**From:** Grace Brannigan (*gracebrannigan_at_gmail.com*)

**Date:** Fri Jan 30 2009 - 10:01:55 CST

**Next message:**Falgun Shah: "pdb and rmsd"**Previous message:**Nicholas M Glykos: "Re: Aligning the distance between two centroids with an axis"**In reply to:**Mert Gür: "Aligning the distance between two centroids with an axis"**Next in thread:**Chris Harrison: "Re: Aligning the distance between two centroids with an axis"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Mert,

This is really a VMD question and should be directed to the VMD mailing

list.

While you're here though, I suggest you check out the "trans" routines

http://www.ks.uiuc.edu/Research/vmd/current/ug/node178.html

in particular "transvec", which will generate the rotation matrix you need,

i.e.

set trans_mat [transvec $v]

and then apply the rotation matrix to your selection by

$sel move $trans_mat

Hope this helps,

Grace

On Fri, Jan 30, 2009 at 5:02 AM, Mert Gür <gurmert_at_gmail.com> wrote:

*> Dear all,
*

*> I have a system composed of two proteins. I defined the first centroid
*

*> (c1) to be the centroid of the Calfa atoms of protein1 . The same way I
*

*> defined the second centroid (c2) to be the centroid of the Calfa atoms of
*

*> protein2 .
*

*> What I would like to do is to align the vector v=c1-c2 with the x axis
*

*> (Could also be y axis or z axis). I think what I need is to rotate my
*

*> protein with respects to this vector. But unfortunately I have no clue how
*

*> to do that. I did some search but I haven't come along any relevant
*

*> information .
*

*> I appreciate any help,hint or source.
*

*> Thanks in advance,
*

*> Mert
*

*>
*

*>
*

*> set allatoms [atomselect top all]
*

*>
*

*> $allatoms set beta 0
*

*>
*

*> set c1atom [atomselect top "chain A and name CA"]
*

*>
*

*> $c1atom set beta 1
*

*>
*

*> $allatoms set occupancy 0
*

*>
*

*> set c2atom [atomselect top "chain B and name CA"]
*

*>
*

*> $c2atom set occupancy 1
*

*>
*

*>
*

*>
*

*> set c1 [lindex [$c1datom get {x y z}] 0]
*

*>
*

*> set c2 [lindex [$c2atom get {x y z}] 0]
*

*>
*

*> vecnorm [vecsub $c1 $c2]
*

*>
*

**Next message:**Falgun Shah: "pdb and rmsd"**Previous message:**Nicholas M Glykos: "Re: Aligning the distance between two centroids with an axis"**In reply to:**Mert Gür: "Aligning the distance between two centroids with an axis"**Next in thread:**Chris Harrison: "Re: Aligning the distance between two centroids with an axis"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:50:27 CST
*