Dear Herman, I am not sure what you really want. Maybe this can help you.
You can get the following numbers out of MAIN 1. comparing a pair of selections. It makes sense only if they are equivalent. > rms b-val select my_selection_1 end select my_selection_2 end 2. Show command does statistics for a given selection. The “bond" keyword considers fluctuations between bonding atoms, whereas without it the selection is considered as one group. > show b-val bond select my_selection end best regards, dusan > On Mar 27, 2015, at 1:00 AM, CCP4BB automatic digest system > <lists...@jiscmail.ac.uk> wrote: > > Date: Thu, 26 Mar 2015 11:32:43 +0000 > From: herman.schreu...@sanofi.com <mailto:herman.schreu...@sanofi.com> > Subject: 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 > Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ <http://bio.ijs.si/sbl/> Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS "Jozef Stefan" e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com <http://www.skype.com/>
