Package: openbabel Version: 1.100.2-2 Severity: normal >From time to time I notice that rasmol or pymol do weird stuff with my molecules.
For instance, the attach pdb file contains a single long chain of 1000 atoms more or less in a straight row. But rasmol splits the line and sends one portion of it in another direction disconnected from the remainder. pymol does likewise. I guess this is happening because of the large size of the coordinates (the largest are around 1000 units). From my original xyz file, I created the pdb file using babel (openbabel). The large end of the pdb file looks like: HETATM 998 C LIG 169 278.606-258.057-1557.890 1.00 0.00 C HETATM 999 C LIG 169 278.332-258.604-1558.640 1.00 0.00 C HETATM 1000 C LIG 0 278.374-257.892-1561.950 1.00 0.00 C (from the original xyz, that's C 278.606 -258.057 -1557.89 C 278.332 -258.604 -1558.64 C 278.374 -257.892 -1561.95 ) You can see the coordinates have run together. I don't know the exact format for pdb files, but it doesn't seem reasonable for the coordinates to run together like this. It's certainly possible for proteins to have coordinates this big. Maybe precision after the decimal place needs to be sacrificed to fit in the extra digit in front of it? Maybe the coordinates need to be given "enough space" rather than being confined to 8-character columns? The protein scientists seem to cheat by chopping up the proteins into fragments. But I was able to find coordinates out there as high as 500, not so far off 1000. Maybe the pdb file format is broken? Drew -- System Information: Debian Release: 3.1 APT prefers unstable APT policy: (990, 'unstable') Architecture: i386 (i686) Kernel: Linux 2.6.10 Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8) Versions of packages openbabel depends on: ii libc6 2.3.2.ds1-20 GNU C Library: Shared libraries an ii libgcc1 1:3.4.3-12 GCC support library ii libopenbabel0 1.100.2-2 Convert and manipulate chemical da ii libstdc++5 1:3.3.5-12 The GNU Standard C++ Library v3 -- no debconf information -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
