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
