Hello
I'm sure this is answered somewhere but I couldn't find it.
The ordering of atoms in a residue in Modeller output as in (a) is different from that usually seen in PDB files (b)
This is a problem when using the output in some other servers. Can the Modeller output be changed?
Thanks
Robin Stamler
Dept Molecular Genetics
University of Cincinnati
(a)
ATOM 1 N ALA B 1 10.145 12.378 3.667 1.00 25.81 1SG N+2
ATOM 2 CA ALA B 1 11.592 12.105 3.515 1.00 25.81 1SG C+3
ATOM 3 CB ALA B 1 12.225 11.817 4.886 1.00 25.81 1SG C+4
ATOM 4 C ALA B 1 11.834 10.932 2.631 1.00 25.81 1SG C+5
ATOM 5 O ALA B 1 11.538 10.968 1.437 1.00 25.81 1SG O+6
(b)
ATOM 586 N ALA A 86 -33.616 77.292 18.556 1.00 27.93 N
ATOM 587 CA ALA A 86 -34.153 76.748 17.311 1.00 27.40 C
ATOM 588 C ALA A 86 -33.329 77.134 16.085 1.00 27.32 C
ATOM 589 O ALA A 86 -32.386 77.921 16.172 1.00 25.96 O
ATOM 590 CB ALA A 86 -35.591 77.205 17.124 1.00 24.83 C
Robin Stamler wrote: > I’m sure this is answered somewhere but I couldn’t find it. > > The ordering of atoms in a residue in Modeller output as in (a) is > different from that usually seen in PDB files (b) > > This is a problem when using the output in some other servers. Can the > Modeller output be changed?
Modeller always outputs atoms in the same order. This is defined by the CHARMM topology library (usually modlib/top_heav.lib) which you can of course alter if you want a different order.
We cannot output atoms in "PDB order" because there is no consistent ordering. If some servers cannot read atoms in different orders, then these servers are broken, and should be fixed.
Ben Webb, Modeller Caretaker
participants (2)
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Modeller Caretaker -
Robin Stamler