Date: Fri Aug 11 2006 - 18:11:07 CDT

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}}


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