[Chimera-users] index out of range

[Francesco Pietra]

Running movie for prmtop/dcd proved extremely slow at amd64, finally
showing the protein in a water box, albeit offering very limited
analysis. Error message: index out of range, error processing "monitor
changes". The log is 16MB!, below the startr and end of the log:

MDTools 1.2 Exp (2005-08-20) by James Phillips.
Trajectory.DCD.MDToolsMarch97.md.help() for more info.
 HomoCoord 1.3 Exp (2005-08-20)
- Constants 1.1 Exp (2004-05-17)
- AtomGroup 1.4 Exp (2007-02-07)
- local 1.1 Exp (2004-05-17)
Unknown OSTYPE ??? set.  Viewing and plotting are disabled.
- Trans 1.2 Exp (2005-08-20)
- DCD 1.10 Exp (2007-02-07)
- Data 1.2 Exp (2005-08-20)
using memory mapping
REMARKS FILENAME=./heat-01.dcd CREATED BY NAMD
REMARKS DATE: 06/03/12 CREATED BY USER: francesco
Model 0 (heat-01.dcd) appears to be a protein without secondary
structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
Traceback (most recent call last):
  File "/usr/local/chimera_Nov3.2011/share/chimera/triggerSet.py",
line 83, in invoke
    self._funcData, triggerData)
  File "/usr/local/chimera_Nov3.2011/share/chimera/Sequence.py", line
1161, in _cacheCheck
    if len(kids) == molecule.rootForAtom(kids[0],
IndexError: list index out of range
Error processing trigger "monitor changes":

....................................
....................................

Traceback (most recent call last):
  File "/usr/local/chimera_Nov3.2011/share/chimera/triggerSet.py",
line 83, in invoke
    self._funcData, triggerData)
  File "/usr/local/chimera_Nov3.2011/share/chimera/Sequence.py", line
1161, in _cacheCheck
    if len(kids) == molecule.rootForAtom(kids[0],
IndexError: list index out of range
Error processing trigger "monitor changes":
IndexError: list index out of range

  File "/usr/local/chimera_Nov3.2011/share/chimera/Sequence.py", line
1161, in _cacheCheck
    if len(kids) == molecule.rootForAtom(kids[0],

See reply log for Python traceback.

Thanks for the attention
francesco pietra