Hari, This is an outright bug that I introduced when adding URL support for files. You can change that one line of code in cgo.py from
if (mode[0:1]=='r') and (string.find(fname,':')>1): to if (string.find(fname,':')>1): in order to solve the problem. 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 > hari jayaram > Sent: Sunday, June 12, 2005 9:29 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] pymol 0.98 and r3d input and getting sec > structure assignments info > > Hello , I tried to open an r3d (raster3d) file in pymol > version 0.98 and I get the following error > > Traceback (most recent call last): > File "/xtal2/pymol/modules/pymol/__init__.py", line 218, in > exec_deferred > cmd.load(a,quiet=0) > File "/xtal2/pymol/modules/pymol/importing.py", line 549, in load > discrete,quiet,multiplex,zoom) > File "/xtal2/pymol/modules/pymol/cmd.py", line 755, in _load > obj = cgo.from_r3d(finfo) > File "/xtal2/pymol/modules/pymol/cgo.py", line 167, in from_r3d > if (mode[0:1]=='r') and (string.find(fname,':')>1): > NameError: global name 'mode' is not defined > > > The same exact r3d file opens up just fine on pymol 0.97. Is > there something I am doing wrong or do I have to do something > different to generate the file to work with 0.98. > > Any help will be greatly appreciated. > > Also I was curious how to get pymol to spit out the > secondary structure assignments it useswhen one says assign > sec structure in the gui. I know this was covered before but > my googling skills are very dull today. So any help in > getting info on the sec str assignments used by pymol for a > particular model will also be greatly appreciated. > Thanks > hari > >
