Re: [PyMOL] Pymol apbs problem

2007-09-21 Thread wgscott
Hi Evan: I ran pdb2pqr by hand and I think the Zn and CTP is problematic: REMARK 5 WARNING: PDB2PQR was unable to assign charges REMARK 5 to the following atoms (omitted below): REMARK 5 7220 ZN in ZN 154 REMARK 5 7221 ZN in ZN 154 REMARK 5

[PyMOL] spectrum, util.rainbow

2004-04-08 Thread wgscott
Hi folks: Why is spectrum and the internal gui (which I assume invokes spectrum) so much faster than util.rainbow ? I like the util.rainbow default color scheme a bit better, but it takes forever for large complexes. Is there a simple way to get spectrum to mimic the rainbow color scheme?

[PyMOL] os x crash bug

2004-03-05 Thread wgscott
Hi folks: I tried to make some symmetry objects of my molecule using the instructions in the manual. MacPymol (0.94b) choked on this, crashing the whole system. (OS X doesn't often crash, but when it does, it ain't pretty). When I rebooted I was unable to log into my account. Fortunately

[PyMOL] Re: PyMOL 0.93 and MacOS X

2003-12-21 Thread wgscott
: +1-831-4593139 (fax) url:

[PyMOL] favorite programming languages

2003-11-24 Thread wgscott
Nat et al: 1. For fortran, there is also an f2py interface: 2. Some things just seem far easier in perl, like is there a one line python-equivalent for this: perl -pi -e 's/old/new/g' myfile.txt ? 3. There is now a python-objective C bridge if you want

[PyMOL] Re: PyMOL-users digest, Vol 1 #354 - 3 msgs

2003-07-03 Thread wgscott
When I installed X-windows pymol 0.90 on OS X using fink and try to run it, I get an error /sw/bin/python: can't open file '/Users/delwarl/pymol/modules/pymol/' another user reported a different such error: /sw/lib/pymol/modules/pymol/ RuntimeWarning: Python C

[PyMOL] python as a satellite virus

2003-04-30 Thread wgscott
Coincidently that was the exact same program that hosed my python installation too. I had set up my computer to run the python based AutoDock Tools interface to the docking program AutoDock. The installer for this program puts its own copy of python as a subdirectory in the main application

[PyMOL] pymol bug?

2003-02-26 Thread wgscott
Hi: I have been making a few rendered movies to give my computer something to chew on at night. This morning I came in to fink failure at step 97 of 120 frames with the following error: MoviePNG: wrote high_closeup_0096.png Ray: tracing 1120x960 = 1075200 rays... Ray: processed 18531

[PyMOL] Apple X11 and pymol display.

2003-01-22 Thread wgscott
Dear Dan: Are you using OS 10.2.3? You won't derive the benefits of the acceleration unless you have 10.2.3. Beyond that, I am at a loss. On my G4 iMac and even on my G3 ibook, x-windows based pymol has gone from virtually unusable to almost as good as the native version (which, by

[PyMOL] Re: PyMOL-manual

2002-12-24 Thread wgscott
On Tuesday, December 24, 2002, at 12:07 PM, wrote: 1. Suggestions for manual - nonspecialists perspective (James L. Kilgore) What I'd like to see written in an accessible form for a non-programmer is 1) A concise-but-ground-up description of

[PyMOL] mixing pymol and powerpoint (or equivalent) in a presentation

2002-11-11 Thread wgscott
-clicking a file to open it. I imagine there is something similar for windows but I don't know what it is. Here is part of my /Users/homedirectory/pymol/alias.pml file to give an idea for how this is implemented: alias 1, os.system(open /Users/wgscott/pymol/part_1/part_1.pps); alias 2, @/Users

[PyMOL] making movies (animated gifs)

2002-10-28 Thread wgscott
There is a program called gif-builder (Mac OS 9 and 10) that is free and uses a variety of input types to make an animated gif which then is platform-independent. Sadly the link is broken but if anyone needs it I can email you mine. Also if you have

[PyMOL] pymol movies (again, sorry) and windows

2002-10-28 Thread wgscott
Dear Stephen Miller: Also, don't overlook the fact that pymol itself is a movie player. In powerpoint you can create what is called a hyperlink to pymol, and then you can just load in your macro (pml script) and your movie starts playing embedded in powerpoint. This is far better because

[PyMOL] Re: PyMOL-users digest, Vol 1 #152 - 6 msgs

2002-09-02 Thread wgscott
Folks, I have made a tough decision. Like many of you, I believe that PyMOL has the potential to become an effective software tool for bioinformatics, structural biology, computational chemistry, cheminformatics, and Science education. However, by myself, working in my spare time, I can not

[PyMOL] OS X pymol version 0.84beta is excellent. Thank you!!!

2002-09-02 Thread wgscott
I just noticed the OS X pymol native update, downloaded and installed it and it is great. It also makes me think that one day I might even install OS 10.2(there was no reason to if pymol didn't work). Nice job Warren! Thanks. Bill Scott William G. Scott Associate Professor Department

Re: [PyMOL] OS X pymol version 0.84beta is excellent. Thank you!!!

2002-09-02 Thread wgscott
I've put a screen-shot here if anyone wants to have a look. Hopefully this will generate a little free publicity... On Monday, September 2, 2002, at 08:02 PM, Bronwyn Carlisle wrote: I second that motion. Very nice. Thank-you Bronwyn