Hi, Thanks for looking into the problem. It would be nice to be able to read trr/xtc trajectories, but then would you also need to add functionality to read the gro file as well? Perhaps other Chimera users would also find these features useful. Thanks, Sabuj Pattanayek Eric Pettersen wrote:
Hi Sabuj, I understand the problem now. My code is not expecting the individual PDB files to have MODEL/ENDMDL records in them (the code is placing these records around each file as it collates them). The result is a mess. I will work on making my code more robust in this regard. There is a fairly easy workaround for you though: don't give the -sep flag to trjconv. You will get a single file containing the frames bracketed by MODEL/ENDMDL records (which is what Chimera would have had to assemble anyhow), which you can read by using the "single file" option of the PDB format trajectory reader. One caveat is that the MD code expects the model numbers to start at 1, not 0, so you will either have to renumber the MODEL records somehow, or delete MODEL 0 from the file. I will also work on handling files where the numbering starts at zero. Do you work with Gromacs trajectories a lot? If you do, I could put reading Gromacs trajectories directly on my to-do list.
--Eric