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I CANT BE SURE of what has happened BUT maprot is a very complicated procedure and your script is trying to do 2 things at once - change the cell and apply the mask. I would try changing the cell first, then generating the mask, then applying it or else: generate mask, apply mask, then change cell. But at every stage look at the result! ( mapslicer or coot or whatever) to make sure you have really achieved what you are aiming for! Eleanor Peter Grey wrote: > Hi all, > > I am trying to cut density from EM map (in a small P1 cell) into big P1 cell > for MR. > > The mask is defined by a certain cut-off level in mapmask : > > mapmask \ > mapin em.map \ > mskout em.msk << eof > MASK CUT 353 > MODE mapin > eof > > I use maprot to cut the density to the big P1 (that has the same grid > spacing as the original small P1). > > maprot wrkin em.map mskin em.msk mapout cut.map << eof > MODE TO > CELL XTAL 1098. 1098. 1098. 90. 90. 90. > GRID XTAL 375 375 375 > SYMM P1 > AVER 1 > ROTA EULER 0.0 0.0 0.0 > TRANS 0.0 0.0 0.0 > END > eof > > When cut.map is read by mapmask the program reports that the minimum of the > map is -310. > > How come the minimum is not the cut-off level used to define the mask ? What > am I missing/Doing wrong ? > > Many thanks in advance for all suggestions and comments, > > Peter. > >