## VMD-L Mailing List

**From:** Reza Salari (*resal81_at_gmail.com*)

**Date:** Wed Jun 22 2011 - 12:50:10 CDT

**Next message:**Axel Kohlmeyer: "Re: APBS installation problem"**Previous message:**Sangita Kachhap: "APBS installation problem"**In reply to:**Axel Kohlmeyer: "Re: Rotating a non-coordinate file"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Thanks. That really helped.

After some search and checking the dxplugin.c file, I wrote a script in

scilab (matlab) to rotate the axes and it seems working. I am attaching the

script below.

Reza Salari

My dx file:

...

origin 0.503 0.503 0.503

delta 1.007 0.000 0.000

delta 0.000 1.007 0.000

delta 0.000 0.000 1.007

..

and for re-orienting the x-axis for 10 degrees, I used the output of

the following script to replace numbers of the first delta line:

point=[1,0,0] angle=10delta=1.007

t=(angle/180.0)*3.14p=[ [1,0,0,point(1,1)]; [0,1,0,point(1,2)];

[0,0,1,point(1,3)]; [0,0,0,1] ]rotx=[ [1,0,0,0]; [0,cos(t),-sin(t),0];

[0,sin(t),cos(t),0];[0,0,0,1] ]roty=[ [cos(t),0,sin(t),0]; [0,1,0,0];

[-sin(t),0,cos(t),0]; [0,0,0,1] ]rotz=[ [cos(t),-sin(t),0,0,];

[sin(t),cos(t),0,0]; [0,0,1,0]; [0,0,0,1] ]

f=rotz*roty*rotx*pout=[f(1,4),f(2,4),f(3,4)]disp(out*delta)

On Wed, Jun 22, 2011 at 6:56 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

*> You cannot change this from within VMD, but you can edit the file
*

*> itself and change the unit cell vectors accordingly. Axel.
*

*>
*

*> --
*

*> Axel Kohlmeyer
*

*> akohlmey_at_gmail.com
*

*> http://goo.gl/1wk0
*

*>
*

*>
*

*> On Jun 22, 2011, at 6:22, Reza Salari <resal81_at_gmail.com> wrote:
*

*>
*

*> > Hello all,
*

*> >
*

*> > I am wondering if there is a way to rotate a dx volume file using
*

*> > the "move" command?
*

*> >
*

*> > If I have a pdb file, I can rotate it around the x axis by running
*

*> > these commands:
*

*> >
*

*> > set prot1 [atomselect 0 "all"]
*

*> > set M [transaxis x 20]
*

*> > $prot1 move $M
*

*> >
*

*> > Now, I have two dx files that belong to the same protein but in two
*

*> > different orientations so I want to re-align one of the dx files.
*

*> > However if I load a dx file to VMD and try to assign it to a variable:
*

*> >
*

*> > set surf1 [atomselect 0 "all"]
*

*> >
*

*> > it fails (probably because the dx file is not a coordinate file and
*

*> > hence atomselect doesn't work for it). I've tried a couple of
*

*> > different options without luck. So I am wondering if it is possible
*

*> > to select a non-coordinate object in the console, for example just
*

*> > using its mol_id or similar attributes and not using atomselect?
*

*> >
*

*> > I appreciate your help in advance,
*

*> >
*

*> > Reza Salari
*

*>
*

**Next message:**Axel Kohlmeyer: "Re: APBS installation problem"**Previous message:**Sangita Kachhap: "APBS installation problem"**In reply to:**Axel Kohlmeyer: "Re: Rotating a non-coordinate file"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]