From: Piter_ <x....@gm...> - 2006-07-06 17:20:20
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Hi all I have some errors if I run script: PyMOL>run c:\pict.pml Traceback (most recent call last): File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 273, in parse parsing.run_file(exp_path(args[nest][0]),pymol_names,pymol_names) File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py", line 407, in run_file execfile(file,global_ns,local_ns) File "c:\pict.pml", line 1 show sticks,tups1 ^ SyntaxError: invalid syntax PyMOL>show sticks,tups1 (if i run it in command line it works) or the same: PyMOL>run c:\pict.pml Traceback (most recent call last): File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 273, in parse parsing.run_file(exp_path(args[nest][0]),pymol_names,pymol_names) File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py", line 407, in run_file execfile(file,global_ns,local_ns) File "c:\pict.pml", line 1 select cyt100,1HRC_Cys8_TUPS_W_1_MD_100 not resn ben+sul+thi+npr+wat+hem ^ SyntaxError: invalid syntax The script: show sticks, tups1 show surface, cyt100 png tups1.png hide sticks, all hide surface, all tups1 and cyt100 are named selections. Thanks for help. Petro |
From: Tsjerk W. <ts...@gm...> - 2006-07-07 10:21:59
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Hi Petro, run expects a python script (.py), whereas you're trying to run a pymol script (.pml). For that you nead '@': @c:\pict.pml Cheers, Tsjerk On 7/6/06, Piter_ <x....@gm...> wrote: > > Hi all > I have some errors if I run script: > > PyMOL>run c:\pict.pml > Traceback (most recent call last): > File "C:\Program Files\DeLano > Scientific\PyMOL/modules\pymol\parser.py", line 273, in > parse > parsing.run_file > (exp_path(args[nest][0]),pymol_names,pymol_names) > File "C:\Program Files\DeLano > Scientific\PyMOL/modules\pymol\parsing.py", line 407, in > run_file > execfile(file,global_ns,local_ns) > File "c:\pict.pml", line 1 > show sticks,tups1 > ^ > SyntaxError: invalid syntax > > PyMOL>show sticks,tups1 (if i run it in command line it works) > > or the same: > > PyMOL>run c:\pict.pml > Traceback (most recent call last): > File "C:\Program Files\DeLano > Scientific\PyMOL/modules\pymol\parser.py", line 273, in > parse > parsing.run_file > (exp_path(args[nest][0]),pymol_names,pymol_names) > File "C:\Program Files\DeLano > Scientific\PyMOL/modules\pymol\parsing.py", line 407, in > run_file > execfile(file,global_ns,local_ns) > File "c:\pict.pml", line 1 > select cyt100,1HRC_Cys8_TUPS_W_1_MD_100 not resn > ben+sul+thi+npr+wat+hem > ^ > SyntaxError: invalid syntax > > The script: > > > show sticks, tups1 > show surface, cyt100 > png tups1.png > hide sticks, all > hide surface, all > > tups1 and cyt100 are named selections. > > Thanks for help. > > Petro > > > > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 |