From: Vermaas, Joshua (
Date: Mon Sep 16 2019 - 18:17:44 CDT


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.


On 2019-09-16 16:46:13-06:00 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.