Hi all,
I am trying to recreate the unit cell assemblage of 4z1r (visible using the PDB
NGL viewer on the website).
After importing my structure and checking the unit cell dimensions, I set the
space group (5 c 2y c 1 2 1 as determined using Maestro) then select “Fill Unit
Cell”. Visually, everything looks good. But unfortunately, all means of
identifying the atom and the corresponding residue is lost in the exported pdb
and matching/replicated atoms as listed together rather than in their
corresponding residue order. I plan on importing this into Gromacs, but in its
current state the .pdb file is impossible to read.
E.g.,
HETATM 1 N UNL 1 3.631 3.685 8.676 1.00 0.00 N
HETATM 2 N UNL 2 165.943 3.685 16.225 1.00 0.00 N
HETATM 3 N UNL 3 89.418 10.655 8.676 1.00 0.00 N
HETATM 4 N UNL 4 80.156 10.655 16.225 1.00 0.00 N
HETATM 5 C UNL 5 4.854 4.502 8.763 1.00 0.00 C
HETATM 6 C UNL 6 164.720 4.502 16.138 1.00 0.00 C
HETATM 7 C UNL 7 90.640 11.472 8.763 1.00 0.00 C
HETATM 8 C UNL 8 78.933 11.472 16.138 1.00 0.00 C
HETATM 9 C UNL 9 6.049 3.864 8.047 1.00 0.00 C
HETATM 10 C UNL 10 163.525 3.864 16.854 1.00 0.00 C
HETATM 11 C UNL 11 91.836 10.833 8.047 1.00 0.00 C
HETATM 12 C UNL 12 77.738 10.833 16.854 1.00 0.00 C
HETATM 13 O HOH 13 5.956 2.719 7.616 1.00 0.00 O
HETATM 14 O HOH 14 163.618 2.719 17.285 1.00 0.00 O
HETATM 15 O HOH 15 91.743 9.688 7.616 1.00 0.00 O
HETATM 16 O HOH 16 77.831 9.688 17.285 1.00 0.00 O
Any idea how to fix this?
I’m beginning to think the only way around this would be to import my
asymmetric unit structure into Gromacs, replicate the protein, identify the
x,y,z location of a central atom from within Avogadro of one of the three
replicated molecules, and perform some basic maths to translate the copies.
Thanks
Anthony
Dr Anthony Nash
Department of Chemistry
University College London
Skeletal Tissue Dynamics Group
Committee member of London Matrix Group @LondonMatrixGrp
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