Dear David,
The following will be of interest:-
*J. Chem. Soc., Faraday Trans.*, 1993, *89*, 2667-2675 (*DOI:
*10.1039/FT9938902667
)
and
Y P Nieh PhD Thesis 1997 available at :- http://ethos.bl.uk/Home.do
[ie just search on his name and the pdf is available.]
All best wishes,
John
On Fri, Dec 2
AC.UK
Subject: [ccp4bb] Rotation
Probably you were wondering what the diffraction patter would look like if you
rotated a lysozyme crystal 360 degrees rather than a fraction of a degree.
Wonder no more.
--
===
All Things Serv
Hi,
I would only suggest using the brute rotation function if you want to use the
"rotate around" option or do something other than a full rotation search,
because the fast search followed by rescoring should give you essentially the
same list of peaks (but faster).
If you want to get a bigger
hi all,
I try to solve the crystal structures of a mult-domain protein with phaser.
I cannot solve the structure by automatic search using domain structure as
the models. I tried to do the rotation search using the fast or brute
rotation function. I defined the rotation search peaks number is 1000
LSQKAB gives something of what you want..
If you fit domain_open to domain_closed after the rest of the structure
is aligned.
you get
the COM of the two domains.
the rotation angles in euler and polar form
I would say the rotation angle was the omega angle and the translation
the difference b
Hi all
I am working with a multidomain protein whcih binds to a ligand. This
protein exist in two different states, a) apo form of the protein is closed
state and b) holo protein is an open state. One of the domain is mobile and
have different conformation compared to its closed conformation. Thi
ALMN can plot the rotation function as a map - although I challenge
anyone to make much sense of it! More or less the same methodology as
MOLREP.
More useful - it lists all peaks generated by the symmetry operators in
Eulerian, and polar angles and gives the direct cosines of the rotation
ax
Hi All,
I want to plot the rotation function that MOLREP uses. I cannot find any
output of rotation function in the logfile or in moIrep.doc. I want to
locate the peaks of the rotation function, that are shortlisted as
solutions, which would help me in understanding the following problem.
My prot
My original posting on this question generated quite a few replies,
for which many thanks.
I found the most useful pointer to the required algorithm was the link
to Mark Gerstein's site given by Ian,
and I have now programmed this in a C++ class using Clipper routines,
which I can make avai
K
> Subject: Re: [ccp4bb] Rotation axis
>
> ROTMAT will also do this. But I am not sure that this is what
> Phil wants?
>
> The superposition transformation includes a translation, so
> there is no
> locus of points that are left unchanged. You can generate an axis of
> rotat
of [EMAIL PROTECTED]
Sent: Tue 7/29/2008 1:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rotation axis
Dear Phil,
Because question keep popping up in the bullitin board about conversion
from a rotation matrix into rotation angles, I decided to take the
relevant subroutines from an old program
implementation (with comments) is in
scitbx/include/scitbx/math/r3_rotation.h
Ralf
- Original Message
From: Phil Evans <[EMAIL PROTECTED]>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, July 29, 2008 1:10:50 AM
Subject: [ccp4bb] Rotation axis
If I've go a superposition transformation (
to:[EMAIL PROTECTED] On
> Behalf Of Ian Tickle
> Sent: Tuesday, July 29, 2008 5:18 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rotation axis
>
> Hi Phil
>
> The rotation axis is the locus of points which the
> transformation leaves
> unmoved, i.e. the eig
be made zero by choosing the right position of
the rotation axis.
Best regards,
Herman Schreuder
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Phil Evans
Sent: Tuesday, July 29, 2008 10:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rotation
Hi Phil
The rotation axis is the locus of points which the transformation leaves
unmoved, i.e. the eigenvector of the transformation matrix which has a
unit eigenvalue. So writing the transformation in homogeneous form for
convenience: x' = Sx you need to solve x' = x, or Sx = x, either
analytica
If I've go a superposition transformation (x' = Rx + t), as it happens
from a superposition in ccp4mg, how do I get the position & direction
of the rotation axis (to draw in a picture)?
I know that any (orthonormal) transformation can be represented as a
rotation about an axis + a screw trans
Ian Tickle schrieb:
<... interesting information about AMORE deleted ...>
Anyway this is all academic now, I always use Phaser which does all this
properly (I have no experience using it for highly ellipsoidal models though).
Cheers
-- Ian
My understanding is that Phaser by default does the
>
> Ian,
>
> I agree with your description, but not quite with your
> conclusion. In the
> original poster's problem one of the cell axes is so short
> that at most a < 20
> Angstrom Patterson outer radius can be used in a
> Patterson-based rotation
> function. This will inevitably lead
The maximum likelihood method used in Phaser doesn't use any cut-off
as it doesn't use the Patterson formulation. It might work better for
such an elongated case
Phil
On 28 Nov 2007, at 17:04, Pietro Roversi wrote:
Dear everyone,
is any of the currently
Ian Tickle schrieb:
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Kay Diederichs
Sent: 02 December 2007 10:07
To: [EMAIL PROTECTED]
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rotation search using the Patterson in
a non-spherical neighbourhood
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Kay Diederichs
> Sent: 02 December 2007 10:07
> To: [EMAIL PROTECTED]
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rotation search using the Patterson in
> a non-spheri
Pietro Roversi schrieb:
Dear everyone,
is any of the currently available
molecular replacement programs capable of accepting a
description of an ellipsoid (rather than the radius of a sphere)
to define the portion of the Patterson around
-- Message d'origine
De: CCP4 bulletin board de la part de Pietro Roversi
Date: mer. 28/11/2007 18:04
À: CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Rotation search using the Patterson in a non-spherical
neighbourhood of the origin
Dear everyone,
is any o
Dear everyone,
is any of the currently available
molecular replacement programs capable of accepting a
description of an ellipsoid (rather than the radius of a sphere)
to define the portion of the Patterson around the origin to be
u
Hello David,
In CCP4mg you can display any arbitrary vector in a variety of display styles
- there is an example in the the online documentation:
http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/vector.html
Liz
On Tuesday 18 September 2007 10:00, David Briggs wrote:
> Good morning ccp4bb-ers!
>
Good morning ccp4bb-ers!
I have two protein-protein complex structures, and the orientation of one of
the components shifts slightly with respect to the other component between
the two structures.
If I run superimpose on the shifting component I get this:
CROWTHER ALPHA BETA GAMMA 12.41607
ALMN will do this ..
It does not have a GUI - Gr
#!/bin/csh -f
#
almn \
hklin /y/people/ccp4/projects/insmon/ins_p1_1,55A-I422cell.mtz \
hklin2 /y/people/jean/Youshang/monomeric/datproc/*mtz <
Hi,
I have two patterson maps created from two observed data sets of similar structures. I
Hi,
I have two patterson maps created from two observed data sets of similar
structures. I want to rotate one map against the other and hence to match them
to get the corresponding rotation function. Does anyone have experience how I
can do that?
Raja
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