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From: Jason V. <jas...@sc...> - 2010-04-09 17:35:38
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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) Jas...@sc...
(o) +1 (603) 374-7120
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From: Maia C. <ch...@ua...> - 2010-04-22 20:25:58
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Hi Jason, 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. 2. Which plugin allows me to move one structure relative to another. (I want to do manual docking of one structure into another). 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 > > |
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From: Jason V. <jas...@sc...> - 2010-04-22 21:16:49
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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) Jas...@sc... (o) +1 (603) 374-7120 |
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From: Robert C. <rob...@qu...> - 2010-04-23 01:55:16
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Hi Maia, Just to add to what Jason said: On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees <jas...@sc...> wrote: > > 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: In case it isn't obvious to you, you can switch between "viewing" mode and "editing" mode simply by left clicking in the bottom-right region of the main PyMOL window where the mouse button functions are described. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |
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From: Maia C. <ch...@ua...> - 2010-04-23 03:44:01
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Thank, Robert, Jason. Finally I figured this out with your help. Maia Robert Campbell wrote: > Hi Maia, > > Just to add to what Jason said: > > On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees > <jas...@sc...> wrote: > > >>> 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: >> > > In case it isn't obvious to you, you can switch between "viewing" mode and > "editing" mode simply by left clicking in the bottom-right region of the main > PyMOL window where the mouse button functions are described. > > Cheers, > Rob > > |
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From: Maia C. <ch...@ua...> - 2010-04-23 19:02:13
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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 >>> >>> >>> > > > > |
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From: Jason V. <jas...@sc...> - 2010-04-23 19:21:35
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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...@ua...> 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) Jas...@sc... (o) +1 (603) 374-7120 |
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