[cctbxbb] cctbx and symmetry: source code

prasun kumar prasun30 at gmail.com
Tue Mar 19 14:25:55 PDT 2013


Dear Luc and Graeme

I have followed, what you all have suggested. I have downloaded and
installed on my PC which is having DEBIAN OS.
Everything is working fine.

Now I am searching for the code which can give me the filled unit cell or
matrix (3X3X3) of unit cell.
I have checked the codes available for the pymol and cctbx working together
(http://pymolwiki.org/index.php/Supercell) or (
http://pymolwiki.org/index.php/SuperSym).
It will be better, if I can get the code which does not use Pymol.
Especially I am concentrating on SuperSym, but when I ran using command
line, it gives segmentation fault (I think I need to remove everything
which is for displaying in Pymol window, not sure though).

Thanx in advance
Prasun Kumar

PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success


On Wed, Mar 20, 2013 at 2:44 AM, Luc Bourhis <luc_j_bourhis at mac.com> wrote:

> Dear Prasun,
>
> My main program is in PERL and I am calling OPENBABEL by installing it on
> my PC and using the system command on UNIX. e.g. system("babel -i pdb input
> file -o cif output file");
>
> Same thing I wanted for cctbx. Since it does alot of other things along
> with unitcell generation, I wanted to have the relevant part of cctbx.
>
> I wanted to make binary of that part, so that I can call it from the main
> program.
>
>
> I got it this time, sorry for being rather thick on that one!
>
> The easiest is definitively to follow Graeme's excellent advice.
>
> Let me spell it out with more details:
>
> 1. Grab a distro of the cctbx that works on the machine you target
>    at http://cci.lbl.gov/cctbx_build and install it.
>    Actually, since your main program is written in Perl, it would be
> rather
>    easy to figure out which OS it is running on, and then to deduce
>    which installer to download, and finally to install the cctbx
> on-the-fly
>    as the program launches for the first time. That way the same Perl code
>    would run on a wide range of Linuxes and versions of MacOS, and even
>    on Windows if you bundle Perl with your program (you would not need
>    to bundle Python as the cctbx installer does that for you on Windows).
>
> 2. system "/path/to/cctbx_build/bin/cctbx.python", "script_of_yours.py";
>    * cctbx_build is one of the directory created by the cctbx installer;
>      again rather easy to have your Perl program find it if it installed
>      the cctbx in the first place!
>    * script_of_yours.py would be a Python script you would devise
>      to generate unit cells: you would be much more productive writing
> that
>      in Python than targeting the cctbx C++ interface, as Graeme and I
> have
>      already pointed out.
>
> HtH,
>
> Luc
>
>
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