. März 2015 15:10
An: Schreuder, Herman RD/DE
Betreff: RE: [ccp4bb] r.m.s.d. ΔB
Hi Herman,
As you state MOLEMAN2 from the USF package will give these…it is old but
linux/mac distribution still work and is easy to install…
read in pdb file and then type ‘bf bo’ and all values you state are printed
Dear Bulletin Board,
A referee wants for the “Table 1” in the supplementary information the
following data:
The r.m.s.d. ΔB (bonded atoms) (Å2)
All protein atoms
Main chain – Main chain
Side chain – Side chain
Main chain – Side chain
r.m.s.d. ΔB (Non-bonded contacts) (Å2)
All protein atoms
Ls,
I dont think these numbers are useful by themselves. It makes more sense
to look at differences in these numbers (between bound atoms in your
protein and in 'the rest of the PDB') as function of as many external
conditions as statistics allow. Then determine averages with SD, and
score
