Maia, Looks like the Ubuntu package is older. Bumps just shows the vdw overlaps, you can work without it.
-- Jason On Fri, Apr 23, 2010 at 3:02 PM, Maia Cherney <ch...@ualberta.ca> wrote: > Hi Jason, > > 1. I am wondering if I have the latest version of pymol. I got it via ubuntu > package. How do I update the pymol version? > > 2. I was trying to do some procedures from the Warren's letter: > > Builder use: > > (1) activate the builder by clicking on the "Builder" button on the > upper window > > (2) click the "Bumps" checkbox > > (3) click the "Sculpt" button > > > When I click on the "Builder" button on the upper window, I do not have the > "Bumps" checkbox and the "Sculpt" button. > I have the autopick, the autozoom and the valence checkboxes. > > That is why I am wondering if I have the same version of pymol. > > Could you also give me some explanation what are polymer or organic, byres > (organic expand 4), and flag fix, not organic > > > Maia > > > Jason Vertrees wrote: >> >> Maia, >> >> >>> >>> 1. How can I undo a plugin. By mistake I tried to plugin a program using >>> a >>> wrong file and now I get an error message every time I open pymol. >>> >> >> Newer versions of PyMOL have a menu option to remove plugins: Plugin > >> Manage Plugins > Remove. You can also remove a plugin by simply >> removing the plugin file. PyMOL stores plugins in the Python >> distribution's "site-packages/pmg_tk/startup" directory. My Mac OS X >> Fink build has them here: >> /sw/lib/python2.5/site-packages/pmg_tk/startup/ >> for example. >> >> If you're on Mac or Linux you can try >> locate pmg_tk/startup >> or >> find / -name yourPlugin.py >> for hints as to the plugin's installed location. >> >> >> >>> >>> 2. Which plugin allows me to move one structure relative to another. (I >>> want >>> to do manual docking of one structure into another). >>> >> >> You don't need a plugin to move objects. Just use SHIFT-middle-mouse >> button drag, while in editing mode. If you're starting from one >> object (eg. protein and ligand come from one file) then split them up: >> >> # example >> fetch 1oky, async=0 >> >> # the protein and ligand are one object; now make them two >> extract myLigand, org >> >> Now you can move the myLigand object independently of other objects. >> >> Good luck, >> >> -- Jason >> >> >>> >>> Maia >>> >>> Jason Vertrees wrote: >>> >>>> >>>> PyMOLers, >>>> >>>> Due to the popularity of using PyMOL as a portal to other programs and >>>> integrating programs with PyMOL, we are developing a new Plugin >>>> Architecture for PyMOL. We have dedicated a page on the PyMOLWiki >>>> http://www.pymolwiki.org/index.php/PluginArchitecture >>>> for this discussion. >>>> >>>> If you have a desire to be involved in how the architecture is >>>> developed please add your contact information to that page (or email, >>>> personally). Even if you don't care much about helping out, you might >>>> want to stop by and let us know which plugin systems you like and >>>> which you don't. >>>> >>>> Thanks, >>>> >>>> -- Jason >>>> >>>> >>>> >> >> >> >> > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
