[Chimera-users] Fwd: index out of range

[Eric Pettersen]

Hi Francesco,
	From the traceback you provided it seems that when you start the MD  
Movie tool and specify your input files, you are selecting something  
other than "Amber" from the "Trajectory format" menu.  Perhaps you  
aren't changing that menu at all and are leaving it on some choice  
other than "Amber".  To use a prmtop/mdcrd you need to change that  
menu to "Amber"!
	The traceback is from an error in the DCD-reading code, which is only  
used for formats other than Amber.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Jan 3, 2011, at 9:01 AM, Francesco Pietra wrote:

> 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
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20110103/65baf0f4/attachment.html>