Re: [ccp4bb] Rotation axis

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: D-Amino acids to L-Amino acids
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-08-03

Next message:
Subject: Re: sequential renumbering of a messed up pdb file
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-08-04

Subject: Re: Rotation axis
From: "Borhani, David" David {- dot -} Borhani {- at -} DESHAWRESEARCH {- dot -} COM
Date: 2008-08-04

Calc-ax (which I mentioned in my post a few days ago) calculates the
position of the rotation axis such that translation perpendicular to
that axis is zero; all remaining translation (if any) is parallel to the
axis.

Dave

David Borhani, Ph.D.
D. E. Shaw Research, LLC
120 West Forty-Fifth Street, 39th Floor
New York, NY 10036
David.Borhani@DEShawResearch.com
212-478-0698
http://www.deshawresearch.com

> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
> Behalf Of Winn, MD (Martyn)
> Sent: Sunday, August 03, 2008 10:39 AM
> To: CCP4BB@JISCMAIL.AC.UK
> 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
> rotation for polar angles from the R which will be quite
> different from t.
> You should be able to translate the rotation axis (change the
> origin of
> the coordinate system) to get a new transformation x' = R'x + t' which
> might be better for visualisation. If Phil's last sentence is
> right, you
> should be able to arrange it so that t' is parallel to the
> rotation axis
> of R'
>
> No, I don't know how to do this off the top of my head, but it sounds
> very similar to the transformations done in the Schomaker and
> Trueblood
> TLS paper.
>
> Or maybe this is over-complicating things ;-)
>
> Martyn
>
> -----Original Message-----
> From: CCP4 bulletin board on behalf of
> Herman.Schreuder@SANOFI-AVENTIS.COM
> 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 from Groningen and
> make a jiffy
> to do these conversions. It is a small fortran program and
> does not need
> any additional libraries or subroutines. The program will take a
> rotation matrix and translation vector and print all kind of rotation
> angles and also the component of the translation vector
> parallel to the
> rotation axis, which is the number you want. All other
> components of the
> translation vector can be made zero by choosing the right position of
> the rotation axis.
>
> Best regards,
> Herman Schreuder
>
>
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Phil Evans
> Sent: Tuesday, July 29, 2008 10:11 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Rotation axis
>
> 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 translation along that axis
>
> I'm sure I've done this before ...
>
> thanks
> Phil
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: D-Amino acids to L-Amino acids
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-08-03

Next message:
Subject: Re: sequential renumbering of a messed up pdb file
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-08-04