Re: Aligning the distance between two centroids with an axis

From: Mert Gür (gurmert_at_gmail.com)
Date: Sat Jan 31 2009 - 02:13:38 CST

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]
>>
>
>

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