I have been reprimanded by the PDB as:
"In this instance we could not recommend matrix formulation because of
the substantial conformational differences between individual
subunits. Only with the full set of coordinates released can other
groups perform independent analyses/evaluation."
both structures have the same split
zmore 3j3y.cif.gz | grep -i split
zmore 3j3q.cif.gz | grep -i split
this doesnt make sense ?
all the split files have REMARK 2 RESOLUTION. NULL ANGSTROMS
while each split file doesnt refer to the parent (which one?)
SPLIT 1VUU 1VUV 1VUW 1VUX 1VUY 1VUZ 1VV0 1VV1 1VV2 1VV3 1VV4 1VV5
1VV6 1VV7
SPLIT 2 1VV8 1VV9 1VVA 1VVB 1VVF 1VVG 1VVH 1VVI
Only this one has a resolution
3J34 REMARK 2 RESOLUTION. 8.60 ANGSTROMS.
i.e. the large files seem to not have a resolution
zmore 3j3y.cif.gz | grep -i resol
_em_3d_reconstruction.resolution ?
_em_3d_reconstruction.resolution_method ?
zmore 3j3q.cif.gz | grep -i resol
_em_3d_reconstruction.resolution ?
_em_3d_reconstruction.resolution_method ?
The two structures appear to be
(i) built on a 8.6Ang EM structure
(ii) from a molecular dynamics run(s) with NAMD
is it a theoretical model
Also at 8.6 Ang one cannot see a 3-10 helix
only in the MD can such a thing come out
The authors cannot have built the EM fitted structure by hand
and found differences - so the EM fitted structure
has to have exact symmetry while the MD structure (why is it in the PDB ?)
may have differences after as they say a 1.5 micro-second MD run
with NAMD
[I am old enough to remember that picoseconds were possible not micro
seconds]
And then how can anyone analyse a normal pdb virus structure which
has incomplete coordinates but symmetry matrices and for the largest
structure in the pdb, i.e.
1m4x 1680 3 # well this has 5040 chains in biomolecule
does anyone really believe 8.6Ang data has differences in symmetry
If one does ? then I must be in dreamland
zcat 3j3q.cif.gz | grep _em > 3j3q
zcat 3j3y.cif.gz | grep _em > 3j3y
diff 3j3q 3j3y
there are no differences apart from vitrification category in one
file and pdb idcodes
they both say
;The model was built using hexamer of hexamers (PDB entry 3J34) and
pentamer of hexamers (computer-based MD model available upon request).
OK so the entire PDB ftp/policy is changed over a theoretical model?
