It sometimes help to use the coot tool NCS ghost control to fit the good chain over the weak. Obviously you must work at a lower contour level than for the good chain..
Of course be careful about the basics.. Is the space group right? is there twinning? Check data quality - anisotropy - tc.. Eleanor On 4 May 2017 at 16:38, Vipul Panchal <panchal.vi...@igib.in> wrote: > Thanks Bert, > > I did understand not to delete such atoms or set occupancy to zero from > forum and literature. However, colleagues in the vicinity informed to take > approaches i mentioned earlier. Therefore, I thought to take opinion from > forum if something has changed recently. > > Thanking, > > > > On Thu, May 4, 2017 at 8:55 PM, Bert Van-Den-Berg < > bert.van-den-b...@newcastle.ac.uk> wrote: > >> This has been discussed before, I guess more than once.... >> >> I think most people (I'm sure i'll be corrected if wrong) would favor not >> removing any atoms or setting occupancies to zero and let the invisible >> atoms be accounted for by high B-factors (either set manually or just >> letting refinement do its thing). >> >> >> Bert >> >> >> ------------------------------ >> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Vipul >> Panchal <panchal.vi...@igib.in> >> *Sent:* 04 May 2017 16:12 >> *To:* CCP4BB@JISCMAIL.AC.UK >> *Subject:* [ccp4bb] Poor density fit. >> >> HI all. >> >> I am solving protein structure with 2.16A resolution. There are two chain >> in an asymmetric unit. I see that in one of the chain, many residues' >> density for side chains is incomplete and therefore results in poor density >> fit. >> >> *I want to know your opinions for the approach I have taken. Figures >> relevant to each approach have been attached herewith.* >> >> *Case1*: There is no experimental density at all. Therefore, i have >> deleted side chains to Gly. >> *Case2*: Though there is incomplete density for Leu, it is enough to >> suggest its rotamer. In this case, as may be seen, i have just set >> occupancy for atoms without density(CG, CD1, CD2) to zero. >> >> Hopeful for the response. >> >> -- >> Vipul Panchal >> Senior Research Fellow, >> Respiratory disease and biology, >> CSIR-IGIB >> (M)-9540113372 >> > > > > -- > Vipul Panchal > Senior Research Fellow, > Respiratory disease and biology, > CSIR-IGIB > (M)-9540113372 >
