Re: [ccp4bb] intrasubunit rotation axis

[Nicolas FOOS]

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.

Re: [ccp4bb] intrasubunit rotation axis

[Paul Emsley]

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.

Re: [ccp4bb] intrasubunit rotation axis

[Eleanor Dodson]

Wont PISA do it? It sorts out the most likely biological unit for you after
applying symmetry operators.
Either submit your coordinates to the EBI PDB server or use the version in
CCP4

Eleanor

On 17 November 2016 at 19:57, 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 searched and there was a FIT program on the DOMOV server, which is not
> active any more.
> If there is some other programs that can do it.
>
> best
>
> Jiri
>
>