Use of the first map during refinement

Submitted by Matthieu on Wed, 2016-03-30 12:02

Forums

Frealign

Hi,

When starting a refinement with frealign using only:
- a stack
- a .par file (XXX_1_r1.par)
- a mparameter file including start_process=2 and end_process=2
it first generates a map with index 1, refine and generate a new map and a new .par file with index 2 (XXX_2_r1).
Is the first map with index 1 (XXX_1_r1.xxx) used in the actual refinement or just an output?
Is is possible to replace this first reconstruction map by another map to be used in the refinement?

Thanks

niko Wed, 2016-03-30 17:47

Yes, this is correct: if for the previous cycle only a .par file is supplied it uses the parameters from this file to calculate a reconstruction before starting a new cycle. If you would like to use a pre-calculated map instead, just copy it into the same place and with the same name as the map that Frealign calculated (e.g. XXX_1_r1.mrc if you are using MRC files).