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Problem analyzing project after replacement final_1.tbl #291

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?

Original project H2_2Ca_64_100.cing.
set x=H2_2Ca_64_100
set ranges=501-850
set stage=rT

1.cing --project $x --ipython --nosave
2.refine --project $x --name $stage --setup --overwrite --superpose $ranges
3.replace the final_1.tbl by the enclosed file.
4.refine --project $x --name $stage --superpose $ranges --psf
5.$x.cing/Refine/$stage/Jobs/generatePSF.csh
6.refine --project $x --name $stage --analyze --overwrite --ipython
7.refine --project $x --name $stage --refine

What is the expected output? What do you see instead?
I expect no errors. There were no errors mentioned in the first 6 steps in the 
terminal.

output:

     Refine version 0.95 (r941)

--------------------------------------------------------------------------------
------------------------------

Finished restoring project <Project H2_2Ca_64_100>
==> Reading configuration
refinePath:     /home/i/workspace/cing/python/Refine
xplor:          /home/i/workspace/xplor-nih-2.27/bin/xplor
parameterFiles: ['parallhdg5.3-merge.pro', 'parallhdg5.3.sol', 
'par_axis_aria.pro', 'ion.param']
topologyFiles:  ['topallhdg5.3-merge.pro', 'topallhdg5.3.sol', 
'top_axis_aria.pro', 'ion.top']
==> Read user parameters H2_2Ca_64_100.cing/Refine/rT/parameters.py

ERROR: path "H2_2Ca_64_100.cing/Refine/rT/Analyzed/refine1_000.pdb" does not 
exist

In addition, there are 19 analyzed_*.log files generated in the directory 
Refine/rT/Jobs. They can also be found in Users/karen/Public/Jobs.

Original issue reported on code.google.com by k.berntsen@student.science.ru.nl on 16 Mar 2011 at 3:44

Attachments:

GoogleCodeExporter commented 9 years ago 
The problem is after step 7 where you're trying to --refine. Weird because the 
error mentions that CING was looking for an already generated pdb file named 
refine... What errors are in the log, in other words, have far did CING/XPLOR 
get?

Original comment by jurge...@gmail.com on 16 Mar 2011 at 4:09

GoogleCodeExporter commented 9 years ago 
Found tab in input which -might- be the cause.

Original comment by jurge...@gmail.com on 22 Mar 2011 at 3:13

GoogleCodeExporter commented 9 years ago 
I got the same errors in the generate.log file, using spaces instead of tabs. 
So this must be something else.

Original comment by k.berntsen@student.science.ru.nl on 22 Mar 2011 at 4:13

GoogleCodeExporter commented 9 years ago 
Strange. Perhaps xplor-nih doesn't allow the ARIA format. To exclude this 
possibility try formatting like below from:

http://restraintsgrid.bmrb.wisc.edu/NRG/MRGridServlet?block_text_type=1-original
&db_username=wattos1&file_detail=1-original&format=ambi&mrblock_id=2864&program=
XPLOR%2FCNS&request_type=block&subtype=NOE&type=distance

ASSI {  671}
   (( segid "    " and resid 63   and name HD1 ))
   (( segid "    " and resid 63   and name HG2 ))
      2.300      .700      .700 peak   671 weight   .10000E+01 volume   .33643E+00 ppm1      1.615 ppm2      1.508
 OR {  671}
   (( segid "    " and resid 63   and name HD2 ))
   (( segid "    " and resid 63   and name HG2 ))

I'll check for more info.

Original comment by jurge...@gmail.com on 22 Mar 2011 at 6:44

GoogleCodeExporter commented 9 years ago 
Using NRG-CING's 1ieh project from:
http://nmr.cmbi.ru.nl/NRG-CING/data/ie/1ieh/1ieh.cing.tgz

and converting to xplor format:
cing -n 1ieh --ipython -v 9

CING 1> p.export2xplor()
==> Exported <DistanceRestraintList "distance_constraint_list" (keep,2241)> to 
"1ieh.cing/Export/Xplor/distance_constraint_list.tbl"

I get the below which I presume was tested but I'm not sure against xplor-nih 
or not.

jd:Stella/leu_janin/ head "1ieh.cing/Export/Xplor/distance_constraint_list.tbl"

assi (resid 92  and name HB*)       (resid 113 and name HG1*)         3.400     
1.600     0.000
  or (resid 111 and name HG2*)      (resid 113 and name HG1*)      
  or (resid 113 and name HG1*)      (resid 114 and name HG2*)      
assi (resid 68  and name HD*)       (resid 70  and name HA)           6.000     
4.100     0.000
  or (resid 68  and name HE*)       (resid 70  and name HA)        
  or (resid 68  and name HZ)        (resid 70  and name HA)        
  or (resid 70  and name HA)        (resid 82  and name HE21)      
assi (resid 49  and name HG)        (resid 51  and name HN)           6.000     
4.500     0.000
  or (resid 51  and name HN)        (resid 60  and name HD*)

Original comment by jurge...@gmail.com on 23 Mar 2011 at 7:48

Attachments:

GoogleCodeExporter commented 9 years ago 
finally I find confirmation this syntax should work in xplor-nih

http://nmr.cit.nih.gov/xplor-nih/xplorMan/node377.html

in the assign paragraph. Check your syntax.

