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<!DOCTYPE html><html lang="zh-CN" data-theme="light"><head><meta charset="UTF-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0,viewport-fit=cover"><title>Brainupdating</title><meta name="author" content="Solver"><meta name="copyright" content="Solver"><meta name="format-detection" content="telephone=no"><meta name="theme-color" content="#ffffff"><meta property="og:type" content="website">
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一 生成jupyter配置文件激活想要jupyter运行的conda环境，运行 jupyter notebook --generate-config命令，生成jupyter_notebook_config.py
二 编辑配置文件运行：vim ~/.jupyter/jupyter_notebook_config.py,在文件末尾添加以下内容：
123456c.NotebookApp.allow_remote_access = True #允许远程连接c.NotebookApp.ip='*' # 设置所有ip皆可访问# c.NotebookApp.password = u'e38443c4916018585a436395dd561ccee7820' # 复制的之前jupyter 启动的tokenc.NotebookApp.notebook_dir = 'path& ...</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/posts/b1becab6.html" title="Python libraries that are frequently used in the Cryo-EM field">Python libraries that are frequently used in the Cryo-EM field</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-08-01T09:22:30.000Z" title="发表于 2024-08-01 17:22:30">2024-08-01</time></span><span class="article-meta tags"><span class="article-meta-separator">|</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/Python/">Python</a><span class="article-meta-link">•</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/CryoEM/">CryoEM</a></span></div><div class="content">This page lists Python libraries which are commonly used to analyze data in the Cryo-EM field or prepare data for deep learning.
Python documentation(simplified Chinese):URL
Pytorch
starfile
mrcfile
os
OpenCV :tutorial
Pillow
sys
Numpy
Pandas
To Be continued
</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/posts/561ec3f6.html" title="Useful Relion and imod Command Tools">Useful Relion and imod Command Tools</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-07-31T15:10:26.000Z" title="发表于 2024-07-31 23:10:26">2024-07-31</time></span><span class="article-meta tags"><span class="article-meta-separator">|</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/CryoEM/">CryoEM</a><span class="article-meta-link">•</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/Relion/">Relion</a></span></div><div class="content">
relion_display:
relion_display --i filename.star This command show mrcfile in filename.star .User should notice that mrcfile path must be same as starfile,if you have moved mrcfile ,then you could create an symbolic link to mrcfile in original folder.
relion_display --gui.This command will open an relion gui,then user could operate file in this gui.
relion_stack_create:
relion_stack_create --i inputpath/filname --o outputpath/filename --one_by_one This command could help you ...</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/posts/a4a6cb9a.html" title="Useful Linux tools">Useful Linux tools</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-07-31T15:06:12.000Z" title="发表于 2024-07-31 23:06:12">2024-07-31</time></span><span class="article-meta tags"><span class="article-meta-separator">|</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/Tools/">Tools</a><span class="article-meta-link">•</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/linux/">linux</a></span></div><div class="content">在安装linux工具时，应该通过创建conda虚拟环境或者docker容器安装，而不是直接安装到系统。尽量保持操作系统纯净，保持运行稳定性，防止安装的各个软件之间依赖冲突或缺失，出现奇怪的bug.
htop:用来查看系统资源分配状态：
安装：
启动：
axel:多线程下载器，倍速提升下载速度：
安装：
启动：
tree:以目录树形式展示文件夹下文件名。
安装：
启动：
parallel:多线程运行bash命令，极大提升任务运行速度。
安装：
启动：
exiftool:快速查看图像元数据
安装：
启动：exiftool image.jpg
eog:linux下图片查看工具
安装：
启动：
To Be Continued ... </div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/posts/undefined.html" title="记录启动jupyter_notebook时也会启动chimeraX的bug">记录启动jupyter_notebook时也会启动chimeraX的bug</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-07-29T09:48:29.000Z" title="发表于 2024-07-29 17:48:29">2024-07-29</time></span><span class="article-meta"><span class="article-meta-separator">|</span><i class="fas fa-inbox"></i><a class="article-meta__categories" href="/categories/debug%E7%B3%BB%E5%88%97/">debug系列</a></span><span class="article-meta tags"><span class="article-meta-separator">|</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/linux/">linux</a></span></div><div class="content">遇到一个很好玩的bug,启动jupyter notebook时，chimeraX也会启动，关掉chimeraX，jupyter notebook也会同时关闭，十分有趣。
在排除了环境本身存在问题后，猜想应该系统配置问题（这俩软件部署在centos 7桌面版），发现chimerax是被~/.local/share/jupyter/runtime/nbserver-83245-open.html 这个html文件启动的，由于 .html 文件关联的应用程序被设置为 ChimeraX，所以两个文件会同时启动。因此需要将html文件的启动软件改为合适的 Web 浏览器，如 Firefox 。
