structure_factors() "d_max" equivalent
Hello All, I'm new to cctbx and trying to get the most rudimentary understanding. I would like to select all of the reflections within a particular resolution shell. This line from the tutorial: f_calc = quartz_structure.structure_factors(d_min=2).f_calc_array() gets all structure factors through the highest resolution of d_min=2 Å (excluding 0 0 0). My question: is there an equivalent to a d_max argument for this function (i.e. a low resolution limit)? James
Hi James,
i think that the method resolution_filter, of miller.array objects, could
do that for you.
Cheers,
Claudia Millán ([email protected])
Institut de Biologia Molecular de Barcelona (IBMB-CSIC)
Barcelona, Spain
2013/3/21 James Stroud
Hello All,
I'm new to cctbx and trying to get the most rudimentary understanding.
I would like to select all of the reflections within a particular resolution shell. This line from the tutorial:
f_calc = quartz_structure.structure_factors(d_min=2).f_calc_array()
gets all structure factors through the highest resolution of d_min=2 Å (excluding 0 0 0).
My question: is there an equivalent to a d_max argument for this function (i.e. a low resolution limit)?
James _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
Hi James, a few options: 1) f_new = f_calc.resolution_filter(d_min=3, d_max=5) 2) d_spacings = f_calc.d_spacings() selection = d_spacings > 3 selection &=d_spacings < 5 f_new = f_calc.select(selection) Pavel On 3/21/13 12:50 AM, James Stroud wrote:
Hello All,
I'm new to cctbx and trying to get the most rudimentary understanding.
I would like to select all of the reflections within a particular resolution shell. This line from the tutorial:
f_calc = quartz_structure.structure_factors(d_min=2).f_calc_array()
gets all structure factors through the highest resolution of d_min=2 Å (excluding 0 0 0).
My question: is there an equivalent to a d_max argument for this function (i.e. a low resolution limit)?
James _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
I realize everyone has an endless to-do list, but this would be
awesome wiki material.
Also note that the binning functionality of cctbx.miller.array
provides a way to generate resolution shells automatically, although
I'd need to check the exact syntax.
-Nat
On Thu, Mar 21, 2013 at 7:34 AM, Pavel Afonine
Hi James,
a few options:
1) f_new = f_calc.resolution_filter(d_min=3, d_max=5)
2) d_spacings = f_calc.d_spacings() selection = d_spacings > 3 selection &=d_spacings < 5 f_new = f_calc.select(selection)
Pavel
On 3/21/13 12:50 AM, James Stroud wrote:
Hello All,
I'm new to cctbx and trying to get the most rudimentary understanding.
I would like to select all of the reflections within a particular resolution shell. This line from the tutorial:
f_calc = quartz_structure.structure_factors(d_min=2).f_calc_array()
gets all structure factors through the highest resolution of d_min=2 Å (excluding 0 0 0).
My question: is there an equivalent to a d_max argument for this function (i.e. a low resolution limit)?
James _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
participants (4)
-
Claudia Millán Nebot
-
James Stroud
-
Nathaniel Echols
-
Pavel Afonine