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@gmail.com> Date: Sun, Jan 2, 2011 at 4:12 PM Subject: index out of range To: chimera <chimera-users@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@Cl-

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

Thanks for pointing me to the correct procedure

francesco pietra

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