Peptide entry fails to generate cv based residue selection

What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.95 (r918)       
AW,JFD,GWV 2004-2011 |
================================================================================
======================
User: jd         on: nmr.cmbi.umcn.nl (darwin/32bit/8cores/2.6.5) at: (87569) 
Tue Feb  1 02:51:15 2011
DEBUG: Using:
DEBUG: inputDir:             
file:///Library/WebServer/Documents/NRG-CING/input/l5
DEBUG: outputDir:            /Library/WebServer/Documents/NRG-CING/data/l5/2l56
DEBUG: pdbConvention:        .
DEBUG: restraintsConvention: .
DEBUG: archiveType:          BY_CH23
DEBUG: projectType:          CCPN
DEBUG: modelCount:           None
DEBUG: storeCING2db:         True
DEBUG: ranges:               cv
Enforcing a redo
copying file: //Library/WebServer/Documents/NRG-CING/input/l5/2l56.tgz to: 
2l56.tgz
Moving CCPN directory from [linkNmrStarData] to [2l56]
==> Importing data from Ccpn project "2l56"
DEBUG: Residue._nameResidue: residue "ACE" not defined in database by 
convention [INTERNAL_1]. Adding non-standard one now.
DEBUG: Residue._nameResidue: residue "NH2" not defined in database by 
convention [INTERNAL_1]. Adding non-standard one now.
Non-standard (residues and their) atoms added:
ACE : C    CH3  O    [ 15]
NH2 : HN1  HN2  N    [ 32]
==> Calculating rmsd's (ranges: 15-32, models: 0-9)
==> Ccpn molecule '2l56' imported
  Warning: could not create torsion information for General_control_protein_GCN4.2.PHI - no linking to prev residue.
  Warning: could not create torsion information for General_control_protein_GCN4.2.OMEGA - no linking to prev residue.
  Warning: could not create torsion information for General_control_protein_GCN4.2.OMEGA - no linking to prev residue.
  Warning: could not create torsion information for General_control_protein_GCN4.17.PSI - no linking to next residue.
==> Ccpn project imported
WARNING: No residues left in rangesByCv for ranges: [A.15-15,A.21-23,A.32-32] 
in rangesByCv after sub selecting for excludeFragmentSize
DEBUG: In residueList2Ranges empty residueList.
Ranges reset from: cv to .
-------------------------------------------------------
==> Saving <Project 2l56>
==> Saved <Molecule "2l56" (C:1,R:18,A:327,M:10)> to 
"2l56.cing/Data/Molecules/2l56"
==> Saving <DistanceRestraintList "distance_constraint_list" (keep,180)> to 
2l56.cing/Data/Restraints/distance_constraint_list.distances
==> Saving <DistanceRestraintList "hBond_constraint_list" (keep,16)> to 
2l56.cing/Data/Restraints/hBond_constraint_list.distances
==> Running shiftx
runShiftx: non-protein residues [<Residue A.ACE15>, <Residue A.NH232>] will be 
skipped.
==> Calculating Q-factors for chemical shift
==> Calculating secondary structure by DSSP
ERROR: Empty list of residues in Whatif
==> Running procheck_nmr
WARNING: In Molecule#ranges2StartStopList, no residues selected from ranges: .
ERROR: In pc failed to get startStopList for ranges: .
ERROR: Procheck.run: Failed to get rangesTxtPlugin for ranges: [.]
Running Wim Vranken's FormatConverter from script 
$CINGROOT/python/cing/Scripts/FC/convertCcpn2Nmrstar.py
==> NMR-STAR project written at 
/Volumes/tera4/NRG-CING/data/l5/2l56/2l56.cing/2l56/Wattos/project.str
==> Running Wattos for an estimated (5,000 atoms/s): 0 hours, 4 minutes and 30 
seconds; please wait
==> Processing the Wattos results into CING data model
==> Calculating restraint information by Queeny
Queeny.initRestraints: adding restraints (# elements = 18937)
WARNING: Queeny.initRestraints: failure to analyze <DistanceRestraint 41>
DEBUG: Queeny.initRestraints: 57 restraints added (# elements = 18937)
==> Saved queeny results to "2l56.cing/2l56/Queeny/queeny.sml"
==> RunTalosPlus: No resonances defined so no sense in running.
==> Superposing: fitted <Molecule "2l56" (C:1,R:18,A:327,M:10)> on 0 atoms 
(residues=., backboneOnly=True, includeProtons=False)
WARNING: Molecule.calculateRMSDs: no selected residues for ranges .
==> Analyzing restraints
==> validateRestraints, output to 2l56.cing/2l56/Cing/restraints.txt
DEBUG: Failed to get the D1D2 hist for <Residue A.ASN16>; skipping. Perhaps a 
non-protein residue was a neighbor?
DEBUG: Failed to get the D1D2 hist for <Residue A.GLY31>; skipping. Perhaps a 
non-protein residue was a neighbor?
==> checkSaltbridges, output to 2l56.cing/2l56/Cing/saltbridges.txt
WARNING: Molecule.calculateRMSDs: no selected residues for ranges .
==> Disulfide analysis, output to 2l56.cing/2l56/Cing/disulfides.txt
==> Analyzing <DistanceRestraintList "distance_constraint_list" (keep,180)>, 
output to 2l56.cing/2l56/Cing/distance_constraint_list.txt
==> Analyzing <DistanceRestraintList "hBond_constraint_list" (keep,16)>, output 
to 2l56.cing/2l56/Cing/hBond_constraint_list.txt
==> Found assigned/overall/fraction for spins:    13C 0/86/0.00   15N 0/26/0.00 
  1H 0/126/0.00
==> Only spins with fraction >= 0.85 will be flagged when missing: {'13C': 
False, '1H': False, '15N': False}
==> Criticizing project: output to "2l56.cing/2l56/Cing/ROG.txt"
DEBUG: In residueList2Ranges empty residueList.
WARNING: _ROGsummary: Funny, no residues encountered
ERROR: Failed to find the procheck summary attribute
==> summary, output to 2l56.cing/2l56/Cing/summary.txt
==> Generating Macros
==> Initializing HTML objects
==> Generating CING HTML code and images.
DEBUG: In residueList2Ranges empty residueList.
WARNING: _ROGsummary: Funny, no residues encountered
ERROR: Failed to find the procheck summary attribute
Creating CING html
CING started at : Tue Feb  1 02:51:08 2011
CING stopped at : Tue Feb  1 02:52:08 2011
CING took       : 59.620 s

