Dear Wei, remember that you might have "something else" in the location occupied by each alternate conformation when it is not occupied by that particular conformation. If you only model two alternate conformations you are saying something like
that space A is occupied 50% of the time by this A conformation and 50% it is vacuum that space B is occupied 50% of the time by this B conformation and 50% it is vacuum It is more likely that you will have space A occupied N% by altConf A and (100-N)% e.g. by water/solvent. And for B you have (100-N)% altConf B and N% e.g. water/solvent. So you will need to model everything marked as N% as altConf A and everything marked (100-N)% as altConf B - including water/solvent. Because this is not yet done, the occupancy refinement might try to explain the non-vacuum density (water/solvent) by increasing the occupancy of each conformation so they sum up to larger than 1. Does that make sense? Cheers Clemens PS: in BUSTER (http://www.globalphasing.com/buster/) you can restrain the summed occupancy to one, which can help clarifying how to model the water/solvent region underneath each conformation ... depending on data quality/resolution of course. I'm sure other refinement programs have a similar feature. PPS: it can be sometimes useful to start refinement once from A=0.1/B=0.9 and a second run with A=0.9/B=0.1. Refinement should reach very similar final values in both cases - which is also a good way of providing confidence in the final results, I think. On Fri, Jul 21, 2017 at 01:10:15AM +0000, Wang, Wei wrote: > Hi Everyone, > > > One quick question: > > > When I do phenix refinement, I see continuous omitted map at one RNA chain > 3'-end (Fig1). > > There is no possibility of next nucleotide because I have built full-length > RNA sequence, which is well fitted into density. > > Hence two conformations is most possible for the last nucleotide. And our > biochemical data also supported the result of two conformations. > > However, I found the occupancy is always > 1.0 (fig2 and fig3), when I did > refinement of occupancy using phenix refinement,. > > I also think about the possibility of small molecules in the crystal buffer. > But in most structures of this protein, there is always no small molecule > here. > > > Any suggestions for occupancy refinement? I will appreciate your great help. > > > Best, > > Wei > > > > [cid:2b30f1a8-2a3a-4483-ac12-310f4bbed70b] > > > > > > -- *-------------------------------------------------------------- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *--------------------------------------------------------------
