| import napari | |
| import numpy as np | |
| class MtModel: | |
| def __init__( | |
| self, | |
| npf: int = 13, | |
| start: int = 3, | |
| space: float = 4.0, | |
| radius: float = 9.8, |
| [ | |
| "FCi27mtaKod38ztmGndn-y8NNz.r.lt6SndqGztz_ztr-ngqQm9aMo9eOnMeJntuNntu", | |
| "D2ei2mgqJz9b-m.mGmPqRyLNNnwmOlt7.ywiGmt-Kndr9otqRywv8o9ePmtiNmd2Sn92Tma", | |
| "6U7vcmPuOn9uLnMaGyM7-nLNNntv9lt6RmtaGmweOyMmJnMmSmgmOo9eOnM6LnMaRmM-Tma", | |
| "lXLf8owyQztiMzwqGnMz7zcNNotb7lwf.m9qGzt6Km.qMngqLndqLo9eOotaNm96Mmt6Tma", | |
| "FCi27y9qOnd-Ny96GmPmOmcNNzwf-lwj-m9mGztz7ytaMnM78n9v-o9ePmM6Rm9-Qn9eTma", | |
| "XlEDumMz7nM7-m9iGogmRmLNNyt_8lwiKz9eGm9-Pm.v7ztiLztz_o9eOnMeQnd-Sodm", | |
| "lXLf8yt-JywmNmPeGm9n9n8NNzgn.lt_8zwqGogz7zgn7zt6SyPr-o9eOnM6Pot2Mn9qTma", | |
| "FCi27zgf8mdqMmMeGnMmMy8NNz9eQlweNy.eGmMiMm96Qmgr9nMb-o9ePmtuRmt6JotmTma", | |
| "FCi27nwmKnMeSodeGm.z.y8NNntz.lt-PywmGy9__ngqQmtiPmtb7o9ePmteJotyJoduTma", |
| # -------------------------------------------------------------------- | |
| # Recursively find pdfs from the directory given as the first argument, | |
| # otherwise search the current directory. | |
| # Use exiftool and qpdf (both must be installed and locatable on $PATH) | |
| # to strip all top-level metadata from PDFs. | |
| # | |
| # Note - This only removes file-level metadata, not any metadata | |
| # in embedded images, etc. | |
| # | |
| # Code is provided as-is, I take no responsibility for its use, |
This document examines how to use RELION 4.0 (beta2 as of writing) with Warp 1.09 and M 1.09 for single particle analysis.
Special thanks to Alister Burt, Pranav Shah and Dimitry Tegunov for discussion on this Twitter thread.
We use the RELION tutorial dataset (beta-galactosidase collected on JEOL CRYO ARM 200, a subset of EMPIAR-10204).
| import numpy as np | |
| def sigmoid(x): | |
| return 1 / (1 + np.exp(-x)) | |
| def neural_network(X, y): | |
| learning_rate = 0.1 | |
| W1 = np.random.rand(2, 4) | |
| W2 = np.random.rand(4, 1) |
| #!/usr/bin/env bash | |
| set -Eeuo pipefail | |
| trap cleanup SIGINT SIGTERM ERR EXIT | |
| script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &>/dev/null && pwd -P) | |
| usage() { | |
| cat <<EOF | |
| Usage: $(basename "${BASH_SOURCE[0]}") [-h] [-v] [-f] -p param_value arg1 [arg2...] |
| /* 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??) | |
| # |
| #!/bin/bash | |
| if [[ ! -d 3DEM ]] | |
| then | |
| mkdir 3DEM | |
| fi | |
| cd 3DEM | |
| curl -s http://mail.ncmir.ucsd.edu/pipermail/3dem/ |\ |
| """ | |
| Script to convert eman2 segmentation hdf maps to imod model files at a user defined contour level. | |
| Requires python>=3.5 as well as having Eman2 and IMOD in the path. | |
| Usage: `python3 tomoseg_to_imod.py -i EXAMPLE.hdf -o EXAMPLE.mod -t 0.8` | |
| Author: Benjamin Barad <benjamin.barad@gmail.com> | |
| """ | |
| import argparse |