[PyMOL] Bind reset to a key?

Hello PyMOL users, I need to bind reset to a key. I tried both PyMOL API way: cmd.set_key('ALT-r', cmd.reset()) and PyMOL commad way: cmd.set_key('ALT-r', cmd.do("reset") But it doesn't work. I bind various things to keys, so I'm certain of the procedure. How could I bind reset to a key?

[PyMOL] conect records?

Hello PyMOL users, I study system which has 160919 residues, and 217021 atoms (it is initially a gromacs' gro file). Is there a way I can display conections correctly in PyMOL? -- With great respect, Boris. -- Precog is a

Re: [PyMOL] How do I get current selection name from python?

abled). > > active_selections = cmd.get_names('selections', 1) > > Hope that helps. > > Cheers, > Thomas > > On Jan 22, 2013, at 2:08 PM, Boris Kheyfets wrote: > > I want to save current selection as a uniquetly-named pdb file. So I > need tempfile of

[PyMOL] How do I get current selection name from python?

I want to save current selection as a uniquetly-named pdb file. So I need tempfile of python. So I write def, and I want it have current selection as default one (not the '(all)'). How do I do that? I think it will be somewhere under cmd.get_session() I read the sources, but couldn't find a sin

Re: [PyMOL] Custom menus and shortcuts?

If you need a global variable, use pymol.stored > Thank You Thomas -- that solves it. Boris. On Tue, Oct 23, 2012 at 9:28 PM, Boris Kheyfets wrote: > Found a solution. > > Basically it is to add > > pmg_tk/startup/newmenu.py > > file with the following content: > >

Re: [PyMOL] Custom menus and shortcuts?

"/home/boris/.pymolrc.py", line 67, in bk_toggles_W if cmd.get("bk_toggles_W"): File "/home/boris/.local/lib/python2.7/site-packages/pymol/setting.py", line 1300, in get raise QuietException QuietException: How can I add the setting to pymol? -- Boris.

[PyMOL] Custom menus and shortcuts?

Hello PyMOL users, Menus = Is there a way I can add custom menu in PyMOL? Ideally I'd like to be able to call both * pml scripts, as well as * full python pymol scrpts Shortcuts = Similarly -- is there a way I can bind exectution of given * pml script, or * full python pymol scri

[PyMOL] Label on top of molecules?

Hello PyMOL users, When I print atom names with label all, name the labels are often behind the spheres (I use balls and sticks representation). I tried moving labels around, but my system is very dence -- and labels generally get under one or another sphere. Is there a way I can print labels

Re: [PyMOL] Can't compile latest svn

acker/?func=detail&aid=3523770&group_id=4546&atid=104546 > > For the moment is not assigned. > > > > Marius > > > > On Mon, May 14, 2012 at 10:22 AM, Boris Kheyfets > wrote: > >> I use PyMOL 1.4.1 which I have compiled myself. Now I'd like to swit

Re: [PyMOL] Clear cached data?

th late on this, but have you tried: > > set defer_builds_mode, 5 > > before loading your trajectory? Setting that value to 3 also helps. > > Cheers, > > -- Jason > > On Thu, Jun 7, 2012 at 12:10 PM, Boris Kheyfets > wrote: > > Hello PyMOL users > > > &g

[PyMOL] Clear cached data?

Hello PyMOL users I'm loading a trajectory file, and when I view it - PyMOL takes a lot of memory. Is there a way I can decrease its amount, or pause a movie and empty the cached frames? I tried to put set cache_frames=0 in .pymolrc, and pause a movie and issue mclean. None helps. With great re

Re: [PyMOL] Periodic boundary conditions?

probably want to calculate densities on a grid >> and get some statistics on mean density and standard deviation. >> >> Cheers, >> >> Tsjerk >> >> On Tue, May 15, 2012 at 4:10 PM, Boris Kheyfets wrote: >>> Thanks to Tsjerk and Thomas >>&g

Re: [PyMOL] Periodic boundary conditions?

Hi Boris, > > if you want to visualize neighboring cells, have a look at one of these > script from the PyMOLWiki: > http://pymolwiki.org/index.php/Supercell > http://pymolwiki.org/index.php/SuperSym > > Or for symmetry mates within a given radius: > http://pymolwiki.org/index.php

Re: [PyMOL] Can I add some path to 'run'?

7;]: >        full = os.path.join(p, filename) >        if os.path.exists(full): >            cmd.do('run ' + full) >            return >    print ' Error: no such file' > cmd.extend('run2', run2) > python end > > Cheers, >  Thomas > > > On 0

Re: [PyMOL] Can I add some path to 'run'?

print sys.path > > There you can see where pymol is looking. > > Or you can this to your .pymolrc in your home folder: > > import sys > sys.path.append("/Path/to/your/Pymol-script/modules") > > Troels Emtekær Linnet > Ved kløvermarken 9, 1.th > 2300 Københa

[PyMOL] Can I add some path to 'run'?

Is there a way I can add a path to 'run' - so not to type the full path to the script when I run it: run /path/to/script.py -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security

[PyMOL] Periodic boundary conditions?

Hello PyMOL users! I was wondering if there's a way to enable periodic boundary conditions in PyMOL? I found a script called lattice.py in the mail archive, but the message is 3 years old - so I thought may there have appeared a built-in solution? Search on pymolwiki reveals nothing. With great

[PyMOL] Can't compile latest svn

I use PyMOL 1.4.1 which I have compiled myself. Now I'd like to switch to the latest version, so I checked out the latest svn, have enabled VMD plugins (and have also increased the fonts). I get the following error during compilation: contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In fu

[PyMOL] PyMOL console font size?

Is there a way to enlarge python's console font size in PyMOL? I've posted this question at stackoverflow. Then it helped me to replace in file /usr/share/pyshared/pmg_tk/PMGApp.py def initializeTk_unix(self):