From: Tristan Croll (
Date: Thu Oct 10 2013 - 00:50:06 CDT


In general I find VMD a joy to work with, but I'd like to note a few issues (some of which I hesitate to call "bugs") to do with VMD and visualisations which are each fairly minor, but nevertheless somewhat annoying.

1. Moving molecules or fragments around with the mouse (i.e. options under mouse/move on the menu): translations work fine, but rotations are another story. When trying to rotate (by shift-clicking and dragging) it is common for the on-screen motion to be way out of line with the mouse movements This has something to do with rotation of the display. I'm playing with it now: when the z axis is pointing right, y axis down and x axis out of the screen, if the display is rotated around the y axis so that x points a few degrees to the right, everything is behaves as normal. A slight rotation of the display so the x axis points off to the left, and everything is haywire - moving the mouse upwards causes the construct to rotate sideways, for instance.

2. When a molecule has graphical representations turned on in the "Graphical Representations" window but display of the molecule is turned off in the "VMD Main" window, those graphical representations are still recalculated at every frame. In general this is no big deal, but when half a dozen or more constructs are loaded, each with complex selections and/or surface representations, things really start to slow down - and it gets to be a pain in the neck going through and turning off all representations one by one.

3. When animating a trajectory against a single-frame volumetric map, the map redraws at every animation step unless the A switch is turned off for that map in the main window. This is fine, except if I then change the axis of rotation by centering on a particular atom in my construct (as I tend to do regularly), all molecules with animation turned off continue to turn on the old axis, making for some very "interesting" graphical effects which can only be fixed by resetting the display.



Tristan Croll
Faculty of Health
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443

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