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render_hkl: render 2D slices of reciprocal space from reflection data

Synopsis

render_hkl [options] ... -p unitcell.pdb file.hkl
render_hkl --help

Description

render_hkl takes a set of reflection data and plots 2D central sections of the reciprocal lattice as circles using a colour scale in a PDF file. You need to provide, at a minimum, the reflection data and a PDB file with at least a CRYST1 line containing the unit cell parameters.

Options

-d h,k,l
--down=h,k,l
Specify the indices for the downward direction of the resulting plot. Default: --down=1,0,0.
-r h,k,l
--right=h,k,l
Specify the indices for the 'right' direction of the resulting plot. The direction will be approximately to the right, the exact direction depending on the unit cell. Default: --right=0,1,0.
--zone=z
Show reflections for which g.r=z, where g is the reflection index (i.e. hkl) and r is the zone axis direction. z hence represents the Laue zone number.
-o filename
--output=filename
Write the output (in PDF format) to filename. Default: --output=za.pdf.
-p unitcell.cell
-p unitcell.pdb
--pdb=unitcell.pdb

Specify the name of the file containing the unit cell information, in PDB or CrystFEL format.

--boost=n
Squash the colour scale by a factor of n. When n=1, the top of the colour scale will represent the highest intensity found in the data set (not the highest intensity found in the projection).
-y pointgroup
--symmetry=pointgroup
Specify the symmetry of the reflection list.
-c scale
--colscale=scale
Use scale as the colour scale. Possible scales are: mono, invmono and colour.
-w weight
--weighting=weight

Colour the reciprocal lattice points according to weight. Possibilities for weight are:

I
The intensities of the reflections
sqrtI
The square roots of the intensities of the reflections. Negative intensities will be set to zero.
count
The numbers of observations of the reflections. The numbers will be corrected for the point group multiplicities of the reflections according to the given symmetry (see --symmetry).
rawcts
The raw numbers of observations of the reflections, without performing the correction described for count.

The default is --weighting=I.

--scale-top=n
Force the top of the colour scale to correspond to a value of n. Any value you give for --boost will be ignored.
--colour-key
Write the selected colour scale out to 'key.pdf' in the current directory.
--res-ring=res
Draw a resolution ring at res Angstroms. You can use this option multiple times to get more than one ring.
--highres=res
Render spots only up to res Angstroms.
--no-axes
Do not draw the reciprocal space axes on top of the plot.

Author

This page was written by Thomas White.

Reporting bugs

Report bugs to taw@physics.org

Copyright and Disclaimer

Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.

Please read the AUTHORS file in the CrystFEL source code distribution for a full list of contributions and contributors.

CrystFEL is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with CrystFEL. If not, see http://www.gnu.org/licenses/.

See also

crystfel check_hkl hdfsee

If CrystFEL is installed on your computer, you can read this manual page offline using the command man render_hkl.