[phenixbb] problems running refinement of shaken model against half map

L. Hielkema l.hielkema at rug.nl
Thu Nov 21 07:27:57 PST 2019

Hi all,

For the validation of my model to my map in phenix 1.17.1 I tried to refine my shaken model (0.5Å) against my half map in phenix real space refine. However, whatever I try I get a weird behaviour in the FSC(Model-map), see the image below. It seems not to be able to reach 0 in the correlation, but keeps getting stuck at 0.1. 

I tried various things to solve this, but unfortunately nothing helps:
- Using the other half map
- Cut of the heterogeneous part of my model and map and refine this
- Used refined data without using a mask for the last iterations
- Used different resolutions to refine against
- Tried data from someone else in the lab (same microscope, same imaging conditions), to check if I am doing something wrong (this gave good results)

When doing the same refinement in Refmac5 in ccpem 1.4 it does seem to work, however I would not like to switch programs, because this will mess up my final model.


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