On Apr 1, 2011, at 4:00 PM, Ed Pozharski wrote:
I need to calculate the electron density values for a list of spatial
locations (e.g. atom positions in a model) using an mtz-file that
already contains map coefficients. To write my own code may be easier
than I think (if one can manipulate mtz columns, isn't the only
problem
left how to incorporate symmetry-related reflections?), but I would
need
an alternative at least for troubleshooting purposes. So,
Does anyone know of a software tool that can calculate point electron
density for every atom in a structure?
If I would have to bring a dependency into this, the best choice for
me
would be clipper libs.
Hi Ed,
You'd have to convert the map to ccp4 or XPLOR format, but once
you've done that it's pretty straightforward to get the values at atom
positions using Chimera, pretty much as described here:
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-March/006202.html
except skipping the part where you average them across a residue.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
