Dmitriy, The very latest beta versions of PyMOL can read .xyz files directly (via the "load" or "load_raw" commands).
http://delsci.com/beta load_raw usage: my_xyz=open("some.xyz").read() cmd.load_raw(my_xyz, 'xyz', "my_xyz") I suspect the chempy XYZ file is limited to reading Tinker's fixed-column XYZ format. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dmitriy > Sent: Friday, November 04, 2005 6:34 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] .xyz file loading problem from chempy module > > Hello everyone > > It seems to be a problem with loading an .xyz file as a chempy model. > For example doing > > from chempy import io > m = io.xyz.fromFile("some.xyz") > > gives: > > chempy: reading "some.xyz". > Traceback (most recent call last): > File "<stdin>", line 1, in ? > File > "/home/dmitriy/pymol/lib/python2.4/site-packages/chempy/__init__.py", > line 185, in fromFile > TypeError: fromList() takes exactly 1 argument (2 given) > > If I've got the right idea whats going on, there should be > fromList(self,list) function in xyz.py which will hide the > Storage one. > Like it's done in pdb.py (it works fine for io.pdb.fromFile) > > I'm trying to establish a communication between my program > and pymol in a simple .xyz format. Sending a list of strings, > creating a chempy model and loading it into pymol will work. > If there is some workaround or a fix for problem mention above. > > Warren, Is it possible to implement a way of passing .xyz > file as a string, not as a list of strings or a file? I've > seen molstr, pdbstr etc. but not xyzstr. > And a short description how to load pdbstr for example it in > this way will be great. > > Thanks > Dmitriy > > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App > Server. Download it for free - -and be entered to win a 42" > plasma tv or your very own Sony(tm)PSP. Click here to play: > http://sourceforge.net/geronimo.php > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
