Your message dated Wed, 30 Nov 2022 17:57:46 +0000 with message-id <[email protected]> and subject line Bug#1022931: Removed package(s) from unstable has caused the Debian Bug report #446750, regarding reading vmol files: coord factor ignored and misdefined to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 446750: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=446750 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---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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--- Begin Message ---Version: 2.4.1-26+rm Dear submitter, as the package viewmol has just been removed from the Debian archive unstable we hereby close the associated bug reports. We are sorry that we couldn't deal with your issue properly. For details on the removal, please see https://bugs.debian.org/1022931 The version of this package that was in Debian prior to this removal can still be found using http://snapshot.debian.org/. Please note that the changes have been done on the master archive and will not propagate to any mirrors until the next dinstall run at the earliest. This message was generated automatically; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]. Debian distribution maintenance software pp. Scott Kitterman (the ftpmaster behind the curtain)
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