Cool! It works! (http://farm8.staticflickr.com/7241/7203500026_8c3755d704_s.jpg: water at the picture do not fill the box along the z direction - that is very bad)
> > On Tue, May 15, 2012 at 6:31 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> Hi Boris, >> >> run lattice.py >> create copy1,all >> shift 1,0,0,copy1 >> create copy2, copy1 >> shift 1,0,0,copy2 >> >> As a side note, don't trust your eyes too much when estimating >> homogeneity. Humans are strongly inclined to see patterns, even if >> they're not there. You 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 <kheyfbo...@gmail.com> wrote: >>> Thanks to Tsjerk and Thomas >>> >>> supercell.py almost fits to my needs: is there a way I can replicate >>> the cell to look exactly the same - I don't want to change the >>> coloring? I tried to call it with >>> supercell 2,1,1, color=None >>> but it doesn't help. >>> >>> SuperSymPlugin12.py: can't make cctbx work: Oops! SuperSym requires >>> cctbx and numeric python to function. Please install these. Error: >>> unable to initialize plugin 'SuperSymPlugin12'. >>> >>> lattice.py: that shift the structure. I want to display some more cells of >>> it. >>> >>> With great respect, >>> Boris. >>> >>> P.S. I have a cell - I'd like to see if its homogeneous. For that I >>> need to put several cells in row - along x,y and z directions. >>> >>> On Tue, May 15, 2012 at 12:20 AM, Tsjerk Wassenaar <tsje...@gmail.com> >>> wrote: >>>> Hi Boris, >>>> >>>> PBC have not yet found their way to the main pymol code. What kind of stuff >>>> do you need? lattice.py is quite convenient for shifting. For (a)symmetry >>>> mates, you can use the scripts suggested by Thomas. If you need something >>>> else, pbc operations are not very hard to script. >>>> >>>> Cheers, >>>> >>>> Tsjerk >>>> >>>> On May 14, 2012 6:08 PM, "Thomas Holder" <spel...@users.sourceforge.net> >>>> wrote: >>>> >>>> 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/Symexp >>>> >>>> Hope that helps. >>>> >>>> Cheers, >>>> Thomas >>>> >>>> On 05/14/2012 05:04 PM, Boris Kheyfets wrote: > Hello PyMOL users! > > I >>>> was >>>> wondering if there's a... >>>> >>>> Thomas Holder >>>> MPI for Developmental Biology >>>> Spemannstr. 35 >>>> D-72076 Tübingen >>>> >>>> ------------------------------------------------------------------------------ >>>> Live Security Virtua... >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
