Re: [ccp4bb] how to convert matrix to angle

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

Previous message:
Subject: Re: how to convert matrix to angle
From: Edward Berry eaberry {- at -} LBL {- dot -} GOV
Date: 2007-07-07

Next message:
Subject: Re: how to convert matrix to angle
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2007-07-07

Subject: Re: how to convert matrix to angle
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-07-07

My understanding of it is the following:

If there are two or more multi-domain proteins of similar structure/function, etc., and if they have a different orientation of a particular domain, then when you superimpose the two structures, they will not superimpose completely because of the domain that is juxtaposed differently in the two proteins with respect to the rest of the protein. The 'angle between domains' would then be the angle through which that domain2 must be rotated to align it with domain1.

This angle would not result in a complete definition of the geometrical transformation required to superimpose the two domains, but it will give a kind of physical/tangible idea of the the relative domain swing between the two proteins.

For example, if the Reverse Transcriptases from mouse and human are superimposed (overall similar protein size, 5 domains: Fingers, Palm, Thumb, Connection and RnaseH), the fingers and palm domains align quite nicely, but there is a swing angle of approx. 70 degrees or so, between the connection domains from the two proteins.

Thanks,
Debanu.

-----Original Message-----
From: Bernhard Rupp [mailto:bernhardrupp@sbcglobal.net]
Sent: Sat 7/7/2007 8:21 PM
To: Das, Debanu; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] how to convert matrix to angle

Not that I want to open a can of worms here...
but could someone explain what is meant
with 'angle between domains'?

Thx, br

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Das,
Debanu
Sent: Saturday, July 07, 2007 7:51 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] how to convert matrix to angle

Hi,
You can also use LSQKAB in CCP4 to get the angle between two similar
domains.

-Debanu.

-----Original Message-----
From: CCP4 bulletin board on behalf of Kay Diederichs
Sent: Sat 7/7/2007 7:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] how to convert matrix to angle

Jiamu Du schrieb:
> Dear all:
> I want to calculate the rotation angle between two similar domains. By
> using Coot, I can superposr the two domain and get the rotation matrix.
> But how to convert this matrix to an angle. Is there any program can
> calculate this ?
> Thanks.
>
Jiamu Du,

If you have the rotation matrix
a11 a12 a13
a21 a22 a23
a31 a32 a33

then

(a11 + a22 + a33 - 1) / 2

is the cosine of the angle you're looking for.

HTH,

Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

CCP4bb navigation

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

Previous message:
Subject: Re: how to convert matrix to angle
From: Edward Berry eaberry {- at -} LBL {- dot -} GOV
Date: 2007-07-07

Next message:
Subject: Re: how to convert matrix to angle
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2007-07-07