VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 16 2019 - 20:11:43 CDT

Hi,
  Josh's description is correct. The axes "origin" relates to the viewport.
For your molecule(s), VMD does automatic translation and scaling to compose
a view that encompasses everything that should be visible when you reset
the view...

By default, when you reset the view, VMD will compute a bounding box for
the active representation on the "top" molecule, and it will then compute
the necessary view transformations such that the center of that bounding
box is brought to the center of the 3-D viewport.

So, if you want to see the origin of your molecule, you might instead
draw your own marker there, e.g. with the graphics "draw" commands such as:
  draw sphere { 0 0 0 } resolution 20 radius 2.0

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 16, 2019 at 11:17:44PM +0000, Vermaas, Joshua wrote:
> Hi,
>
> The "origin" refered to by the display->axes->origin option is for the
> viewport, NOT the molecule. This is clear if you put the molecule into
> translate mode ("t") and move it around. The axes won't move with the
> molecule! Basically, "origin" is if you want the axes in the middle of the
> image, rather than in one of the corners like the default.
>
> -Josh
>
>
>
> On 2019-09-16 16:46:13-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Dear all,
>
>
>
> I generated a pdb file using charmm, and here is the xyz statistics
> information:
>
>
>
> XMIN = -0.056054 XMAX = 95.323813 XAVE = 47.498205
>
> YMIN = -0.301661 YMAX = 95.280182 YAVE = 47.337873
>
> ZMIN = -0.575130 ZMAX = 95.194181 ZAVE = 47.494812
>
>
>
> From the information clearly the origin (0, 0, 0) is at the corner of
> the box, not the center of it. I also checked the pdb file inside and
> indeed almost all x y z values are positive. However, when I opened the
> pdb file with VMD and displayed axes (by Display -> Axes -> Origin), the
> axes always showed up in the center of the box, which is far away from
> (0, 0, 0). So do I have a misunderstanding of "origin" in VMD? In this
> case, why is it not in the corner of the box?
>
>
>
> Thank you all very much.
>
>
>
> M.M
>
>
>
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/