From: John Stone (
Date: Fri Aug 11 2006 - 22:27:58 CDT

  That's odd. What version of VMD were you running?
When I ran the commands you provided in both VMD 1.8.4 and in the test
builds of VMD 1.8.5, it displayed perfectly in my sessions.

It is possible that some other step/operation caused the axes to get
out of sync, what happens if you select: Display->Reset View
Do the axes line up properly?

Generally speaking this isn't expected, but it is possible to get
things out of sync by toggling molecules as fixed, and then rotating
the display, for example. If/when such a thing occurs, you can do
Display->Reset View (or press the '=' key in the graphics window),
or type the command "display resetview" in the console.
If resetting the view doesn't resolve this discrepancy, let me know and
we'll figure out what happened there.


On Fri, Aug 11, 2006 at 07:11:07PM -0400, wrote:
> Dear John & VMDers,
> I've made a long and thin membrane with the membrane plugin of x= 200 and y=30
> (commands used below). Then I filled it up with water molecules, 30A above and
> 30A beneath the lipid bilayer using the solvate plugin.
> The final dimensions of the system are 200, 35, 120 in x, y and z axis,
> according to measure minmax function. The dimensions seem right, as the lipid
> bilayer is about 60A high. My confusion is, the orientation of the reference
> axes in the display window shows the system as if the dimensions were 200, 120,
> 35 in x, y and z. In other words, I'm seeing the y axis in the display where, I
> thought, the z axis should be and viceversa.
> I'm almost sure I've read another thread months ago about the same optical
> dilema but I couldn't find it in the mailing list. As I'm a big fan of VMD I'm
> still not sure I'm correct in what I see, so I attached a .jpeg screenshot. In
> the left bottom the reference axes, and, in the system, I roughly measured the
> distances along the water box shape lines for clarity. Am I right?
> The commands I used are:
> membrane -l POPC -x 200 -y 30
> set todo [atomselect top all]
> measure minmax $todo # then I added 30 to z-max and subtracted 30 from the z-min
> solvate membrane.psf membrane.pdb -s WT -minmax {{-50.6 -49.3 -57.7} {150.75
> -15.86 58.06}}
> Gonzalo.
> -------------------------------------------------
> Este mensaje fue enviado por:

NIH Resource for Macromolecular Modeling and Bioinformatics
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