[Chimera-users] list index out of range

[Eric Pettersen]

Hi Paula,
     Chimera expects a PSF/DCD combo, not a PDB/DCD combo.  The  
underlying package I use for DCD support, MD Tools for Python, does a  
good job of handling PSF files but its PDB file support leaves a lot  
to be desired, which is why the PDB part is omitted from Chimera.   
Nonetheless, I hacked up a couple of the MD Movie files to sort of  
handle your PDB file.  I say "sort of" because I had to add CONECT  
records to your file or else all the trajectory bonds would be missing.
     I will probably work on making it possible to use a PDB file in  
general instead of a PSF file for the next release (or maybe the one  
after).
     So appended is two replacement files for your Chimera  
distribution (DCD.py and md_AtomGroup.py) and your PDB file with  
CONECT records added (x.pdb).  DCD.py and md_AtomGroup.py should go  
in <your chimera install dir>/share/Trajectory/DCD and <install>/ 
share/Trajectory/DCD/MDToolsMarch97 respectively, replacing files of  
the same name.  You may want to copy the originals somewhere because  
you will lose the ability to use PSF/DCD combinations after putting  
in these hacked versions.
     In case you need to add CONECT records to other PDB files, you  
can do this pretty easily in Chimera.  After opening the PDB file in  
Chimera, use the command:

     pdbrun nouser conect cat > filename.pdb

which will create filename.pdb in your Chimera startup directory  
(though "filename.pdb" could be a full path if you wanted it to go  
elsewhere).  The above command will only work on Unix-based systems  
since "cat" is a Unix command.

--Eric

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


On Oct 24, 2005, at 7:09 PM, Paula Petrone wrote:

> Hi,
>
> I am trying to load in an MD-ensemble, using a pdb and an X-plor  
> file .dcd.
> For some reason, it gives me "IndexError: list index out of range".
>
> I generated the .dcd file myself (with Fortran). VMD program seems  
> to have no problem with it.
> Is it a format problem? Is it a bug? Any suggestion?
>
> Thanks a lot! (I attach the files)
>
> paula


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