Subject: RE: A little geometrical problem

From: "Shobe, Dave" <[email-masked]>
Date: Thu, 28 Feb 2002 13:22:49 -0500

I don't have a program to recommend, but if you're building your own here is
an idea.  The problem is related to converting from spherical to Cartesian
coordinates.  With CA as the origin and the C-CA bond along the (negative) z
axis, we have in terms of *local* Cartesian coordinates (xloc, yloc, zloc):

zloc = r * cos(180° - alpha)
yloc = r * sin(180° - alpha) cos(beta)
xloc = r * sin(180° - alpha) sin(beta)

with r, alpha, beta equaling the CA-CB distance, the C-CA-CB bond angle, and
the N-C-CA-CB torsion angle.  

Now that you have (xloc, yloc, zloc) you need to convert them into the
coordinates being used for the molecule.  This is a Cartesian to Cartesian
conversion so it's just a matter of finding the right matrix to multiply the
vector by.

--David Shobe
Süd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  [email-masked]

Don't bother flaming me: I'm behind a firewall.

-----Original Message-----
From: Logean Antoine [mailto:[email-masked]]
Sent: Thursday, February 28, 2002 11:44 AM
To: [email-masked]
Subject: CCL:A little geometrical problem

A little geometrical problem :

Taken a residue in a PDB file, how can I calculate the Cartesian
coordinates of CB when I know the coordinates of N, CA and C, the angle
N-CA-CB, C-CA-CB and the bond length CA-CB ? 

It seems to be trivial but I am unable to find a solution !

I am sure that somebody can help me.

In advance thank you

LOGEAN Antoine                              

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