RE: [PyMOL] "show surface" and the "get_view" cmd

Dr. Delano, Thank you for the information. --- Warren DeLano wrote: > Douglas, > > It is the molecular or "Connolly" surface: the > surface that would be traced > out by the *surfaces* of waters in contact with the > protein at all possible > positions. > > There's nothing in PyMOL that would

[PyMOL] building pymol rpm

Hi, Anyone out there have a spec file (or srpm) for building a pymol v0.98 RPM on CentOS-4 or Fedora Core 3? I succeeded in building a monolithic pymol RPM (~11MB) on CentOS by basically wrapping the standalone pymol-0_98rc3-bin-linux-x86-glibc23.tgz, but this resulted in an executable that w

Subject: [PyMOL] ray-trace stereoview

Alejandro, Someone a while back wrote a beautiful script to do this for us. I posted it on the wiki. Check out http://www.pymolwiki.org/index.php/Stereo_Ray It should have all the information you'll need. HTH, -- Jason On Fri, 2005-06-10 at 20:19 -0700, pymol-users-requ...@lists.sourceforge.

[PyMOL] Re: pdb-l: protein visualization/interaction tools?

Hi Marty, Sorry if this misses your point, but it is possible to translate molecules independantly in pymol: http://sourceforge.net/mailarchive/message.php?msg_id=11658301 However, that won¹t help if you want to show overlap. To do this, you would have to repeatedly call translate and distan

[PyMOL] Pymol/ABPS

Hi, I'd like to know what charges Pymol uses when generates a pqr file from a pdb. The follow-up would be is whether there was a way to change this, say if one wanted to use charmm charges rather than amber. It seems that APBS hates chain IDs. Is that really so, or just my imagination? Thanks

Re: Subject: [PyMOL] ray-trace stereoview

Additionally, if you have the ImageMagick suite of tools on your machine (most Linux distros come with it) you can use the 'montage' program to stitch the two images together automagically. Just add the lines: print "Creating the stereo image" montage = '"montage +frame +shadow +label -tile 2

[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 dis