Quanta, multisubunit enzyme setup. Help

[Bob Funchess]

Gregory M. F. Watson wrote:
> 
> I have
> the pdb coordinate file (1RSC) for RubisCO.  This file includes the
> coordinates for a large (L) and a small (S) subunit.  Various
> transformation matrices are included in the pdb ...
> My understanding is that Quanta can
> handle these transformations and generate the desired multimeric
> structures ...

One reason you can't find anything in the QUANTA documentation about
this is because QUANTA can't do it directly unless the other subunit can
be generated by a crystallographic symmetry operation (based on my own
experience, I'd say this is very seldom the case with PDB files; they're
almost always related by noncrystallographic symmetry).  You also have
to have the crystal modelling option, which is not part of the basic
QUANTA package.

However, it's a common thing to want to do, so I wrote a little CHARMm
script a while back to handle it.  You set a few CHARMm variables to
tell it what the MATRIX records say, and then stream the script to
transform the coordinates.  It doesn't actually generate a copy, but you
can write out the new coordinates and then read both molecules into
QUANTA to make the dimer (or more-mer, but then you need to run the
script once for each transformation matrix).

You can get the script from MSI's web site; look at
http://www.msi.com/support/ssb/9412.html in the "Scientific Support
Solutions" section, or by anonymous FTP at
ftp://ftp.msi.com/pub/vendor/biosym/outgoing/xform.str.Z.

    Regards,
              Bob Funchess

-- 
Dr. Robert B. Funchess                    bobf at msi.com
Senior Scientist, Scientific Support      Voice (619) 458-9990 x738
Molecular Simulations Inc.                FAX   (619) 458-0431
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