VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_vitae.cmm.upenn.edu)
Date: Tue Apr 04 2006 - 14:26:01 CDT

On Mon, 3 Apr 2006, Peter Hamm wrote:

> Hi
>
> When I try to load the attached cube file into VMD, I get a warning:
>
> WARNING: Coordinates will be rotated to comply
> with VMD's convention for periodic display...

peter, this message appears, so that VMD can display
periodic images for non-orthorhombic cell correctly.
the periodicity code, currently assumes, that the a-vector
is collinear with the x-axis and the b-vector is in the
xy-plane.

>
> Even more so, when I combine more than one of such file to a
> trajectory, that rotation is different for each file. I am an absolute
> newcomer to VMD, but this just doesn't make sense to me. Does
> anybody have an idea how to avoid this?

how did you generate the cube files?
what version of VMD are you using?

please make sure, that the cell vector description
in your cube file is correct. there is quite a bit of
confusion about what is a correct cube file. here is
a format description the underlies the VMD implementation:

C THE FORMAT IS AS FOLLOWS (LAST CHECKED AGAINST GAUSSIAN 98):
C
C LINE FORMAT CONTENTS
C ===============================================================
C 1 A TITLE
C 2 A DESCRIPTION OF PROPERTY STORED IN CUBEFILE
C 3 I5,3F12.6 #ATOMS, X-,Y-,Z-COORDINATES OF ORIGIN
C 4-6 I5,3F12.6 #GRIDPOINTS, INCREMENT VECTOR
C #ATOMS LINES OF ATOM COORDINATES:
C ... I5,4F12.6 ATOM NUMBER, CHARGE, X-,Y-,Z-COORDINATE
C REST: 6E13.5 CUBE DATA
C
C ALL COORDINATES ARE GIVEN IN ATOMIC UNITS.

if you have files, that are conformant, but do not display
correctly, can you try to upload them to the VMD biofs
(via a biocore account)? this way, you'd also get access to
updated alpha/beta builds of VMD...

if this is too much hassle (it is worth it, though), you
can also send them to me (privately only) and i'll see
if there is a way to fix them or the cubefile reader.
might take a few days, though, since i am currently
'on the road'.

regards,
     axel.

>
> Many thanks in advance
>
> Peter Hamm
>
>
>
>
> ---------------------------------------------------------
> Peter Hamm
> Physikalisch Chemisches Institut
> Universität Zürich
> Winterthurerstr. 190
> CH-8057 Zürich
> Switzerland
> Tel: ++41/1/63 54431
> Fax: ++41/1/63 56838
>
> 

--
=======================================================================
Axel Kohlmeyer    e-mail: akohlmey_at_cmm.upenn.edu, tel: ++1-215-898-1582
     Center for Molecular Modeling    --    University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.