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
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
I've put a screen-shot here if anyone wants to have a look.
http://chemistry.ucsc.edu/~wgscott/xtal/page6.html
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
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
http://www.macupdate.com/info.php/id/235 but if anyone needs it I can
email you mine.
Also if you have
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
-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
On Tuesday, December 24, 2002, at 12:07 PM,
pymol-users-requ...@lists.sourceforge.net 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
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
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
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
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/__init__.py'
another user reported a different such error:
/sw/lib/pymol/modules/pymol/__init__.py:300: RuntimeWarning: Python C
Nat et al:
1. For fortran, there is also an f2py interface:
http://cens.ioc.ee/projects/f2py2e/
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
: +1-831-4593139 (fax)
url: http://chemistry.ucsc.edu/~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
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?
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
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