CrystFEL

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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

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/.