Dear Bulletin Board, The correct answer came from Ashley Pike (see below). Moleman2 calculates indeed exactly the values our reviewer wants to see! There must be some Uppsala connection here….
Best regards, Herman Von: Ashley Pike [mailto:[email protected]] Gesendet: Donnerstag, 26. März 2015 15:10 An: Schreuder, Herman R&D/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 out – this is the only software I am aware of that gives these values so I guess the reviewer is a moleman/moleman2 user fan! Ash From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of [email protected]<mailto:[email protected]> Sent: 26 March 2015 11:33 To: [email protected]<mailto:[email protected]> Subject: [ccp4bb] r.m.s.d. ΔB 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
