marinegor

Data

I'm using trajectory and topology for an 1us run generated according to lysozyme in water tutorial and used later in this publication. It a full-atom xtc trajectory containing 25690 atoms in total.

Both trajectory and topology can be accessed here: https://zenodo.org/record/8349796

Hardware

Drive

marinegor

# Unmount the database image
fusermount -u $TMPDIR/alphafold_data

marinegor

#!/usr/bin/env python3

import mrcfile
import click
from typing import Optional
from pathlib import Path
import numpy as np

@click.command()
@click.argument("input_map")

marinegor

#!/usr/bin/env python3

'''
usage: get_empair_raw_folder.py [-h] [--quiet QUIET] url         

positional arguments:  
  url            EMPAIR raw data folder link (for example, http://ftp.ebi.ac.u    
                 k/empiar/world_availability/10025/data/14sep05c_raw_196)
optional arguments:            
  --quiet QUIET  Whether to write loggin messages

marinegor

#!/usr/bin/env python3

from hypothesis import given
from hypothesis.strategies import lists, integers


def zeros_inplace(xs):
    if not xs:
        return

marinegor

Introduction

Serial femtosecond crystallography, currently, doesn't have a gold-standard model for scaling of still (zero degrees rotation partial reflection intensities) images [1]. There is a Bayessian approach for it [2], but it lacks the opportunity to work with CrystFEL format directly, which we are currently using.

[1] https://royalsocietypublishing.org/doi/10.1098/rstb.2013.0330 [2] https://github.com/Hekstra-Lab/careless/

Workflow

• Dry lab: 5/5
• Wet lab: 0/5
• Methodology oriented: 4/5

marinegor

#!bin/bash

for i in `seq 1 139`; do
  echo "------------Downloading run ${i}/139-------------"
  wget -c http://portal.nersc.gov/archive/home/projects/cxidb/www/141/runs/run${i}.tar.gz
done

marinegor

                    GNU GENERAL PUBLIC LICENSE
                       Version 3, 29 June 2007

 Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
 Everyone is permitted to copy and distribute verbatim copies
 of this license document, but changing it is not allowed.

                            Preamble

  The GNU General Public License is a free, copyleft license for

marinegor

#!/usr/bin/env python

from __future__ import print_function
import os
import sys

input_stream = sys.argv[1]

if input_stream == '-h':
  echo "Usage: python explorestream.py output.stream"