Traceback (most recent call last):
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 355, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 259, in main
    doWattos=doWattos, doTalos=doTalos):
  File "/Users/jd/workspace35/cingStable/python/cing/core/classes.py", line 990, in validate
    validateFastest = validateFastest, validateCingOnly = validateCingOnly, validateImageLess = validateImageLess)
  File "/Users/jd/workspace35/cingStable/python/cing/core/validate.py", line 125, in validate
    project.generateHtml(htmlOnly = htmlOnly)
  File "/Users/jd/workspace35/cingStable/python/cing/core/classes.py", line 1008, in generateHtml
    return generateHtml(self, htmlOnly = htmlOnly)
  File "/Users/jd/workspace35/cingStable/python/cing/Libs/html.py", line 606, in generateHtml
    project.molecule.html.generateHtml(htmlOnly=htmlOnly)
  File "/Users/jd/workspace35/cingStable/python/cing/Libs/html.py", line 2388, in generateHtml
    self._generateCingHtml(htmlOnly=htmlOnly)
  File "/Users/jd/workspace35/cingStable/python/cing/Libs/html.py", line 2133, in _generateCingHtml
    if createHtmlCing(project):
  File "/Users/jd/workspace35/cingStable/python/cing/Libs/html.py", line 112, in createHtmlCing
    moleculePlotSet.renderMoleculePlotSet( printLink, createPngCopyToo=True  )
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/matplib.py", line 2047, in renderMoleculePlotSet
    if not convert2Web(self.pathPngList, outputDir = head, doPrint = False, doFull = False):
  File "/Users/jd/workspace35/cingStable/python/cing/Libs/Imagery.py", line 152, in convert2Web
    pathFirst = path[0]
IndexError: list index out of range

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Original issue reported on code.google.com by jurge...@gmail.com on 1 Feb 2011 at 10:44
AlphaBetaTest / cing

Peptide entry fails to generate cv based residue selection #278
