Or to put it slightly differently: the masking of symmetry-related
density works (only) when the cell and symmetry of the map is the same
as the cell and symmetry of the atoms for the mask.
Paul.
Bernhard Lohkamp wrote:
Hi,
you dont say how you obtained you map. Usually in Coot, thanks to
clipper, the maps extend over the whole "crystal space", i.e. you have
the same map in all asu. However this only works if the map is either
generated by Coot itself (from an mtz file) or if you read a map file
which covers only/exactly the asu (or unit cell). I assume you didnt use
either of these. So, please try that and you will get the same, masked
map around all molecules incl the symmetry related ones. Alternatively
you could write out the symmetry related molecules and masked them again.
B
Hi all,
I am looking for a strategy to obtain a density map which only contain
densities where no assignment was made in the model.
When I load a PDB file and its corresponding density map to coot, I
can mask all regions contain the model. And then several parts were
left around the edge of the model.
However, these parts are not totally the one where no assignments was
made, because some of them belong to the adjacent asymmetric unit
part. I can display these parts by using " cell and symmetry" function
in coot and can see the model overlap with the map.
But how can I also make masks on them and let only the part where no
assignments was made left from the whole map. That is how to mask the
model and also its images.
Thanks
