  : B  94 TYR OH  : B  97 THR OG1 : B  99 LYS NZ  : B 102 ASN : B 103 ASN

  : B 111 TYR OH  : B 113 SER OG  : B 116 THR OG1 : B 119 HIS : B 120 THR OG
1
  : C  19 SER OG  : C  23 GLN : C  24 ASN : C  31 ASN : C  32 SER OG

  : C  33 LYS NZ  : C  34 SER OG  : C  36 MET CE  : C  38 HIS : C  40 GLN

  : C  46 THR OG1 : C  47 GLN : C  48 ASN : C  50 GLN : C  52 THR OG
1
  : C  54 TYR OH  : C  55 LYS NZ  : C  58 TYR OH  : C  60 LYS NZ  : C  62 SER OG

  : C  64 LYS NZ  : C  65 SER OG  : C  68 THR OG1 : C  70 THR OG1 : C  73 SER OG

  : C  75 THR OG1 : C  76 GLN : C  78 SER OG  : C  79 GLN : C  88 THR OG
1
  : C  90 TYR OH  : C  91 ASN : C 102 THR OG1 : C 106 THR OG1 : C 110 SER OG

  : C 113 THR OG1 : C 116 SER OG  : D  19 SER OG  : D  23 GLN : D  24 ASN

  : D  26 SER OG  : D  31 ASN : D  32 SER OG  : D  33 LYS NZ  : D  34 SER OG

  : D  36 MET CE  : D  38 HIS : D  40 GLN : D  46 THR OG1 : D  47 GLN

  : D  48 ASN : D  50 GLN : D  52 THR OG1 : D  54 TYR OH  : D  55 LYS NZ

  : D  58 TYR OH  : D  60 LYS NZ  : D  62 SER OG  : D  64 LYS NZ  : D  65 SER OG

  : D  68 THR OG1 : D  70 THR OG1 : D  73 SER OG  : D  75 THR OG1 : D  76 GLN

  : D  78 SER OG  : D  79 GLN : D  88 THR OG1 : D  90 TYR OH  : D  91 ASN

  : D 102 THR OG1 : D 106 THR OG1 : D 110 SER OG  : D 113 THR OG1 : D 116 SER OG

  : E  19 SER OG  : E  23 GLN : E  24 ASN : E  31 ASN : E  32 SER OG

  : E  33 LYS NZ  : E  34 SER OG  : E  36 MET CE  : E  38 HIS : E  40 GLN

  : E  46 THR OG1 : E  47 GLN : E  48 ASN : E  50 GLN : E  52 THR OG
1
  : E  54 TYR OH  : E  55 LYS NZ  : E  58 TYR OH  : E  60 LYS NZ  : E  62 SER OG

  : E  64 LYS NZ  : E  65 SER OG  : E 

Re: [ccp4bb] problems with molprobity in coot

[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 > cc_list = clst.cliques();
//cerr << "start: " << cc_list.size() << endl;
 for (std::list< std::list >::iterator cc =
cc_list.begin(); cc != cc_list.end(); ++cc) {
//cerr << "start2" << endl;
int nscnt = xyz.orientClique(*cc, ExhaustiveLimit);
if (nscnt > 0) { Tally._num_adj += nscnt; }
else { // too many permutations, make note
  ReturnCodeGlobal = ABANDONED_RC;
}
 }

Where ABANDONED_RC is elsewhere defined as 1.

This is the only obvious place in the "reduce" code I can find where
ReturnCodeGlobal is set to something other than 0.  I'm not sure what
they mean (in the comment) by "too many permutations," though.  Do you
think this is a fatal error that calls for not running "probe"?
Otherwise, I might try to just work around this by modifying the Coot
source to ignore the return value of "reduce."

Thanks again,
Tom

On Mon, Oct 12, 2009 at 1:54 PM, Paul Emsley  wrote:
> Thomas Cleveland 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).
>>
>
> OK, so that's some meat to chew on...
> Interesting things AFAICS:
>
> BL WARNING:: reduce didnt run ok, so stop here!
>
>
> It is convention in the Unix world that a program that runs without errors
> exits with a status of 0.  This is not happening when you run reduce from
> within WinCoot - it is not clear to me why that is. I raise a doubt over
> your installation of reduce.  Or it might be that reduce exits with a random
> status in Windows and you are unlucky.
>
> Regards,
>
> Paul.
>
>

Re: [ccp4bb] problems with molprobity in coot

[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

 std::list< std::list > cc_list = clst.cliques();
//cerr << "start: " << cc_list.size() << endl;
 for (std::list< std::list >::iterator cc =
cc_list.begin(); cc != cc_list.end(); ++cc) {
//cerr << "start2" << endl;
int nscnt = xyz.orientClique(*cc, ExhaustiveLimit);
if (nscnt > 0) { Tally._num_adj += nscnt; }
else { // too many permutations, make note
  ReturnCodeGlobal = ABANDONED_RC;
}
 }

Where ABANDONED_RC is elsewhere defined as 1.

This is the only obvious place in the "reduce" code I can find where
ReturnCodeGlobal is set to something other than 0.  I'm not sure what
they mean (in the comment) by "too many permutations," though.  Do you
think this is a fatal error that calls for not running "probe"?
  


It seems unlikely, but I can't think what else it could be.



Otherwise, I might try to just work around this by modifying the Coot
source to ignore the return value of "reduce."
  


OK, xxx/share/coot/python/generic_objects.py: lines 202:

if (reduce_status):

to

if (True):

I guess should do it.

Paul.

Re: [ccp4bb] problems with molprobity in coot

[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 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  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
>  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
>  .  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
> >
> >
>
>