Dear Vipul, the first thing I would check is why one chain has good and the other chain has poor side chain density. Are the B-factors of one chain much higher than of the other? Does one chain have more/better crystal contacts to stabilize its position in the crystal? Is the structure well-refined (e.g. R~20%; Rfree~25%)?
If this has all been checked, I would do as Bert suggested and leave the side chains intact and let the B-factors take care of the disorder. However, this is a very contentious issue, with probably 50% of the board members in favor of leaving the side chains intact and the other 50% in favor of truncating undefined side chains. Both approaches have their merits and I would do what you personally feel is the best, rather than setting off another mega-thread on this subject. You could try to google previous threads on this issue if you are interested! ;-) Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Vipul Panchal Gesendet: Donnerstag, 4. Mai 2017 17:13 An: CCP4BB@JISCMAIL.AC.UK Betreff: [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
