From: Michael Morgan (
Date: Mon Sep 16 2019 - 16:44:47 CDT

Dear all,


I generated a pdb file using charmm, and here is the xyz statistics


    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.