Hi Arjen, thank you so much! Yes, I am working with coot, and you just solved a problem that bothered me for days!
We found the same box also on the R/RC button on the toolbar. It’s called Refinement Weight. Best regards, Anne On 28 Feb 2017, at 17.36, arjen jakobi <xtalst...@gmail.com<mailto:xtalst...@gmail.com>> wrote: Dear Anne, You do not mention it, but from your description I infer that you are using Coot? EM potential maps differ in characteristic properties from crystallographic maps. The problem you describe likely comes from inappropriate weighting of the map term in the refinement target. You may need to reduce the matrix weights on the map (Extensions -> Refine -> Set Refinement Options). Best, Arjen On 28 February 2017 at 15:40, Ries, Anne <anne.r...@helsinki.fi<mailto:anne.r...@helsinki.fi>> wrote: Hi, I am working with a cryo EM map at 4.2 A and would like to de novo build a model into the map. As our map is initially calculated in .mrc format, we converted it into .mtz format. I used a poly-Ala helix .pdb file as a model to begin with. I opened the .pdb of the helix and the .mtz map in coot. Up to here everything works fine, map is nicely displayed, follows changes of the sigma value. I can do a rigid body fit of the helix within the map, works just fine. When I try to do a realspace refinement though, the geometry window shows very bad values and the message “Incorrect chiral volumes” for each of the amino acids. Apart from the bad values, the realspace refine zone does not appear as a grey copy of the area, that can be dragged around. Instead single atoms or other artefacts, which can be dragged around, appear around the helix. Accepting the real space refinement deletes the respective part of the chain and keeps the single atoms and artefacts. Our helix is a right handed standard helix and our map has the correct handedness (we even inverted the map to check, but still get the same error). We also deleted the initial helix and built a new helix with coot and we tried to build beta strands in other parts of the same map in coot. It always yields the same error. Has anybody seen that before? Best regards, Anne
