Dear Eleanor, Yes, thanks for pointing it out - i will give it a shot absolutely and see how it works - still curious about making a mask for map calculation though…:)
Best, Tommi On Feb 10, 2017, at 1:30 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> wrote: Well - in my experience it gives much clearer density for missing features.. E On 10 February 2017 at 10:59, Kajander, Tommi A <tommi.kajan...@helsinki.fi<mailto:tommi.kajan...@helsinki.fi>> wrote: Dear Eleanor, I will try that, just wondering if excluding solvent masking completely doenst have detrimental effect on the overall quality of the map? Tommi On Feb 10, 2017, at 12:43 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> wrote: Certainly if you are using REFMAC with an incomplete model you should specify SCALE TYPE BULK SOLVENT NO Otherwise it assumes any density outside the given model is to be effectively screened out.. Eleanor On 10 February 2017 at 09:37, Kajander, Tommi A <tommi.kajan...@helsinki.fi<mailto:tommi.kajan...@helsinki.fi>> wrote: Hi All, Was there a convenient way to make a solvent mask for a region with a model - its been a while - and use that to generate maps (i have a domain that is only partially visible, could not be found be molecular replacement), its there though. Could be that its not well ordered, but I was wondering if the bulk solvent masking is just wiping it out. (basicly something like half a domain, e.g. half of individual beta-strands, are missing.) resolution is bit limited (at best 3 Å) so automated building and refinement doesnt work terribly well. I could just place a model there and make a mask somewhere and include in map calculation? Thanks for suggestions, tommi
