[Chimera-users] Fwd: index out of range

Francesco Pietra chiendarret at gmail.com
Mon Jan 3 09:01:40 PST 2011


hello:
While I have solved how to show chloride ligands  in case of allh
protein, the movie still fails in my hands.

I have installed the daily built

chimera-alpha-linux_x86_64.bin
Size: 86507786 bytes
MD5: 8f899c8b0ad19b3e8ae5a406d597cc41

getting the same error on prmtop/inpcrd:

You are now running Chimera version 1.6 (build 32219).
Your previous version was 1.5 (build 30702).
Check the release notes for new features and other info.
(To access the release notes, use the Help menu to bring up the User's Guide.
Then click the 'Documentation index' link and you will then see a link
for the release notes.)
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)
<type 'exceptions.IndexError'> Exception in Tk callback
  Function: <function command at 0x3fe0ed8> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "/usr/local/chimera/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)

for files that are correctly handled by VMD (I have also tried
prmtop/inpcrd files that were correctly handled by chimera a couple of
years ago, getting now the same 'out of index error'. As the other
files for a would-be-publication have already been prepared with
chimera, I would like to solve the issue for the remaining figures.

Thanks

francesco


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Sun, Jan 2, 2011 at 4:12 PM
Subject: index out of range
To: chimera <chimera-users at cgl.ucsf.edu>


Hello:
Two not new questions.

(1) I am trying to read prmtop/mdcrd files from Amber MD with chimera
alpha version 1.5 (build 30702) 2010-06-10 23:51:24 GMT, getting
"index out of range" (the files are correct, they open with VMD)


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)
Traceback (most recent call last):
 File "/usr/local/chimera/lib/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
   return apply(self.func, args)
 File "/usr/local/chimera/share/chimera/baseDialog.py", line 342, in command
   getattr(s, buttonFuncName(txt))()
 File "/usr/local/chimera/share/chimera/baseDialog.py", line 560, in OK
   self.Apply()
 File "/usr/local/chimera/share/Trajectory/EnsembleLoader.py", line 92, in Apply
   self.callback)
 File "/usr/local/chimera/share/Trajectory/DCD/__init__.py", line 72,
in loadEnsemble
   addTrajKw=self.addTrajKw)
 File "/usr/local/chimera/share/Trajectory/DCD/__init__.py", line 85,
in loadEnsemble
   ensemble = DCD(psf, dcd, startFrame, endFrame)
 File "/usr/local/chimera/share/Trajectory/DCD/DCD.py", line 24, in __init__
   mdtMol = md.Molecule(psf=psfPath)
 File "/usr/local/chimera/share/Trajectory/DCD/MDToolsMarch97/md_AtomGroup.py",
line 356, in __init__
   nrecs = int(psfrec[0])
IndexError: list index out of range
IndexError: list index out of range

 File "/usr/local/chimera/share/Trajectory/DCD/MDToolsMarch97/md_AtomGroup.py",
line 356, in __init__
   nrecs = int(psfrec[0])
See reply log for Python traceback.
************************************************

(2) Although I suppose I used in the past ATOM ATTRIBUTES to display
chloride anion at its standard radius in preparing figures for
publication, I just get it now as a tiny dot as set by MODELLER. That
with proteins without or with non-polar hydrogens.

For example

TER    6750      LYS A 426
ATOM   6751  Cl- Cl- A 427     -31.021   4.748  41.205  1.00  6.32          Cl
TER    6752      Cl- A 427
ATOM   6753  N   LEU B   1     -13.959  20.979 -35.226  1.00 63.95         N

I can't remember how to specify the chloride radius in command

sel :427 at Cl-

************************************************

Thanks for pointing me to the correct procedure

francesco pietra




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