Re: [PyMOL] Pymol apbs problem

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

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 schem

[PyMOL] os x crash bug

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] pymol x-windows version for Mac OS X

Howdie, Citizens: Jack Howarth very kindly got a current version of X-windows pymol working on Mac OS X via fink. These files work for 10.3 and python 2.3, and he also has some that work with python2.2.x http://chemistry.ucsc.edu/~wgscott/xtal/xtalfink/pymol.info http://chemistry.ucsc.edu

[PyMOL] pymol and powermate

Hi Zac: Thanks for sharing this. I just bought one of these for MacOSX and it works great with O. Will your python script, along with powermate.py, work on other platforms like OSX where the default driver/kernel extensions that come with the powermate have been installed, or is this specifi

[PyMOL] Re: PyMOL 0.93 and MacOS X

67 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax) url: http://chemistry.ucsc.edu/~wgscott/

[PyMOL] favorite programming languages

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

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

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 API

[PyMOL] question about new os x version

Hi: I just installed the new os x version of pymol. I had been invoking pymol with full screen using the following command: /Applications/PyMOL/Darwin/pymol.com -q -e This avoids the multiple icons and terminal screens and just opens up pymol to full screen mode. In the previous version the

[PyMOL] python as a satellite virus

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 dir

[PyMOL] pymol bug?

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 grap

[PyMOL] fink and povray

Regarding povray installation with fink: fink installs povray 3.5 without a problem for me. However, if you look at the file /sw/fink/10.2/stable/main/finkinfo/graphics/povray-3.50b-1.info you find the following dependencies: BuildDepends: libtiff, libjpeg, libpng, dlcompat-dev Depends: x11,

[PyMOL] Apple X11 and pymol display.

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] x-windows pymol on OS X

Oh, and if you already have installed pymol with fink, you don't need to do anything apart from installing Apple's X-windows. William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of Calif

[PyMOL] x-windows pymol, fink and os x

Awesome! I was hoping Apple's new release might have this impact. In my hands the X-windows version of pymol on OS X went from unusable to almost as fast as the native version. Apple's GLUT driver can now bind to the hardware drivers under X11 at the same time as the Tcl/Tk external GUI

[PyMOL] Re: PyMOL-manual

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 wh

[PyMOL] pymol and mmtk

to this please let me know. BTW if you want to install mmtk via fink on OS X I have an install script here: http://chemistry.ucsc.edu/~wgscott/xtal/xtalfink_html.html Thanks in advance. Bill Scott William G. Scott Associate Professor Department of Chemistry and Biochemistry and The

[PyMOL] Color plotting of electron density contours?

Hi Folks: Is there a way to display a cross-section of electron density (false)-color-coded for electron density? In other words, I would like to produce a 2-D plot that looks like a contour map (eg: output of CCP4 npo) but color-coded with respect to electron density. A continuum, if poss

[PyMOL] PyObjC for OS X

Howdie Citizens: There is a new PyObjC web page at http://pyobjc.sourceforge.net/index.php complete with a truly tasteful icon. <> Has anyone made use of this (pyobjc, not the photo) yet? Bill William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center

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

n use the open filename command as the equivalent of double-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,

[PyMOL] (no subject)

Hi Lieven: I don't have windows pymol or access currently to a windows machine, so I will have to tell you how I did it on the Mac version and then hope it is essentially identical with windows. I did this about 6 months ago in order to hyperlink quicktime to Powerpoint in XP. I am assuming

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

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 you

[PyMOL] making movies (animated gifs)

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

[PyMOL] Re: PyMOL input

I've been using the commands and a lobotomized 1-button mouse. It would ge a great question for the pymol users email list. Anybody know of an improvement mouse-wise for OS X? On Friday, September 6, 2002, at 12:31 PM, Scott Classen wrote: Dr. Scott I just installed the OSX version of PyMO

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

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 Bronwy

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

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

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

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 br

[PyMOL] pymol on OS 10.1

Hi Warren, et al: I just returned from a conference where I gave my first pymol-based presentation on an ibook G3 500MHz using the native version (the X-windows version, as previously noted, was impossibly slow). I have to say it was a resounding success. I used it to present both structures