RENDER_HKL(1)

💅 RENDER_HKL(1) — bestie edition 🎀

okay so this is render_hkl(1) from the General Commands Manual — yes, the whole "General Commands Manual" vibe, we're in the big leagues now ✨

🌸 NAME 🌸

render_hkl — render 2D slices of reciprocal space from reflection data 💫

🦋 SYNOPSIS 🦋

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

render_hkl --help

💖 DESCRIPTION 💖

so render_hkl takes your reflection data and plots 2D central sections of the reciprocal lattice as circles, using a colour scale, into a PDF file. iconic, honestly 🌈

the bare minimum you gotta give it: the reflection data, and a PDB file with at least a CRYST1 line holding the unit cell parameters. that's the entry fee, no cap 💅

✨ OPTIONS ✨

• -d h,k,l, --down=h,k,l — sets the indices for the downward direction of the plot. default: --down=1,0,0 🫶
• -r h,k,l, --right=h,k,l — sets the indices for the 'right' direction of the plot. heads up: the direction is only approximately to the right — the exact direction depends on the unit cell. default: --right=0,1,0 🎀
• --zone=z — shows reflections for which g.r=z, where g is the reflection index (i.e. hkl) and r is the zone axis direction. so z is literally the Laue zone number 💫
• -o filename, --output=filename — writes the output (in PDF format) to filename. default: --output=za.pdf 📄
• -p unitcell.cell, -p unitcell.pdb, --pdb=unitcell.pdb — names the file containing unit cell information, in PDB or CrystFEL format 🔍
• --boost=n — squashes the colour scale by a factor of n. when n=1, the top of the colour scale represents the highest intensity found in the data set (not the highest intensity found in the projection). lowkey important distinction, remember it 👀
• -y pointgroup, --symmetry=pointgroup — specifies the symmetry of the reflection list 🧚
• -c scale, --colscale=scale — uses scale as the colour scale. possible scales are: mono, invmono and colour 🌸
• -w weight, --weighting=weight — colours the reciprocal lattice points according to weight. the possibilities for weight are:
  • I — the intensities of the reflections
  • sqrtI — the square roots of the intensities of the reflections. negative intensities get set to zero 🚫
  • count — the numbers of observations of the reflections. these numbers get 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, with no correction done, i.e. without performing the correction described for count

the default is --weighting=I ⭐

• --scale-top=n — forces the top of the colour scale to correspond to a value of n. any value you give for --boost will be ignored 💀
• --colour-key — writes the selected colour scale out to 'key.pdf' in the current directory 🎨
• --res-ring=res — draws a resolution ring at res Angstroms. you can use this option multiple times to get more than one ring — stack 'em, collect 'em 🍓
• --highres=res — renders spots only up to res Angstroms 🔥
• --no-axes — does not draw the reciprocal space axes on top of the plot 🙈

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👑 AUTHOR 👑

this page was written by Thomas White 💜

😭 REPORTING BUGS 😭

report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel> 🫶

🌈 COPYRIGHT AND DISCLAIMER 🌈

copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.

render_hkl, and this manual, are part of CrystFEL.

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(7), check_hkl(1)

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and that's the whole page bestie, mwah 💋 — this one's straight out of the CrystFEL General Commands Manual, page render_hkl(1) (the footer's literally just the same RENDER_HKL(1) again, so no spicy version-or-date tea to spill) 🎀✨