Original comment by jurge...@gmail.com on 23 Mar 2011 at 7:51

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
I tried to put the or's on the next line. I still got errors in the 
generatePSF.log file about the dihedrals. in the analyze.log files the original 
error disappeared, but I got other errors instead.

X-PLOR>{*=======================================================================
===*} 
 X-PLOR>{*========================= READ THE EXPERIMENTAL DATA =====================*} 
 X-PLOR>{*==========================================================================*} 
 X-PLOR>set message off echo off end 
 NOE: allocating space for   30000 restraints.
 %NOESET-ERR: error in selection - no atoms spec.
 %NOE-ERR: problem at  2669  -999.000  -999.000  -999.000  -999.000
 %NOESET-ERR: error in selection - no atoms spec.
 %NOE-ERR: problem at  2670  -999.000  -999.000  -999.000  -999.000
 %NOESET-ERR: error in selection - no atoms spec.
 %NOE-ERR: problem at  2671  -999.000  -999.000  -999.000  -999.000
 %NOESET-ERR: error in selection - no atoms spec.
 %NOE-ERR: problem at  2672  -999.000  -999.000  -999.000  -999.000
 %NOESET-ERR: error in selection - no atoms spec.
 %NOE-ERR: problem at  2673  -999.000  -999.000  -999.000  -999.000
 %NOESET-ERR: error in selection - no atoms spec.
 %NOE-ERR: problem at  2674  -999.000  -999.000  -999.000  -999.000
 %NOESET-ERR: error in selection - no atoms spec.
 %NOE-ERR: problem at  2675  -999.000  -999.000  -999.000  -999.000
 %NOESET-ERR: error in selection - no atoms spec.
 %NOE-ERR: problem at  2676  -999.000  -999.000  -999.000  -999.000
 %CSTRAN: allocating space for   10000 assignments.
 %POWELL-ERR: all atoms fixed. No action
 %POWELL-ERR: all atoms fixed. No action

I try to go in and see what happens next.

Original comment by k.berntsen@student.science.ru.nl on 23 Mar 2011 at 9:03

GoogleCodeExporter commented 9 years ago 
After refinement this error can be found in the analyze_**.log and the 
refine_**.log. What does this error mean?

When I go on and do:
refine --project $x --name $stage --parse --best 10 --sort Enoe
refine --project $x --name $stage --import

the first action doesn't display any errors, when I run the second one, I get:

--------------------------------------------------------------------------------
------------------------------

     Refine version 0.95 (r941)

--------------------------------------------------------------------------------
------------------------------

Finished restoring project <Project H2_2Ca_64_100>
==> Reading configuration
refinePath:     /home/i/workspace/cing/python/Refine
xplor:          /home/i/workspace/xplor-nih-2.27/bin/xplor
parameterFiles: ['parallhdg5.3-merge.pro', 'parallhdg5.3.sol', 
'par_axis_aria.pro', 'ion.param']
topologyFiles:  ['topallhdg5.3-merge.pro', 'topallhdg5.3.sol', 
'top_axis_aria.pro', 'ion.top']
==> Read user parameters H2_2Ca_64_100.cing/Refine/rT/parameters.py

==> Restoring <Project H2_2Ca_64_100> ... 
==> Restoring whatif results
ERROR: runWhatif: no molecule defined
==> Restoring procheck results
ERROR: runProcheck: no molecule defined
ERROR: validateModels: no molecule defined
ERROR: checkForSaltbridges: no molecule defined
ERROR: Project.Summary: Strange, there was no molecule in this project
==> Generating Macros
ERROR: makeMolmolMacros: no molecule defined
ERROR: makeMolmolMacros: no molecule defined
ERROR: mkYasaraMacros: no molecule defined
WARNING: No molecule found in project in getSummaryFromProject
==> Importing coordinates from 
H2_2Ca_64_100.cing/Refine/rT/Refined/refine1_%03d.pdb, models [0, 1, 2, 3, 4, 
5, 6, 7, 8, 9]
Traceback (most recent call last):
  File "/home/i/workspace/cing/python/Refine/refine.py", line 615, in <module>
    mol = importFromRefine( config, parameters, project )
  File "/home/i/workspace/cing/python/Refine/refine.py", line 56, in importFromRefine
    project.molecule.initCoordinates()
AttributeError: 'NoneType' object has no attribute 'initCoordinates'

Is this the result of the previous error?

Original comment by k.berntsen@student.science.ru.nl on 23 Mar 2011 at 11:21

GoogleCodeExporter commented 9 years ago 
  File "/home/i/workspace/cing/python/Refine/refine.py", line 56, in importFromRefine
    project.molecule.initCoordinates()
AttributeError: 'NoneType' object has no attribute 'initCoordinates'

This means that project.molecule is a None object. In other words it, the 
molecule has not been initialized/read. A CING molecule is required before the 
coordinates of a PDB file can be added to it I think.

Original comment by jurge...@gmail.com on 23 Mar 2011 at 11:43

GoogleCodeExporter commented 9 years ago 
By repeating this measurements I don't get the error in comment 9 again. I 
haven't found the difference yet. The one in comment 8 is still there.

Original comment by k.berntsen@student.science.ru.nl on 29 Mar 2011 at 9:24

GoogleCodeExporter commented 9 years ago 
Let's fix this further offline.

Original comment by jurge...@gmail.com on 11 Apr 2011 at 12:20