No! the "divide by 2" part is for a 2-fold rotation- not 8*.
Sorry, and hope the O.P. didn't waste any time trying to implement this.
Edward A. Berry wrote:
> Would this work?
> Take the rot-trans operator from superpose or lsqman and express
> the rotation matrix as polar coordinates of rotation axis (and angle about it).
> Get the rotation axis as direction cosines, which will be a vector along
> the rotation axis of the matrix. Now take the component of the
> translation vector along that rotation axis, and subtract from the
> translation vector, to get the component of the translation vector
> which is orthogonal to rotation axis. Divide that by two and,
> as a vector from the origin, it defines a point on the
> rotation axis. Add any multiple of the rotation axis vector to
> this and it gives another point on the rotation axis.
> Test these points by operating on them with the orig
> rot-trans operator, they should just move along the rotation axis
> by the screw component of the rotation
>
> WENHE ZHONG wrote:
>> Dear members,
>>
>> I would like to have your ideas if there is any way to identify a rotation centre of
>> domain in two different states using CCP4 or other program.
>>
>> The situation is: the domain of the protein will rotate between two different states
>> (depending on substrate binding) around 8 degree, and it is (nearly) clearly that the
>> domain is rotated around a rotation centrel. So the question is how to identify this
>> "rotation centre" in this 3D model? The ideal is to identify a region of residues in the
>> domain which are most closed to the rotation centre.
>>
>> The tool I am using right now is the "superpose" tool in CCP4 package. The output which I
>> think mightbe uesful is:
>>
>> CENTROID OF "WORKING" MOLECULE : 157.812 152.396 -70.778
>> CENTROID OF "WORKING" MOLECULE :(fractional) 157.812 152.396 -70.778
>> CENTROID OF "REFERENCE" MOLECULE: 157.251 151.877 -70.874
>> CENTROID OF "REFERENCE" MOLECULE:(fractional) 157.251 151.877 -70.874
>> Distance between CENTROIDS : 0.770
>> Direction cosines of vector between CENTROIDS: 0.729 0.674 0.124
>>
>> I would say the “CENTROID" it mentioned above, such as (157.251 151.877 -70.874), is
>> possibly near to the "rotation centre". I would like to have your opinion though. Thank
>> you.
>>
>> King regards,
>> Wenhe
>
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