Hello Warren and pymol users, Thanks for your help on what to fix to get r3d working in 0.98 with linux . .. but I still have one problem How do I get a cgo.pyc to replace the cgo.pyc which has the bug in it. Sorry I dont understand anything about the inner workings of pyhton to replace the faulty cgo.pyc with a new fixed cgo.pyc and I use the static build provided by the website.
Also how do I get the list of ss elements assigned by util.ss Thanks a lot for your help Hari On 6/13/05, Warren DeLano <war...@delanoscientific.com> wrote: > > 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 > > > > > > >
