VMD-L Mailing List

From: Erin L. (erinl_at_chem.ubc.ca)
Date: Thu Nov 18 2010 - 14:23:06 CST

Hello,

I'm new to VMD and having trouble with particle positions in triclinic unit
cells. I've written my own program and make output in both .xsf (using
www.xcrysden.org/doc/XSF.html as a guide) and .xyz file format.

My problem is that the two files, when loaded into VMD, give me different
visualizations of the crystal. I've narrowed down the problem to the .xsf
file coordinate positions are not consistent from input to visualization,
but I'm not sure why. How can I fix or reconcile this? I would prefer to
keep using the .xsf format because the files are much smaller.

I've made up a minimal example with only one non-orthogonal angle. The .xsf
and VMD Query results are below. I should note that the unit cell vectors
in the .xsf seem to work just fine. The command "pbc box" in the Tk Console
draws the unit cell as specified and it matches the lattice from the .xyz
file. I'm using VMD 1.8.6 (Linux, 64 bit), but have also checked it on VMD
1.8.7 (Linux, 32 bit). Any thoughts or pointers would be appreciated.

Thank you for your time,

Erin

------------

sample .xsf file:

-------------
CRYSTAL
PRIMVEC
   5.000 0.000 0.000
   0.000 5.000 0.000
   0.000 2.500 4.330

 # 5.000 5.000 5.000 (a, b, c lengths)
 # 60.000 90.000 90.000 (alpha, beta, gamma angles)

PRIMCOORD
 4 1
          12 0.000 0.000 0.000
          12 2.500 0.000 0.000
          12 0.000 2.500 * 0.000 *
          12 0.000 *1.250 2.165*
--------------

VMD Coordinate Query results on the .xsf unit cell particles:

--------------

0.00 0.00 0.00
2.50 0.00 0.00
0.00 2.50 *1.25*
0.00 * 5.00 4.665*

-------------