Re: [Jmol-users] Is there command to rotate protein to show the particular residue

[Jeff H. <jh...@de...>]

Would it be possible to add an invisible atom in front of the protein and rotate the protein until the distance from the selected residue to the invisible atom is minimized?


***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jh...@de...
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On Jun 7, 2011, at 5:40 PM, Robert Hanson wrote:

> yeah, for that you are going to have to do some scripting. It's a classic problem -- that of finding the "best" view of a particular part of a protein. I think if you have a particular protein in mind, it should be possible, but it's really a very big challenge. 
> 
> What I was trying to point out there is that you should learn a bit about how Jmol uses quaternions. These are direct measures of orientation, and that's precisely what you need here. They can be multiplied and inverted like matrices, and they are just very convenient.  So you would do some constructing of quaternions and combine them as desired to get the view you want. An illustration of this is at the Klotho site, where I am using quaternions to orient molecules that are coming from a database and have all sorts of odd orientations. 
> 
> http://chemapps.stolaf.edu/klotho
> 
> Basically, you can define a little "xyz frame" in the form of a quaternion using any three atoms:
> 
> Var q = quaternion({atomno=1} {atomno=2} {atomno=3})
> 
> and then you can use that to do all sorts of interesting things.
> 
> 
> On Tue, Jun 7, 2011 at 7:17 AM, M K <se...@gm...> wrote:
> Thanks, I have tried this. This is great, but not completely what I need.
> As I understand this command (moveto quaternion {<residue unmber}) sets the residue as the center of rotation and moves it to the center of the window. Unfortunately, residue can be shadowed by other residues of protein.
> What I need is to bring the desired residue to the front. This residue should not be new center of rotation.
> OK, if there is no appropriate command I guess I can write script to rotate molecule in desired way - to bring particular residue to the front of view. 
> For this I should calculate rotational angles that is needed.
> So, my question is where is the zero points of rotational angles?
> 
> 
> 2011/6/7 Robert Hanson <ha...@st...>
> Ah, sure. For this I would recommend using quaternion rotation. Basically each amino acid is assigned an xyz frame that is positioned in a way that depends upon the setting of the "quaternionFrame" -- C, P, or N. Then the moveto command has the keyword QUATERNION, which can be followed by a residue number:
> 
> set quaternionFrame "C"
> moveto quaternion {5}
> 
> This orients the molecule relative to that residue. 
> 
> 
> On Mon, Jun 6, 2011 at 5:57 PM, M K <se...@gm...> wrote:
> Dear all,
> 
> Form my web-page that incorporates Jmol applet I would like to issue command to show particular residue of protein (to rotate molecule by the appropriate angle) in response to the pressing the button by user.
> Is there the appropriate command in Jmol? 
> If not, I guess I could write a script which rotate molecule by the appropriate angel. But where is the zero angle of molecule? How is it defined?
> 
> Thanks,
> seven32
> 
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> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> If nature does not answer first what we want,
> it is better to take what answer we get. 
> 
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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> EditLive Enterprise is the world's most technically advanced content
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