Re: [PyMOL] Periodic boundary conditions?

[Boris K. <khe...@gm...>]

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 <ts...@gm...> 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 <khe...@gm...> 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 <ts...@gm...> 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" <sp...@us...>
>>>> 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