Re: [ccp4bb] Calculation of angle between two helix of different subunits
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 Accurate description of helices, including curvature and bending, and determination of interhelical angles are essential for analysis of the three-dimensional fold and functionally important conformational changes in helical proteins. Here, a new computational method is presented that allows determination of angles between any helical stretches, the radius of curvature of curved helices, bending angle of bent helices, as well as symmetry relations within the protein molecule, using main chain atom coordinates. The method has been applied to describe changes in interhelical angles in calmodulin upon interaction with a target peptide, which reveals the conformational changes at a higher precision. Because subtle changes in helix-to- helix packing and interhelical angles often underlie significant functional transitions in proteins, this approach can serve as a useful tool for characterization of such conformational changes at an exceedingly high accuracy and thus provide detailed insight into the structure-function relationship of proteins. PMID: 18602867 [PubMed - indexed for MEDLINE] On Apr 15, 2009, at 9:38 AM, peter hudson wrote: 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 different subunit in different orientation. Suggestiona would be appreciated. Thnaks in advance Peter Young-Tae Lee, Ph. D. Research Associate David Goodin lab Dept. of Molecular Biology The Scripps Research Institute
Re: [ccp4bb] Calculation of angle between two helix of different subunits
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 angle between two 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 of different subunits 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 different subunit in different orientation. Suggestiona would be appreciated. Thnaks in advance Peter
Re: [ccp4bb] Calculation of angle between two helix of different subunits
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 is attempting to define said vectors for helices of different subunit[s] in different orientation[s]. James
Re: [ccp4bb] Calculation of angle between two helix of different subunits
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 vectors in the first place, especially when one is attempting to define said vectors for helices of different subunit[s] in different orientation[s]. On second thought it's only slightly less trivial than the angle calculation: (1) decide the C-alphas of the helix (e.g. DSSP) (2) do PCA on their coordinates (3) the first principle component defines the direction of the helix.
Re: [ccp4bb] Calculation of angle between two helix of different subunits
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 stuff up into a distributable program Phil On 16 Apr 2009, at 10:46, James Stroud wrote: 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 vectors in the first place, especially when one is attempting to define said vectors for helices of different subunit[s] in different orientation[s]. On second thought it's only slightly less trivial than the angle calculation: (1) decide the C-alphas of the helix (e.g. DSSP) (2) do PCA on their coordinates (3) the first principle component defines the direction of the helix.
Re: [ccp4bb] Calculation of angle between two helix of different subunits
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 product' or something similar). Cheers, Charlie -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310, 35 Stirling Highway Crawley WA 6009, Australia
Re: [ccp4bb] Calculation of angle between two helix of different subunits
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 modern ;-)
On Thu, Apr 16, 2009 at 07:21:45PM +0800, Charlie Bond wrote:
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 product' or
something similar).
Cheers,
Charlie
--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310, 35 Stirling Highway
Crawley WA 6009, Australia
--
***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--
* BUSTER Development Group (http://www.globalphasing.com)
***
#!/bin/sh
version=Time-stamp: 2009-04-16 12:47:59 vonrhein
#
# Copyright 2008 by Global Phasing Limited
#
# All rights reserved.
#
# Author(2008) Clemens Vonrhein vonrh...@globalphasing.com
#
# Contact buster-deve...@globalphasing.com
#
#--
# BEGIN OF USER INPUT
#--
#--
# END OF USER INPUT
#--
echo 2
echo
2
echo 2
echo Copyright (C) 2008 by Global Phasing Limited 2
echo 2
echoAll rights reserved. 2
echo 2
echo
2
echo 2
echo Contact: buster-deve...@globalphasing.com 2
echo 2
ShortVersion=`echo $version | cut -f2- -d':' | sed s/
[a-z0-9][a-z0-9][a-z0-9]*//g`
echo Program: `basename $0` version ${ShortVersion} 2
echo 2
echo
2
echo 2
#--
# BEGIN OF SCRIPT
#--
usage () {
echo
echo USAGE: $0 Ax Ay Az Bx By Bz
echo
echo Ax Ay Az : XYZ coordinates of vector A
echo
echo Bx By Bz : XYZ coordinates of vector B
echo
}
[ $# -ne 6 ] usage exit 1
echo $@ | awk 'BEGIN{
PI = 4*atan2(1,1)
DTOR = PI/180
RTOD = 180/PI
}
function Sin(x){ return sin(x*DTOR) }
function Cos(x){ return cos(x*DTOR) }
function Tan(x){ return Sin(x)/Cos(x) }
function ASin(x) { return atan2(x,sqrt(1 - x * x))*RTOD }
function ACos(x) { return atan2(sqrt(1 - x * x),x)*RTOD }
function ATan2(y,x){ return atan2(y,x)*RTOD }
{
ax=$1;ay=$2;az=$3
l=sqrt(ax*ax+ay*ay+az*az)
x1=ax/l;y1=ay/l;z1=az/l
bx=$4;by=$5;bz=$6
l=sqrt(bx*bx+by*by+bz*bz)
x2=bx/l;y2=by/l;z2=bz/l
dot=x1*x2+y1*y2+z1*z2
ang=ACos(dot)
printf( %15.5f%15.5f\n,ax,bx)
printf( angle between %15.5f and %15.5f = %15.5f degree\n,ay,by,ang)
printf( %15.5f%15.5f\n,az,bz)
printf(\n)
}'
#--
# END OF SCRIPT
#--
Re: [ccp4bb] Calculation of angle between two helix of different subunits
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 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 modern ;-) On Thu, Apr 16, 2009 at 07:21:45PM +0800, Charlie Bond wrote: 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 product' or something similar). Cheers, Charlie -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310,? 35 Stirling Highway Crawley WA 6009, Australia -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Calculation of angle between two helix of different subunits
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 angle between two vectors! Honestly, Pet I don't think many job interviews for crystallographers these days include a question on how to calculate the angle between two vectors. Sure a background in math, physics, or computation is a valuable asset, but it is no longer essential as it was 2-3 decades ago. Crystallographers may have dumbed down in the math department but they have smartened up in other areas. Bart
Re: [ccp4bb] Calculation of angle between two helix of different subunits
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. Won't get you no job, though. Cheers, BR
[ccp4bb] Calculation of angle between two helix of different subunits
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 different subunit in different orientation. Suggestiona would be appreciated. Thnaks in advance Peter
