Check out also this paper.
---
Comput Biol Chem. 2008 Oct;32(5):370-4. Epub 2008 Jul 7.
Determination of helix orientations in proteins.
Tatulian SA.
Biomolecular Science Center, University of Central Florida, 12722
Research Parkway, Orlando, FL 32826, USA. statu...@mail.ucf.edu
vectors!
Honestly,
Petr
From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of peter hudson
[peter.hudson.pe...@gmail.com]
Sent: Wednesday, April 15, 2009 6:38 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Calculation of angle between two helix
On Apr 16, 2009, at 1:18 AM, Leiman Petr wrote:
I am not sure if it possible to understand _anything_ in
crystallography if it is not clear how to calculate an angle between
two vectors!
More difficult is deciding exactly how to define said vectors in the
first place, especially when one
On Apr 16, 2009, at 2:29 AM, James Stroud wrote:
On Apr 16, 2009, at 1:18 AM, Leiman Petr wrote:
I am not sure if it possible to understand _anything_ in
crystallography if it is not clear how to calculate an angle
between two vectors!
More difficult is deciding exactly how to define said
I suspect that PCA will only give you a good estimate of the helix
direction with a long helix. I've done it (less elegantly perhaps) by
superimposing an ideal helix which has its axis along z, then
extracting angles from the superposition matrix. However I'm afraid
I've not packaged this
I've previously done it by using the centroids of the Calphas from the
first 4 residues and last 4 residues of the helix to define the vector
(7 residues might be better if the helix is long enough). It seemed to
work well enough by eye.
From then on it is simple vector algebra (google 'dot
Hi,
And if you want a simple and trivial awk script (based on that
google'ing that Charlie described): save attached file in your path,
make it executable and run it e.g. as
% vecang 1.23 3.45 6.78 9.87 7.65 5.43
Cheers
Clemens
PS: sorry it isn't in python/scheme or something similarly
What are you doing?
Write this as an iPhone App! Charge $0.99 and you will be set! :-)
Of course, I will need my $0.02 per App comission for giving the idea out.
Thanks,
Chris
On Thu, 16 Apr 2009, Clemens Vonrhein wrote:
Hi,
And if you want a simple and trivial awk script (based on that
Leiman Petr wrote:
Every other week this question comes up!
This is Geometry 101 or beginner's geometry!!!
http://www.euclideanspace.com/maths/algebra/vectors/angleBetween/index.htm
I am not sure if it possible to understand _anything_ in crystallography if it is not clear how to calculate an
I don't think many job interviews for **crystallographers** these days
include a question on how to calculate the angle between two vectors.
I'd change that to **Structural biologists**. If you call yourself a
bona fide crystallographer, probably a good idea to have the
basic math handy.
Hello all
I am interested to know about any programme which can calculate the angle
between the helices of different subunit not the consecutive helices. I know
about helixang which is a ccp4 supported programme but, i am not sure that
does it calculate the relative angle between the two helix of
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