Package: viewmol
Version: 2.4.1-11
Severity: normal
Babel can convert data files to viewmol format (.vmol). The vmol file
so produced appears correct.
However reading it into viewmol, the molecule gets contracted by a
factor of a Bohr radius (0.529 Ang).
For instance dihydrogen phosphate:
$title
dihydrogenphosphate ion
$coord 1.0
0.03224100000000 -0.00595000000000 -0.07012400000000 P
1.64667200000000 0.05724700000000 -0.17487200000000 O
-0.24436100000000 -1.58692300000000 -0.28265500000000 O
-0.33758300000000 0.30240100000000 1.31263100000000 O
-0.49193500000000 0.70014500000000 -1.24085700000000 O
1.87625600000000 0.31179000000000 -1.04869100000000 H
-0.34684200000000 -1.98488400000000 0.56118500000000 H
$end
Viewmol measures the OH distances to be "0.4967 Ang" rather than 0.938
Ang. Notice the line "$coord 1.0". The '1.0' is supposed to be the
factor converting the given coordinates into Angstroms (see
file:///usr/share/doc/viewmol/html/node32.html ), so 1.0 in this case
- coordinates are already in Angstroms. But for some reason a Bohr
factor is applied regardless.
Furthermore changing the factor in this line appears to have no effect.
-- System Information:
Debian Release: lenny/sid
APT prefers unstable
APT policy: (990, 'unstable'), (1, 'experimental')
Architecture: i386 (i686)
Kernel: Linux 2.6.22 (PREEMPT)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages viewmol depends on:
ii lesstif2 1:0.95.0-2.1 OSF/Motif 2.1 implementation relea
ii libc6 2.6.1-5 GNU C Library: Shared libraries
ii libgl1-mesa-glx [libgl1 7.0.1-2 A free implementation of the OpenG
ii libglu1-mesa [libglu1] 7.0.1-2 The OpenGL utility library (GLU)
ii libpng12-0 1.2.15~beta5-2 PNG library - runtime
ii libtiff4 3.8.2-7 Tag Image File Format (TIFF) libra
ii libx11-6 2:1.0.3-7 X11 client-side library
ii libxext6 1:1.0.3-2 X11 miscellaneous extension librar
ii libxi6 2:1.1.3-1 X11 Input extension library
ii libxmu6 1:1.0.3-1 X11 miscellaneous utility library
ii libxp6 1:1.0.0.xsf1-1 X Printing Extension (Xprint) clie
ii libxt6 1:1.0.5-3 X11 toolkit intrinsics library
ii python 2.4.4-6 An interactive high-level object-o
ii python-support 0.7.4 automated rebuilding support for p
ii python2.4 2.4.4-6 An interactive high-level object-o
ii zlib1g 1:1.2.3.3.dfsg-6 compression library - runtime
viewmol recommends no packages.
-- no debconf information
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