[FeLiXe]

Hi!

I am looking for a quick way to open several molecules in PyMol without having to open all of them separately. Does someone know how to do that? Best would be to open them from the command line but I think this only works for one molecule ('pymol molecule.ext')

thanks

(I don't know where a chemical software question goes. but this is the closest I could think of)

[sjb]

I'm not totally sure (thought I saw a magazine article the other day, it's now disappeared into the pile by the desk - will have a look later, but I think something like xargs is possibly the way to go (http://unixhelp.ed.ac.uk/CGI/man-cgi?xargs)

S

[sjb]

I'm not totally sure (thought I saw a magazine article the other day, it's now disappeared into the pile by the desk - will have a look later, but I think something like xargs is possibly the way to go (http://unixhelp.ed.ac.uk/CGI/man-cgi?xargs)

S

OK, have now found the article - try file1.ext file2.ext (etc) xargs pymol . Or even something like ls *.ext | xargs pymol which (I think will open all files with *.ext in pymol)

[FeLiXe]

pretty cool, thanks
I'll try that out tomorrow

[Yggdrasil]

From a linux terminal, if all of the files are in the same dirrectory, you can type:

pymol *.pdb

(or whatever extension you're using)

and pymol will open up all of the files in your current dirrectory with the .pdb extension.

[sjb]

pretty cool, thanks
I'll try that out tomorrow

Any luck? Yggdrasil's approach may be easier - don't have pymol here to test.

S

[FeLiXe]

What I finally did is that I wrote a .pymolrc into the folder. The advantage is that I can do some more things that way, like showing the cartoon or showing sticks.
I tried out "pymol *.pdb" and it did not work. I will try out your commands on monday when I am at work. it would be interesting to see how it works. It's just that I thought of the pymolrc before I read your posts

[FeLiXe]

I think the problem is that pymol doesn't recognize that I am trying to enter multiple molecules. it thinks that I am entering one long name with spaces in between ls *.ext writes the "correct" string but pymol doesn't recognize it as several molecules