Re: [PyMOL] density map
Hi Steve, You'll need to provide more information if you want to have a chance on a helpful thought. Maybe you could link the .pdb file and the .xplor map and show what O does to it. Cheers, Tsjerk On Dec 7, 2007 3:57 PM, W.M. B. wrote: > Hi, All > > I'm trying to make a picture of active site with density map. When I > loaded the pdb and xplor map, I found that map and model are in the diffrent > position. But in O, they are fine. Would anyone give me a hint how to fix > it. > > Thanks > > Steve > > - > SF.Net email is sponsored by: > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
Re: [PyMOL] apbs plugin for macpymol
Thanks to Michael and Warren for a quick and correct but somewhat baffling solution. In OSX, one renames an application and it starts up looking quite dissimilar from before. I'm still new to the Gospel according to Steve, and I wouldn't mind enlightenment. In any case, using MacPyMOL as PyMOLHybrid also solves the problem of physically separating the viewer from the external gui, without which one couldn't fully harness the power of multiple screens. A side note regarding Michael's instructions: APBS doesn't require fink. (I haven't even figured out what fink is yet. Some sort of yum for OSX?) One can just download the Mac OSX binary from WUSTL and install it as per default. Works like a charm, as does APBS itself. Much better than on my Fedora 7 system, I'm embarrassed to admit ;-) Andreas Michael Lerner wrote: I would like to use apbs from within PyMOL. I have downloaded and installed the latest version of apbs, and apbs_tools.py exists in $PYMOL_PATH/modules/pmg_tk/startup/. However, I find no "plugins" entry in any of the PyMOL menus. I think that you need to rename the application bundle to "PyMOLX11Hybrid" in order to use plugins. Am I blind or daft? But the question I'd really like to have answered is how do I get abps to work. I would suggest 1) register APBS here http://agave.wustl.edu/apbs/download/ 2) Install fink ( http://finkproject.org/ ) and then use it to install apbs (e.g. by typing "fink install apbs" on the command line). hope that helps, -michael I'm using educational MacPyMOL, which "integrates and extends Open-Source PyMOL 1.0r1". Thanks. Andreas
[PyMOL] density map
Hi, All I'm trying to make a picture of active site with density map. When I loaded the pdb and xplor map, I found that map and model are in the diffrent position. But in O, they are fine. Would anyone give me a hint how to fix it. Thanks Steve
[PyMOL] Fit sequence to structure with pymol
Hello everybody. Does anybody know how to perform sequence to structure fit with pymol? For example this feature in swiss-pdb-viewer is called "Fit" or "Magic fit". So, 1/ Is there a command to fit sequence to pdb& 2/ If yes, could I specify the region to fit on? Thanks!
Re: [PyMOL] apbs plugin for macpymol
> I would like to use apbs from within PyMOL. I have downloaded and > installed the latest version of apbs, and apbs_tools.py exists in > $PYMOL_PATH/modules/pmg_tk/startup/. However, I find no "plugins" entry > in any of the PyMOL menus. I think that you need to rename the application bundle to "PyMOLX11Hybrid" in order to use plugins. > Am I blind or daft? But the question I'd > really like to have answered is how do I get abps to work. I would suggest 1) register APBS here http://agave.wustl.edu/apbs/download/ 2) Install fink ( http://finkproject.org/ ) and then use it to install apbs (e.g. by typing "fink install apbs" on the command line). hope that helps, -michael > > I'm using educational MacPyMOL, which "integrates and extends > Open-Source PyMOL 1.0r1". > > Thanks. > > > Andreas > > - > SF.Net email is sponsored by: > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner
[PyMOL] apbs plugin for macpymol
Hey all, I would like to use apbs from within PyMOL. I have downloaded and installed the latest version of apbs, and apbs_tools.py exists in $PYMOL_PATH/modules/pmg_tk/startup/. However, I find no "plugins" entry in any of the PyMOL menus. Am I blind or daft? But the question I'd really like to have answered is how do I get abps to work. I'm using educational MacPyMOL, which "integrates and extends Open-Source PyMOL 1.0r1". Thanks. Andreas
