[phenixbb] how to move one domain of a protein in respect to another?

Pavel Afonine pafonine at lbl.gov
Tue Feb 15 22:47:25 PST 2011


this will be trivial to do in the next available PHENIX nightly build:


phenix.pdbtools model.pdb rotate_about_axis.axis="chain A and resseq 
1:123 and (name CA or name CB)" rotate_about_axis.atom_selection="chain 
A and resseq 1" rotate_about_axis.angle=35


rotate_about_axis.axis defines the rotation axis (must be two points in 
rotate_about_axis.atom_selection defines the atoms that will be rotated 
about the axis;
rotate_about_axis.angle defines rotation angle in degrees.

Instead of specifying atom selection string in rotate_about_axis.axis, 
you can give it coordinates of two points:

phenix.pdbtools model.pdb rotate_about_axis.axis="1.234 2.345 4.567 
-2.321 3.765 0.001" rotate_about_axis.atom_selection="chain A and resseq 
1:123" rotate_about_axis.angle=35

Let me know if there are any problems or questions.

phenix.pdbtools available in PHENIX GUI too.


On 2/9/11 11:57 AM, Tatyana Sysoeva wrote:
> Dear all,
> I am working with a protein which form homooligomeric assembly. Each 
> subunit of the assembly consists of 2 subdomains. I would like to 
> create chimeras with the subdomains moved with respect to each other, 
> keeping the linkers.
> I am wondering what would be the easiest way to do this?
> Any suggestions are welcome!
> Sincerely,
> Tanya

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