[Chimera-users] index out of range

[Francesco Pietra]

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