**From:** Mert Gür (*gurmert_at_gmail.com*)

**Date:** Sat Jan 31 2009 - 02:13:38 CST

**Next message:**Arturas Ziemys: "combining abf reaction path"**Previous message:**Chris Harrison: "Re: Aligning the distance between two centroids with an axis"**In reply to:**Chris Harrison: "Re: Aligning the distance between two centroids with an axis"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

You are right, its an VMD question . I am really sorry about that.

Thanks a lot, the script you have sent worked.

Best,

Mert

On Sat, Jan 31, 2009 at 5:31 AM, Chris Harrison <char_at_ks.uiuc.edu> wrote:

*> Mert,
*

*>
*

*> Your question is really a VMD question and therefore, to yield better and
*

*> more responses, it's best to post similar questions to vmd-l.
*

*>
*

*> 1. Check out the matrix commands in the vmd manual; ie transvec, vecsub,
*

*> etc.
*

*>
*

*> 2. Check out the Orient script, written for similar problems, at:
*

*> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/
*

*>
*

*> 3. A hastily written example soln to a similar problem:
*

*> proc align_p1p2_to_z { p1 p2 } {
*

*> # p1 and p2 should represent more than one atom
*

*>
*

*> set p1pos [lindex [$p1 get {x y z}] 0 ]
*

*> set p2pos [lindex [$p2 get {x y z}] 0 ]
*

*> set vec [vecsub $p1pos $p2pos]
*

*>
*

*> set alat [atomselect top all]
*

*>
*

*> set M [transvec $vec]
*

*> $alat move $M
*

*>
*

*> set M2 [transaxis y -90]
*

*> $alat move $M2
*

*> }
*

*>
*

*>
*

*> C.
*

*>
*

*>
*

*> --
*

*> Chris Harrison, Ph.D.
*

*> Theoretical and Computational Biophysics Group
*

*> NIH Resource for Macromolecular Modeling and Bioinformatics
*

*> Beckman Institute for Advanced Science and Technology
*

*> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
*

*>
*

*> char_at_ks.uiuc.edu Voice: 217-244-1733
*

*> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
*

*>
*

*>
*

*>
*

*> On Fri, Jan 30, 2009 at 4:02 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:**Arturas Ziemys: "combining abf reaction path"**Previous message:**Chris Harrison: "Re: Aligning the distance between two centroids with an axis"**In reply to:**Chris Harrison: "Re: Aligning the distance between two centroids with an axis"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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