Re: Bond Angles and Hybridization

From: Uncle Al (UncleAl0_at_hate.spam.net)
Date: 01/01/05 

Date: Sat, 01 Jan 2005 12:17:41 -0800

budullewraagh wrote:
>
> thanks for your input. problem is that out of all those links all i
> found was the basic structure involving the structure without bond
> angles and lengths and without hybridization
>
> i cant find those anywhere

Why would they tabulate any of it? All the information is directly
and indirectly inside the structure files. Let's try this again,

   1) You download the *.mcm structure file for DNA, or any structure
file for DNA. The ID and 3-space coordinates of every atom within the
structure are provided. That is what a structure file is, plus
frou-frou and idiosyncratic this and that depending on format.

   2) You have chemical modeling software in your PC. HyperChem-Lite
is excellent and inexpensive and ships with a small snippet of DNA as
an example. Purchase, borrow, steal and install or use what you want.

   3) If and as necessary you use WinBabel or Babel or whatever to
convert the *.mcm file or any structure file of whatever format to an
acceptable format for your chemistry software. Or use native file(s)
in your modeling software provided by the vendor as examples.

   4) THE SOFTWARE CALCULATES DISTANCES, ANGLES, AND DIHEDERAL ANGLES
as requested - and with a legitimate number of significant figures.

If you are a glutton for punishment you can look into any structure
file with a wordprocessor, grab the 3-space coordinates, and do the
trig yourself. Structure data in HyperChem-Lite using the Selection
tool takes about 0.03 seconds/request. You could push each through a
calculator in under a minute once you get the patter down. You do NOT
want to do it by hand.

I have a battery of custom-written software to manipulate *.hin files
from HyperChem for input into a graph theory connectivity analysis.
Even with software custom written for me the process is a royal pain
in the ass for manipulating 20 files. Doing it by hand requires days
vs. about 2 hours. I've done it by hand. Doing it by hand sucks. A
programmer only has to get it right once. 

-- 
Uncle Al
http://www.mazepath.com/uncleal/
 (Toxic URL! Unsafe for children and most mammals)
http://www.mazepath.com/uncleal/qz.pdf

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