On 10/15/06, Margaret Luk-Paszyc <mags@pharm.stonybrook.edu> wrote:
Hello --

Can someone please advise me?
I'm a new user of PyMol trying to get the kabsch alignment
script to work. I only installed the main pymol installer
(v 0.99r6), and I have copied the kabsch.py script as the
wiki said.  However, I can't find this Numeric.py you are
referring to in the wiki... The wiki infers that the
Numeric.py script is a native part of the installer, but I
don't seem to have it in my folders anywhere.  Obviously,
kabsch doesn't want to run either.  I am running PyMol
v0.99r6 on RHE4 (intel32).

I'm a bit of a newbie when it comes to the more advanced
tools with PyMol, so maybe I forget to install something?
Does it require the APBS plugin to work?

Any help would be appreciated.

Thanks!

Sincerely yours,
Maggie L.-P.
SUNY Stony Brook


Hi Maggie,

Numeric.py is usually located (on Windows platforms) under  "C:\Program Files\DeLano Scientific\PyMOL\modules\Numeric"

If you see the wiki, this is also listed under the "Notes" section of the Kabsch wikipage.

The changes you need to make to Numeric.py are also listed in the same section.

Here is a direct link: http://pymolwiki.org/index.php/Kabsch

Best,
Shiven