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?
fft to calculate the map, then mapman with the "peek value" command.
Give it a pdb file (fek.pdb) with the coordinates of the atoms,
it returns a pdb file with electron density at those points in
the B-factor column. Several options for interpolating map values to the
chosen point, iirc.
Something like:
setenv MAPSIZE 5000000
/data/trp/berry/usf/rave/lx_mapman -b <<eof
re m1 d.map CCP4
!norm m1
!pick level 5.2
!pick peaks m1 danopeaks.pdb pdb
peek value m1 fek.pdb fepkhght.pdb int
quit
eof
If I would have to bring a dependency into this, the best choice for me
would be clipper libs.
Thanks in advance,
Ed.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
