Thank you Eleanor and Kevin, Eleanor suggested separating the two tasks. Eventually, I changed the cell with maprot and then used MAPMAN to zero the map below the cut-off level.
Kevin described how maprot works and suggested down-scaling the map to have more reasonable values for densities. These two suggestions give slightly different results. When the mask is applied in maprot the distribution of densities close to the cut-off level is smoothened. Peter. On Mon, Aug 3, 2009 at 10:26 AM, Eleanor Dodson <c...@ysbl.york.ac.uk>wrote: > 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. >> >> >> > >
