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<div style="font-family: sans-serif; font-size: 16px">Any Fourier map without an F000 term will analytically have a mean value of 0.<br>
<br>
Lynn<br>
<br>
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<div style="font-family: sans-serif; font-size: 14px"><b>From: </b>Nathaniel Echols <nechols@lbl.gov><b><br>
To: </b>cctbx mailing list <cctbxbb@phenix-online.org><b><br>
Sent: </b>Tue, Oct 16, 2012 17:22:17 GMT+00:00<b><br>
Subject: </b>Re: [cctbxbb] Patterson map data structure<br>
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<div class="PlainText">On Tue, Oct 16, 2012 at 6:47 AM, Dmytro Guzenko<br>
<Dmytro.Guzenko@pharm.kuleuven.be> wrote:<br>
> rmap = pmap.real_map_unpadded()<br>
> n_real = pmap.n_real()<br>
> unit_cell = pmap.unit_cell()<br>
> grid2cart = maptbx.grid2cart(n_real,unit_cell.orthogonalization_matrix())<br>
><br>
> n_points_total = n_real[0]*n_real[1]*n_real[2]<br>
> cart_coord = flex.double(flex.grid(3,n_points_total))<br>
> p_weight = flex.double(n_points_total)<br>
><br>
> for plain_ind,grid_point in enumerate(flex.nested_loop(n_real)):<br>
> cart_coord[0,plain_ind],cart_coord[1,plain_ind],cart_coord[2,plain_ind] = grid2cart(grid_point)<br>
> p_weight[plain_ind] = rmap[grid_point]<br>
<br>
There are better arrays for storing the coordinates, e.g.:<br>
<br>
cart_coord = flex.vec3_double(flex.grid(n_real))<br>
p_weight = flex.double(rmap.size())<br>
<br>
for plain_ind,grid_point in enumerate(flex.nested_loop(n_real)):<br>
cart_coord[grid_point] = grid2cart(grid_point)<br>
p_weight[plain_ind] = rmap[grid_point]<br>
<br>
> By the way, I noticed that many weights are negative, is this possible in a patterson map or am I doing something wrong?<br>
<br>
This is normal - I believe it's a Fourier series termination error,<br>
but I still don't fully understand the reason. An Fobs map will have<br>
the same problem; the mean will always be approximately zero.<br>
Technically, if the map were perfect with no missing data, it would be<br>
uniformly positive, but that's never actually the case. There are<br>
ways to "fix" the map so it's all-positive, such as maximum entropy<br>
cleanup, but in practice I think we just ignore the negative values<br>
(at least for Fobs/2mFo-DFc maps - not sure how Patterson maps are<br>
usually handled).<br>
<br>
-Nat<br>
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