Validation error after coordinate replacement

[GoogleCodeExporter]

What steps will reproduce the problem?
Below is the code which causes a problem. I tried to replace the coordinates of 
my cing-project and validate it. I got an error when I tried the validation.

set x = H2_2Ca_64_100
cing --project $x --ipython
CING 1> m.initCoordinates()
CING 
2>m.importFromPDB('/home/i/tmp/karenVCdir/2fwu3models.pdb',convention='IUPAC')
CING 3> exit()
cing -n $x --validateFastest2.

What is the expected output? What do you see instead?
I expect a validation report. I got an IndexError

Please use labels and text to provide additional information.

Original issue reported on code.google.com by k.berntsen@student.science.ru.nl on 1 Mar 2011 at 10:40

Attachments:

• 2fwu3models.pdb

[GoogleCodeExporter]

[deleted comment]

[GoogleCodeExporter]

[deleted comment]

[GoogleCodeExporter]

[deleted comment]

[GoogleCodeExporter]

Looking at it now.

Original comment by jurge...@gmail.com on 1 Mar 2011 at 10:45

• Added labels: Type-Defect, Priority-High, Component-CING, Usability

[GoogleCodeExporter]

Does the original project before modifications validate? Use validateFastest 
for speed. Or iCing.

Original comment by jurge...@gmail.com on 1 Mar 2011 at 10:48

[GoogleCodeExporter]

Then the trouble seems to be:

jd:stella/~/workspace/ cing -n $x --validateFastest
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.95 (r934)       
AW,JFD,GWV 2004-2011 |
================================================================================
======================
User: jd         on: stella.cmbi.umcn.nl (darwin/64bit/2cores/2.6.6) at: 
(16213) Tue Mar  1 12:09:22 2011
==> Restoring <Project H2_2Ca_64_100> ... 
==> Restoring whatif results
CING started at : Tue Mar  1 12:09:18 2011
CING stopped at : Tue Mar  1 12:09:32 2011
CING took       : 14.096 s

Traceback (most recent call last):
  File "/Users/jd/workspace35/cing/python/cing/main.py", line 853, in <module>
    main()
  File "/Users/jd/workspace35/cing/python/cing/main.py", line 705, in main
    project = Project.open(options.name, status='create')
  File "/Users/jd/workspace35/cing/python/cing/core/classes.py", line 466, in open
    return Project.open(name, 'old', restore = restore)
  File "/Users/jd/workspace35/cing/python/cing/core/classes.py", line 587, in open
    pr.restore()
  File "/Users/jd/workspace35/cing/python/cing/core/classes.py", line 742, in restore
    f(self, o)
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Whatif.py", line 1223, in restoreWhatif
    project.runWhatif(parseOnly=True)
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Whatif.py", line 1135, in runWhatif
    if whatif._processWhatifSummary(pathPdbOut):
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Whatif.py", line 417, in _processWhatifSummary
    ensembleValueList[modelIdx] = value
IndexError: list assignment index out of range

Original comment by jurge...@gmail.com on 1 Mar 2011 at 11:09

[GoogleCodeExporter]

Work around:

Remove manually the following directories:
Dssp/
Macros/
Procheck/
Queeny/
Shiftx/
Wattos/
Whatif/
X3DNA/
talosPlus/

and not the others in H2_2Ca_64_100.cing/refine1

Fyi working with CING:

drl = p.distances[0]
dr = drl[0]
dr.distances 

# Get fourth Leu from molecule
r = m.residuesWithProperties('LEU')[3]
# Get list of distance restraints from this specific residue
drl = r.distanceRestraints

# Dive into the code for specific properties
E.g. loop over distance restraints;
CING 29> for dr in drl:
    print dr.violations

Original comment by jurge...@gmail.com on 1 Mar 2011 at 11:33

• Changed state: Started

[GoogleCodeExporter]

Karen, I assume that you're happy with. Feel free to change the status of such 
an issue to closed for next time.

Original comment by jurge...@gmail.com on 16 Mar 2011 at 5:12

• Changed state: Fixed