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@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