biochem_fan biochem-fan

ORTEP style thermal ellipsoid in PyMOL

Draw thermal ellipsoids in a style similar to ORTEP.

thermal_ellipsoid selection, [cgo_name, [draw_rings]]

This document examines how to use RELION 4.0 (beta2 as of writing) with Warp 1.09 and M 1.09 for single particle analysis.

We use the RELION tutorial dataset (beta-galactosidase collected on JEOL CRYO ARM 200, a subset of EMPIAR-10204).

Warning: this is my personal messy ad-hoc note. Not intended for production installation. Instruction by @kalinialab is probably better.

	import numpy as np
	import sys

	# Usage: cat indexing5/mille-run/mille-data-.bin \| dials.python ~/scripts/rmsd_from_millepede.py \| tee indexing5/RMSD
	# TODO: Use online standard deviation calculation
	# TODO: Make this more general

	NPANELS = 9
	residuals = [[] for x in range(NPANELS * 2)]

	#!/bin/bash

	JOB=$1

	for f in */$1/dials.scale.log; do
	DIR=`dirname $f \| cut -d/ -f1,2`
	awk '/cc_ano/ {f=1; b=999; next}
	f==1 && $13 > 0.3 {b = $2;}
	f==1 && $13 <= 0.3 {printf FILENAME" "b" "; exit}' $f
	grep "Best sol" $DIR/dials.cosym.log\| tr -d '\n'

	# A simple project to show including /opt/homebrew/include
	# in the GCC search path breaks OpenMP because GCC picks up
	# libomp headers for LLVM.
	# https://github.com/3dem/relion/issues/913#issuecomment-1263499265

	# On Mac OS X:
	# CC=gcc-12 cmake ..; make; ./omp_test # hangs
	# CC=gcc-12 cmake .. -DAVOID_JPEG=ON; make; ./omp_test # OK
	# gcc-12 -o omp_test ../main.c -fopenmp; ./omp_test # OK

	# Group particles by time by @biochem_fan
	# GPLv3; contact me if you want other license

	import sys
	import numpy as np
	from collections import OrderedDict

	def load_star(filename):
	from collections import OrderedDict
	# This is not a very serious parser; should be token-based.

	/* BoxNet2D runner
	* Based on Warp 1.0.7 by Dimitry Tegunov https://github.com/cramerlab/warp/
	* Command line interface and Linux port by @biochem_fan
	* Licensed under GPLv3
	*/

	using System;
	using System.IO;
	using System.Linq; // for toList()
	using System.Diagnostics; // for Stopwatch

	# This has been merged to the dxtbx (with many updates).
	# See https://github.com/cctbx/dxtbx/blob/main/src/dxtbx/format/FormatROD.py.

	# This dxtbx class has been renamed to FormatTIFFMultipage.py and the latest version is now hosted in
	# https://github.com/GKLabIPR/MicroED/blob/main/scripts/FormatTIFFMultipage.py.