[MMTK] Rotating parts of the side-chain of a residue

Konrad Hinsen hinsen at cnrs-orleans.fr
Wed Jan 21 12:34:26 CET 2004

On Wednesday 21 January 2004 11:27, Urban Hafner wrote:

> the moment I'm trying to find out what is the easiest way to change the
> side-chain of a residue to have specific chi1 - chi4 angles. My idea was
> to just use rotateAroundAxis(self,point1,point2,angle) to change the
> existing angles (as I'm starting with a protein from a PDB file). But

That is my suggestion as well.

> I'm
> not sure what rotateAroundAxis does. Does it rotate the whole protein
> (which would be useless for my purpose) or is it possible to take part
> of the protein and it just rotates that part (which would mean I could

It is a method which works on the object it is called on. This can be a whole 
protein, a residue, a sidechain, or an aritrary selection via a Collection 
object. In your case, you would have to use the general case via a 
Collection. For example:

sidechain = protein[0][10].sidechain
atoms = Collection([sidechain.CG, sidechain.HG])
atoms.rotateAroundAxis(ref_atom_1.position(), ref_atom_2.position(), angle)

> Or am I just heading for the wrong direction and there is some other
> easy way to change to side-chain (mind you, I'm just a student)?

There are of course other ways, but I can't think of a simpler one. Three 
lines doesn't look so bad!

Konrad Hinsen                            | E-Mail: hinsen at cnrs-orleans.fr
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