biochem_fan biochem-fan

## list.sh
#!/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'

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

## CMakeLists.txt
# 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

## FormatTIFFTVIPS.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.

## NOTES.md

      
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                Warp-RELION4-M Protocol
              
          
    RELION interoperabiity with Warp and M

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.
Special thanks to Alister Burt, Pranav Shah and Dimitry Tegunov for discussion on this Twitter thread.
Download the movies

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

  
## NOTES.md

      
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              March 13, 2024 07:29
            
              
                AlphaFold2 without Docker
              
          
    Warning: this is my personal messy ad-hoc note. Not intended for production installation.
Instruction by @kalinialab is probably better.
My environment


Cent OS 7.0
CUDA 11.2
Without root accoumt

Directories


## group_by_time.py
# 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.

## BoxNet2DRunner.cs
/*  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

## atom2svg.py
# atom2svg.py by @biochem_fan
# VERSION: 210224
# License: GPLv2 or later (ask me if this is inconvenient for you)
#
# LIMITATIONS:
# - This supports only a single chain. If you have more chains, shift residue IDs and merge chains.
#
# TODO:
# - Residue numbers (how to pack??)
#

## Compile_WarpLib_on_Linux.md

      
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                Warp on Linux
              
          
    Tested Environment


Ubuntu 20.04 LTS
CUDA 11.6
GCC 9.4.0
Mono 6.12.0

Be careful with your driver and runtime version!
For example, when I tried to run a binary compiled with CUDA 9.2 on a machine with CUDA runtime 9.0, it said 'DeviceCount = 0'.
	#!/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'
	# This has been merged to the dxtbx (with many updates).
	# See https://github.com/cctbx/dxtbx/blob/main/src/dxtbx/format/FormatROD.py.
	# 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
	# 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.
	# 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
	# atom2svg.py by @biochem_fan
	# VERSION: 210224
	# License: GPLv2 or later (ask me if this is inconvenient for you)
	#
	# LIMITATIONS:
	# - This supports only a single chain. If you have more chains, shift residue IDs and merge chains.
	#
	# TODO:
	# - Residue numbers (how to pack??)
	#