Hi Juan, Regarding your last question: yes, you can open an “MD metafile” at the command line. It’s basically a text file with the information you would otherwise input into the MD Movie dialog. You can indicate that file type with prefix md: or movie: , for details see:

http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#metafile also mentioned here http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#molstruct

That might partly avoid your other issues since you would just specify pathname to the metafile, and within the metafile, you would give pathnames of the actual input files relative to the metafile location.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 30, 2015, at 9:47 AM, Eiros Zamora, Juan j.eiros-zamora14@imperial.ac.uk wrote:

Dear Chimera experts, I am working with Mac OS X version 10.11.1 and Chimera 1.10.2

I use Chimera to visualize MD trajectories. Usually I launch the program through the command line. I’ve got a pretty deep hierarchy of directories to keep my data organized, so I’ve been trying to look for a way to make Chimera keep the path of the directory where I launched it from, with no success.

What I mean is, if I launch it from a given directory and then try to load MD NetCDF files with the “MD Movie” option, is there a way for it to show me the files in the directory where I opened it from?. Because now what it does is show me the ones from the last time I used this.

Also, is there a way to load the topology and trajectories directly from the command line? I have looked for this option but haven’t found anything. Thanks for your help Juan