On Tue, 2011-04-12 at 22:54 -0400, Edward A. Berry wrote:
What about doing the Fourier summation at the precise location
requested,
in order to not calculate the map or interpolate at all?
Input would be the mtz file rather than map file.
eab
One advantage of map interpolation is speed -
Dear Tim,
On Mon, 2011-04-11 at 10:44 +0200, Tim Gruene wrote:
since you pointed it out I wonder if there is any reasonable (i.e.
w.r.t. data
error/ resolution) difference between the interpolated values and the
calculated
value. I actually doubt that
That should depend on the quality of
On Fri, 2011-04-08 at 18:06 -0700, Pavel Afonine wrote:
phenix.map_value_at_point map_coeffs.mtz label=2FOFC point=1 2 3
point=4 5 6
Cool. Afaiu, this is interpolation. A useful extension would be
automatic picking of (x,y,z) from a pdb-file (a la mapman), although a
determined person can
Hi Ed,
yes, this is the eight-point interpolation, but since you can select to
choose very small grid step for the map calculation (grid_step parameter), I
hope this should be ok. If necessary, I can add an option so it will give
you the map value at the closest grid point instead of
Pavel Afonine wrote:
Hi Ed,
yes, this is the eight-point interpolation, but since you can select to
choose very small grid step for the map calculation (grid_step
parameter), I hope this should be ok. If necessary, I can add an option
so it will give you the map value at the closest grid point
That is exactly what HYDENS is doing. A good interpolation with small
grid steps should be equally good but with current computers and just a
few hundred or even thousand points to evaluate, a classical Fourier
summation is pretty fast and, for me, easier to program than a proper
cubic-spline
Hi Ed,
yes, this is one of possible ways of doing this. Although I doubt it will
make any (significant) difference in practice compared to other options. All
mentioned methods should normally result in similar values.
Pavel.
On Tue, Apr 12, 2011 at 7:54 PM, Edward A. Berry ber...@upstate.edu
Dear Ed,
since you pointed it out I wonder if there is any reasonable (i.e. w.r.t. data
error/ resolution) difference between the interpolated values and the calculated
value. I actually doubt that
Cheers, Tim
On Fri, Apr 08, 2011 at 12:07:21PM -0400, Ed Pozharski wrote:
Thanks to everyone
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
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
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
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
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
Hi Ed,
if you are familiar with CCTBX then
map_value = map_data.eight_point_interpolation(site_fractional)
Also, there is a similar method that will just give you the density value at
closes grid point.
Let me know if interested, and I can send you a 10 lines Python
script-example that will do
Hi Ed,
I wrote a short program name HYDENS that takes a PDB file and an H K L
amplitude phase file for a full hemisphere of data. You can make the
latter from an MTZ with sftools. The program is on my website at
http://129.128.24.248/highlights.html. There is a linux executable as
well as
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