[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
Hi,
this will be trivial to do in the next available PHENIX nightly build:
http://www.phenix-online.org/download/nightly_builds.cgi
Examples:
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
where
rotate_about_axis.axis defines the rotation axis (must be two points in
space);
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.
Pavel.
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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