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Submitted By: Geoff Hutchison (ghutchis)
Assigned to: Nobody/Anonymous (nobody)
Summary: PDB format on 1000+ angstrom coordinates
>From time to time I notice that rasmol or pymol do weird stuff with
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
HETATM 999 C LIG 169 278.332-258.604-1558.640 1.00 0.00
HETATM 1000 C LIG 0 278.374-257.892-1561.950 1.00 0.00
(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.