Re: [PyMOL] Periodic boundary conditions?

[Tsjerk W. <ts...@gm...>]

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