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 on Z and RMS Z.
Also, look at our recent BDB article in PEDS (Vol 27, Iss 11 457-462),
because not every B-factor in the PDB is what you would expect it to be.
Gert
On 26/03/15 12:32, herman.schreu...@sanofi.com wrote:
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
Using google I found at that some of these numbers could be calculated
with Moleman, although I am not sure to what extend this program is
still maintained.
Older versions of Refmac would calculate r.m.s.d. ΔB’s for main chain
and side chain bonds, which I guess would be the “Main chain – Main
chain” and “Side chain – Side chain” values requested. However, what
would should I think of the “Main chain – Side chain” values;
differences between Calpha and Cbeta atoms?
What would be the use of these numbers? The standard CCP4 validation
programs, or any validation program I know, do not calculate these
numbers, so they do not seem to be extremely important. If somebody
could point me to a program which could calculate these number without
too much effort, I would be happy to do it. Otherwise, I would still
be willing to go the extra mile if someone could convince me that it
is useful to have these numbers.
Thank you for your help!
Herman
