[PyMOL] Symmetry Expansion

PyMOLers, A bug was brought to my attention to day in the symmetry expansion command (try it on 2bop). If you have issues with the symexp command in your work, please check out the hastily-written and really-slow, but correct (for my test cases), manual symmetry expansion script: http://pymolwiki

[PyMOL] Fwd: feature request: supercell construction

forgot to also send to the list. -- Forwarded message -- From: Nicolas Bock Date: Thu, Apr 15, 2010 at 15:46 Subject: Re: [PyMOL] feature request: supercell construction To: Thomas Holder Hi Thomas, On Thu, Apr 15, 2010 at 03:42, Thomas Holder wrote: > Hi Nick, > > > I notic

Re: [PyMOL] how to install pymol in Mac?

The error below shows that you don't have gcc, which means you have to install Apple's Developer tools to compile pymol. That said, the easiest way right now is probably using macports. Follow the instructions at http://www.macports.org/install.php for installing macports, then you can run "port i

Re: [PyMOL] pymol and freemol

It's not too hard to configure PDB2PQR and APBS in Ubuntu or any other Linux distro: For PDB2PQR: Extract binaries from tarball, e.g. "tar xvzf pdb2pqr-1.4.0.tar.gz" copy or move extracted directory to desired location, e.g. "mv pdb2pqr-1.4.0 /usr/local/xtal" Enter pdb2pqr directory, e.g. "cd

Re: [PyMOL] Pymol and APBS

Dear Michael, First, let me thank you for your time and effort in providing the community with your contributions. I do sincerely appreciate your hard work and your willingness to share it with us all. Without the contributions of users such as yourself, PyMOL's stature and utility would be far le

Re: [PyMOL] pymol and freemol

On Thu, Apr 15, 2010 at 11:53:06AM -0600, Maia Cherney wrote: > I downloaded apbs and pdb2pqr, but I don't know how to install them on > my ubuntu 9.04. Is it possible to make an easy to install release? > For now, could you please send me the instruction. apbs is available in Ubuntu (via Debian

Re: [PyMOL] pymol and freemol

Hi David, I downloaded apbs and pdb2pqr, but I don't know how to install them on my ubuntu 9.04. Is it possible to make an easy to install release? For now, could you please send me the instruction. Maia David Hall wrote: > In my incentive build, freemol is present with the following readme:

Re: [PyMOL] Pymol and APBS

On Thu, Apr 15, 2010 at 10:30 AM, Shiven Shandilya < shiven.shandi...@gmail.com> wrote: > Sorry to be knocking down APBS+PyMOL integration like this, but IMHO VASCo > does a stellar job as far as integrating outside programs with PyMOL goes. > > I initially wrote the PyMOL/APBS plugin for my own u

Re: [PyMOL] Pymol and APBS

Hi, Which version of PyMOL, APBS and PDB2PQR are you using? If you send me a PQR file off-list, I can take a closer look at what's going on. Thanks, -Michael On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming wrote: > Hi all, > > I've been trying to get APBS Tools and/or APBSTools2 running for a

[PyMOL] how to install pymol in Mac?

Dear pymol users, I had to install pymol on my Macbook. I downloaded the files from SouceForge.net. When I typed as following I got error messages: python setup.py build install running build running build_py running build_ext building 'pymol._cmd' extension gcc -fno-strict-aliasing -Wno-long-do

[PyMOL] psw full screen , on screen menu and see typed commands in full screen mode

Hi I can get the animations launched from inside powerpoint to show up and go between my stored scenes. Is there some way to toggle on the internal_gui display from this full screen mode. I know the command set internal_gui,1 But when I type it on the full screen molecule, nothing happens. Othe

Re: [PyMOL] Pymol and APBS

Hi Jon, Perhaps you could look at VASCo http://genome.tugraz.at/VASCo/ I have found it to work extremely well on Windows and Linux platforms. You not only get electrostatics but also hydrophobic surface coloring, and all without the APBS and Python "hassles and headaches". Sorry to be knocking

[PyMOL] Pymol and APBS

Hi all, I've been trying to get APBS Tools and/or APBSTools2 running for a few weeks now on multiple linux systems (RedHat and Fedora). I've Installed MALOC and APBS Tools. I can start up Pymol through Phenix, load a .pqr generated from a PDB2PQR server, start APBS Tools, set the grid, but whe

Re: [PyMOL] pyMol executing python script: file path

Dear Mr. Hall, thank you very much for your help. This really works (I have tested it now on windows). Regards, Petr Benes 2010/4/15 David Hall : > I think you'll be saddened to discover that if you try what Petr (the > original poster) was doing, sys.argv[0] won't work. > > $ cat test.py > print

Re: [PyMOL] feature request: supercell construction

Hi Nick, > I noticed a few things: > > - when I run "supercell 2, 1, 1" I get another cell outline along the > a axis, but no atoms are shown in the second cell. Do I have to run > another command for them to show up? the script does not create symmetry mates. The "symexp" command can create sym

Re: [PyMOL] pyMol executing python script: file path

I think you'll be saddened to discover that if you try what Petr (the original poster) was doing, sys.argv[0] won't work. $ cat test.py print sys.argv[0] $ pymol -qrc test.py PyMOL>run test.py,main /sw/lib/pymol-py26/modules/pymol/__init__.py This quite clearly gives the behavior that Petr had is