Hi Ed,
thanks for nice summary! Just a quick update while on this subject:
(using nightly build dev-724 an up) you will be able to get density value at
a given point using just one command:
phenix.map_value_at_point map_coeffs.mtz label="2FOFC" point="1 2 3"
point="4 5 6"
where you can specify as many points as you wish. You can request to use
either sigma or volume scaled map, as well as you can specify the grid_step
for map finess. You can use a parameter file if the number of points is too
large to be specified in the command line.
Pavel.
On Fri, Apr 8, 2011 at 9:07 AM, Ed Pozharski <[log in to unmask]> wrote:
> Thanks to everyone for their suggestions. The closest solution was
>
> 1. Expand dataset in P1 using SFTOOLS (keyword EXPAND)
> 2. Write it out in text file
> (WRITE data.hkl format(3i5,2f16.3) col col1 col2)
> 3. Use program HYDENS (Bart Hazes)
>
> It should be noted that the current version of HYDENS only works in
> orthorhombic spacegroups (although there may be a workaround of
> pre-calculating fractional coordinates with coordconv and then setting
> the unit cell to 1x1x1).
>
> This was the only solution that actually calculates electron density at
> the atomic positions. The rest of options were all to calculate the map
> and then interpolate it to the select (x,y,z). Several options exist
> for that (in the order they were received):
>
> 1. MAPMAN (PEEK keyword) (Gerard Kleywegt, James Holton, Edward Berry)
> 2. CCTBX (Pavel Afonin)
> 3. COOT (density_at_point, probably uses clipper libs) (Paul Emsley)
> 4. CHIMERA ("Values at Atom Positions") (Eric Pettersen)
>
> On Fri, 2011-04-01 at 11:16 -0400, 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.
> >
> > Thanks in advance,
> >
> > Ed.
> >
> >
>
> --
> "Hurry up before we all come back to our senses!"
> Julian, King of Lemurs
>
