Re: BALLView: new package version
On Sun, 28 Jan 2007, Andreas Moll wrote:
there is a now a new improved package version available.
Got it and builded the package. My main concerns are solved and
I would regard the package nearly ready for upload. There is just
one issue if I run the demo I get the following output:
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/BALL/index.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/BALL/index.html
reading PDB file...
Read 454 atoms from file "/usr/share/BALL/data/structures/bpti.pdb"
applying molecular properties ...
> normalized names
> generated missing bonds
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo01.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo01.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo02.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo02.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo03.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo03.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo04.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo04.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo05.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo05.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo06.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo06.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo07.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo07.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo08.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo08.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo09.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo09.html
Calculated 15 H-bonds
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo10.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo10.html
Could not delete Representation while update is running!
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo11.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo11.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo12.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo12.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo13.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo13.html
Set up the force field for 892 atoms with parameters from /usr/share/BALL/data/Amber/amber96.ini.
Minimizing 892 of 892 atoms.
final RMS gradient : 25.544510 kJ/(mol A) after 20 iterations
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo14.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo14.html
Canonical MD simulation System has potential energy -8454.06 kJ/mol at time 0 ps
Canonical MD simulation System has temperature 0 at time 0 ps
final RMS gradient : 31.285550 kJ/(mol A) after 30 iterations
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo15.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo15.html
FDPB: creating array of charged atoms...
FDPB: creating bounding box...
FDPB::setup: grid border: 5
FDPB::setup: grid:(-11.0954 64.6133 -13.4265)/(38.7545 114.463 36.4234)
grid dimensions: 50x50x50
Boundary points: 4639
creating phi grid...
creating charge grid...
creating boundary...
Debye length = 3.40282e+38 m
ionic strength = 0
calculating effective dipole...
assigned negative charge: -89.9301 at (13.0115/88.8805/9.14098)
assigned positive charge: 95.9301 at (13.0568/88.4927/9.57466)
setting up xy-planes...
setting up xz-planes...
setting up yz-planes...
setting up some arrays...
calculating charged grid points...
number of charged grid points: 2792 (2.10477%)
starting iterations.
Iteration 10 RMS: 0.0109379 MAX: 0.301846
Iteration 20 RMS: 0.00386107 MAX: 0.10198
Iteration 30 RMS: 0.00139456 MAX: 0.0308396
Iteration 40 RMS: 0.000493385 MAX: 0.0136791
Iteration 50 RMS: 0.000216491 MAX: 0.00432247
Iteration 60 RMS: 8.21957e-05 MAX: 0.00185032
Iteration 70 RMS: 2.86647e-05 MAX: 0.000657082
Iteration 80 RMS: 1.40924e-05 MAX: 0.000297308
Iteration 90 RMS: 5.34581e-06 MAX: 9.80496e-05
Converged.
final energy after 91 iterations: 16709.2 kJ/mol
reaction field energy: -7012.63 kJ/mol
Finished FDPB grid
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo16.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo16.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo17.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo17.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo18.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo18.html
Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/tutorial01.html' for reading
Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/tutorial01.html
Editor is empty, aborting...
So it seems you have to do a little bit more fiddling around with symlinks.
BTW, you did fine with dh_link but I personally regard it easier if you
use debian/<pkgname>.links files and calling dh_link without any argument.
It's a question of style but in case you want to switch to cdbs or something
like that this method would be more convenient.
Kind regards and thanks for your fine work
Andreas.
--
http://fam-tille.de
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