HI Matthias, Sounds like you almost had it right. However, you have to use the “open” command to open the metafile. The “md” part is just a format specifier for the open command, not a command in itself. (command list: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>) Summary: To bypass the MD Movie input-files dialog you would create a “metafile” which is just a short plain text file of the same things you would enter into that dialog. The "startup and input" section of the MD Movie help has a couple examples of metafile contents: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...> Your metafile would just contain something like this: namd(prmtop/dcd) D:\structure.psf D:\structure_MD001.dcd …and you’d open it with command: open md:metafile-name …where metafile-name is a pathname if it is not in the current working directory. However, I suspect that pathname with a colon might cause problejms. Chimera command “cd” changes the current working directory, so if giving the pathname directly in the open command causes a problem, instead use “cd” to go that folder and then just use the metafile name in the open command. I’m a little uncertain of what you’ll need to do, since I’m not a Windows user. On Mac, all my pathnames don’t have colons in them so it’s not an issue. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2018, at 7:58 PM, Matthias Fellner <matthias.fellner@otago.ac.nz> wrote:
Good day
I successfully loaded NAMD psf/dcd files into chimera (version 1.13.1) using the tools MD movie interface. As I have many runs and each has multiple dcd files I wanted to use a script to load the different runs, instead of manually picking all the files through the interface each time. I tried to follow the limited instructions of the MD Movie homepage but failed to get anywhere. I tried some versions of this command: md: D:\script.txt or movie: D:\script.txt
The command md appears to try to start MDA (MultiDomain Assembler), the command movie wants some other unrelated inputs. I am also not sure if the script command would even work like this:
namd(psf/dcd) D:\structure.psf structure_MD001.dcd - D:\
Any advice is appreciated Thank you Matthias Fellner