Hi,
not certain to understand the question. In chimera, you can create axis
(for example in alpha helix) or directly draw one and do the angle
measurement between differents axis. I imagine that you can create the
"same axis" in both of your monomer and measure the angle between these
axis.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
On 17/11/2016 23:48, Paul Emsley wrote:
> On 18/11/2016 03:57, chemocev marker wrote:
>> Hi All
>>
>> I am interested to measure the symmetry axis of individual sub-unit
>> (chain A & chain B)
>> along with the symmetry axis of the heterdimer (AB). Each chain is
>> also 2 fold axis, and I
>> can measure by removing 1 chain and measure for the other and then
>> combine all the symmetry
>> axis in the 1 PDB file. Is there is a way to do it with out removing
>> the either chain.
>
> I'm not sure that I fully understood the question, but you could try
> Coot's
> superpose_with_atom_selection, where you can specify the residue
> selection for the superposition
>
> e.g.
>
> Calculate -> Scripting -> Python
>
> superpose_with_atom_selection(0, 0, '//A/1-200', '//A/201-400', 1)
>
> will produce output like this:
>
> | 0.9705, -0.0469, -0.2365|
> | 0.2359, 0.3887, 0.8907|
> | 0.05015, -0.9202, 0.3883|
> ( 37.8, -17.18, 13.83)
> Rotation - polar (omega,phi,kappa) 81.2326 -171.0041 68.0547
> Rotation - euler (alpha,beta,gamma) 104.8719 67.1530 -93.1198
> Translation - Angstroms 37.8021 -17.1809 13.8283
> INFO: core rmsd achieved: 0.4517 Angstroems
> number of residues in reference structure: 200
> number of residues in moving structure: 200
> number of residues in aligned sections (reference): 200
> number of residues in aligned sections (moving): 200
> number of aligned residues: 200
>
>
> Paul.
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