Thanks for your mail. I did two things: (i) typed the entire path starting from /home/../../draw_cell.py (ii)"cd /home/../../" and then "run draw_cell.py.
It still gives me the same error of not finding cctbx. I checked if I am in the correct directory by typing "pwd" and got the correct answer. When I do "ls draw_cell.py" it prints the filename. I guess the problem is that pymol cannot recognise cctbx, even though my path to cctbx are correctly set as I can run cctbx commands from any directory. Is there a resolution ? or I need to reinstall pymol ? Thanks again, Vivek Ranjan On Fri, Jul 9, 2010 at 4:01 PM, Paul Rigor (uci) <paul.ri...@uci.edu> wrote: > Hi, > Your assumptions are correct, as I've copied and tested your code, which > works fine from the current working directory where I ran the pymol start > script. It's probably a quirk w/ your installation? Otherwise, you can just > specify the full path to your script or "cd" into the folder... either way. > Goodluck, > Paul > On Fri, Jul 9, 2010 at 11:01 AM, Robert Campbell > <robert.campb...@queensu.ca> wrote: >> >> On Fri, 09 Jul 2010 13:46:57 -0400 Vivek Ranjan <vran...@gmail.com> wrote: >> >> > Hello, >> > >> > I am trying to run a simple python script from Pymol and cannot run it: >> >> <snip> >> >> > I saved the above in a file named "axes.py" and put it in the same >> > directory from where I type "pymol" (on ubuntu linux). Then I type >> > "run axes.py" in pymol command bar. I get the following error message: >> > >> > ***************************************** >> > Traceback (most recent call last): >> > File "/usr/local/lib/python2.6/dist-packages/pymol/parser.py", line >> > 334, in parse >> > parsing.run_file(path,self.pymol_names,self.pymol_names) >> > File "/usr/local/lib/python2.6/dist-packages/pymol/parsing.py", line >> > 455, in run_file >> > execfile(file,global_ns,local_ns) >> > IOError: [Errno 2] No such file or directory: 'axes.py' >> > ******************************************************************* >> > >> > Any help ? >> >> Try typing the command "pwd" within PyMOL to see if it reports that you >> are >> in the directory that you think you are. Also try typing "ls axes.py" to >> see >> if it can see it. Are you sure you haven't made a typo in the name of the >> file? Otherwise I don't see why what you have done shouldn't work. >> >> Cheers, >> Rob >> -- >> Robert L. Campbell, Ph.D. >> Senior Research Associate/Adjunct Assistant Professor >> Botterell Hall Rm 644 >> Department of Biochemistry, Queen's University, >> Kingston, ON K7L 3N6 Canada >> Tel: 613-533-6821 Fax: 613-533-2497 >> <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > -- > Paul Rigor > http://www.ics.uci.edu/~prigor > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Thank you and Regards, Vivek Ranjan ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
