VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Thu Sep 21 2023 - 12:50:19 CDT

Hi Camila, you were very close to solutions.

I wrote you a script with comments to compute the angle to a plane.
Please let me know if it works for you.

Friendly regards,
Diego.

On Wed, Sep 20, 2023 at 9:25 AM Castro Martinez, Camila <
camila.castro_at_tu-dortmund.de> wrote:

> What I need is to compute the angle between the vector and the plane
> itself. Is that possible?
>
>
> Camila
> ------------------------------
> *De:* Vermaas, Josh <vermaasj_at_msu.edu>
> *Enviado:* miércoles, 20 de septiembre de 2023 15:06:25
> *Para:* Castro Martinez, Camila
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Asunto:* Re: vmd-l: Angle between a vector and a plane
>
>
> Can I ask another question then? The arccosine between two vectors is
> related to the angle between the two vectors. Wouldn’t the quantity you are
> calculating then be the angle between a vector and the vector normal to the
> plane, not the plane itself? That could very well be a small number if
> ChimeraX is giving you the angle between the vector and the plane itself,
> which is giving you a number near 90 degrees. So numerical issues
> notwithstanding, its at least plausible to me that your code is correct,
> but that you are comparing two different quantities. ChimeraX might be
> giving you the angle between the plane and a specific vector, and your VMD
> code is giving you the angle between a specific vector and the vector
> normal to the plane.
>
>
>
> -Josh
>
>
>
> *From: *"Castro Martinez, Camila" <camila.castro_at_tu-dortmund.de>
> *Date: *Wednesday, September 20, 2023 at 8:16 AM
> *To: *"Vermaas, Josh" <vermaasj_at_msu.edu>
> *Subject: *Re: vmd-l: Angle between a vector and a plane
>
>
>
> I just used 1 or 2 or 3 as an example. The expression
>
>
>
> set v1 [atomselect top "residue 1"]
> set v2 [atomselect top "residue 2"]
>
>
>
> is for one vector, and the other expression
>
>
>
> set n1 [atomselect top "residue 1"]
> set n2 [atomselect top "residue 2"]
> set n3 [atomselect top "residue 3"]
>
>
>
> is for other three residues that form the plane. Are not the same residues
> at all. Maybe I should have put
>
>
>
>
>
> set n1 [atomselect top "residue 3"]
> set n2 [atomselect top "residue 4"]
> set n3 [atomselect top "residue 5"]
>
>
>
> so that it is better understood.
>
>
>
> Camila
> ------------------------------
>
> *De:* Vermaas, Josh <vermaasj_at_msu.edu>
> *Enviado:* miércoles, 20 de septiembre de 2023 13:54:23
> *Para:* Ashar Malik; Castro Martinez, Camila
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Asunto:* Re: vmd-l: Angle between a vector and a plane
>
>
>
> Definitely in radians. acos -1 gives you pi, not 180, but I think that is
> accounted for by "conv". I think this is coming from your definitions for
> p1 and p2. As written, p1 is the vector from residue 1 to 2, and p2 is the
> vector from residue 2 to 3. That will usually be an angle > 90 degrees, and
> so the cross product won't be as well behaved as if p1 and p2 are made by
> vectors that share an origin. To be honest, as written, the answer should
> be 0, not 70, since residue 1 and 2 are used to define the vector AND the
> plane, so both 10 and 70 are clearly wrong here.
>
> -Josh
>
> On 9/20/23 05:13, Ashar Malik wrote:
>
> Not sure I recall this correctly, but isn’t the angle supposed to be
> handled in radians? Might be wrong but woke a look.
>
>
>
>
>
>
>
> On Wed, 20 Sep 2023 at 6:37 PM, Castro Martinez, Camila <
> camila.castro_at_tu-dortmund.de> wrote:
>
> Dear all
>
>
> I'm looking to calculate the angle between a vector and a plane over a
> trajectory using tcl script. The code I've been using is the following:
>
>
> set outfile [open output.dat w]
> set nf [molinfo top get numframes]
>
> #for the vector
> set v1 [atomselect top "residue 1"]
> set v2 [atomselect top "residue 2"]
>
> #for the plane
> set n1 [atomselect top "residue 1"]
> set n2 [atomselect top "residue 2"]
> set n3 [atomselect top "residue 3"]
>
> for { set i 0 } { $i < $nf } { incr i } {
>
> $v1 frame $i
> $v2 frame $i
> set com1 [measure center $v1]
> set com2 [measure center $v2]
> set m2 [vecsub $com2 $com1]
> set m2mag [veclength $m2]
>
> $n1 frame $i
> $n2 frame $i
> $n3 frame $i
> set com3 [measure center $n1]
> set com4 [measure center $n2]
> set com5 [measure center $n3]
> set p1 [vecsub $com4 $com3]
> set p2 [vecsub $com5 $com4]
> set cn [veccross $p1 $p2]
> set cnmag [veclength $cn]
>
> set dotp [vecdot $m2 $cn]
> set theta [expr $conv * acos($dotp / ($m2mag * $cnmag))]
> if { $theta > 90.0 } {
> set theta [expr 180.0 - $theta]
> }
>
> puts $outfile "[expr ($i + 1)] $theta"
> }
>
> close $outfile
>
> This commands actually worked, but the results are not what I expected.
> When I checked in Chimera for example the angle should be 70°, and the
> angle calculated with this script was 10°. This is clearly not correct.
> Where have I gone wrong in the code? or am I missing something? Thanks in
> advance
>
>
>
> --
>
> Josh Vermaas
>
> vermaasj_at_msu.edu
>
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>
> Michigan State University
>
> vermaaslab.github.io
>
>
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> ist ausschließlich für den Adressaten bestimmt. Sollten Sie nicht der für
> diese E-Mail bestimmte Adressat sein, unterrichten Sie bitte den Absender
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> durch Übermittlung eines solchen Schriftstücks per Telefax erfolgen.
> Important note: The information included in this e-mail is confidential. It
> is solely intended for the recipient. If you are not the intended recipient
> of this e-mail please contact the sender and delete this message. Thank
> you. Without prejudice of e-mail correspondence, our statements are only
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> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics
Leach Science Center
Auburn University
dgomes_at_auburn.edu
+1 (334) 559-4016