步骤1：确保目录存在首先，确保 ~/.local/share/applications 目录存在。如果不存在，需要手动创建它：
1mkdir -p ~/.local/share/applications
步骤2：创建或修改 mimeapps.list接下来，需要确保 mimeapps.list 文件存在，并且包含正确的内容。您可以手动编辑这个文件：
打开终端。
输入以下命令以编辑或创建 mimea ...</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/posts/676dd596.html" title="Resume">Resume</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-05-15T09:19:57.000Z" title="发表于 2024-05-15 17:19:57">2024-05-15</time></span><span class="article-meta tags"><span class="article-meta-separator">|</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/Resume/">Resume</a></span></div><div class="content">Chenhui ZhangE-mail : 12032627@mail.sustech.edu.cn
EducationSouthern University of Science and Technology
Master of Science, Biology
Sept. 2020 – July 2023
Supervisor: Yingxia Liu(Professor) and Liang Yang(Professor)
Lanzhou University
Bachelor of Science, Biology
Sept. 2016 – July 2020
Primary fields of research
Cryo-Electron Microscopy
Pocket prediction a ...</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/posts/4abd0723.html" title="使用python脚本提高雅思生词学习效率">使用python脚本提高雅思生词学习效率</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-03-31T07:00:53.000Z" title="发表于 2024-03-31 15:00:53">2024-03-31</time></span><span class="article-meta"><span class="article-meta-separator">|</span><i class="fas fa-inbox"></i><a class="article-meta__categories" href="/categories/python/">python</a></span><span class="article-meta tags"><span class="article-meta-separator">|</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/Tools/">Tools</a><span class="article-meta-link">•</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/%E9%9B%85%E6%80%9D/">雅思</a></span></div><div class="content">背景在准备雅思阅读的过程中，及时记录不认识的生词是非常重要的。由于纸笔的效率太低，我更喜欢利用电脑将生词记录在文本文件中。但是在记录的过程中，发现了一个很大的痛点：复制粘贴单词需要频繁的切换软件界面。这样会影响专注程度,减慢学习效率。为了解决这个问题，我写了三个python脚本去除页面切换，并且对收集的单词做清洗和规范化处理，最后可进行批量翻译。
做个简单介绍：
复制粘贴脚本。运行之后会在后台监听粘贴板，当我们选中并复制单词之后，自动将复制的单词写入脚本中设置好的文档中。
整理脚本。通过将第一步复制的单词统一大小写，去重，去掉空行，实现规范化处理。
批量翻译脚本。对第二步的单词进行批量翻译，翻译结果写入单词的本行。
使用（运行之前仔细看注释！！！）复制粘贴运行脚本之前，修改脚本中的写入文本路径，如果路径中没有命名的文件，代码会自己创建该文件。
123456789101112131415161718192021import pyperclipimport time# 获取剪贴板内容clipboard_content = pyperclip.paste()while True: ...</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/posts/230c341e.html" title="Gromacs使用技巧">Gromacs使用技巧</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-03-25T04:40:41.000Z" title="发表于 2024-03-25 12:40:41">2024-03-25</time></span><span class="article-meta"><span class="article-meta-separator">|</span><i class="fas fa-inbox"></i><a class="article-meta__categories" href="/categories/%E5%88%86%E5%AD%90%E5%8A%A8%E5%8A%9B%E5%AD%A6%E6%A8%A1%E6%8B%9F/">分子动力学模拟</a></span><span class="article-meta tags"><span class="article-meta-separator">|</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/Gromacs/">Gromacs</a><span class="article-meta-link">•</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/%E7%A7%91%E7%A0%94/">科研</a><span class="article-meta-link">•</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/Tools/">Tools</a></span></div><div class="content">安装
安装之前要检查是否存在旧版本gromacs,避免出现环境变量冲突。
可通过conda或者docker快速安装gromacs，但是，这样的安装方式存在局限性，版本选择不灵活，而且容易出现bug,比如不能运行charmgui搭建的模拟体系，这种安装方式适合入门时学习tutorial，快速把Gromacs运行起来。
源码编译安装是最推荐的一种安装gromacs的方式，编译安装的gromacs最契合运行的硬件，bug少，运行稳定，可非常自由的选择安装版本以及相关配置，缺点是安装过程容易报错。在编译安装的时候，最关键的是gcc编译器版本，ubuntu下通过创建合适的gcc conda环境解决与系统自带gcc版本冲突的问题，centos可通过update-alternatives工具实现gcc多版本控制。
在选择安装版本的时候，应该考虑服务器的配置，如果有gpu,那就安装gpu版本的，纯cpu版本的模拟速度远落后于cpu加速版本，gromacs任务属于是计算型任务，算法简单，gpu可以分担大部分计算。
体系搭建
搭建蛋白md体系最重要的是选择合适的输入文件。开始搭建体系之前，要检查蛋白骨架 ...</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/posts/d623811.html" title="hexo + butterfly搭建静态网站记录">hexo + butterfly搭建静态网站记录</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-03-18T05:51:02.000Z" title="发表于 2024-03-18 13:51:02">2024-03-18</time></span><span class="article-meta"><span class="article-meta-separator">|</span><i class="fas fa-inbox"></i><a class="article-meta__categories" href="/categories/%E7%BD%91%E7%AB%99%E8%AE%B0%E5%BD%95/">网站记录</a></span><span class="article-meta tags"><span class="article-meta-separator">|</span><i class="fas fa-tag"></i><a class="article-meta__tags" href="/tags/%E7%BD%91%E7%AB%99/">网站</a></span></div><div class="content">安装步骤主要安装流程参考：Hexo+GitHub搭建个人博客教程（2023最新版）_hexo github个人网站教程-CSDN博客
报错解决安装过程报错解决：
在创建name.github.io仓库之后，需要在settings-pages路径下手动设置该仓库的页面链接，save之后，等几分钟便可看到链接；
hexo d上传网页文件夹到github仓库之后看不见内容。这是因为在教程中设置的上传分支为master,然而仓库的默认分支为main,所以，分支需要对应上，修改一致便可以解决。
部署hexo框架之后，更换网站主题为butterfly的时候报错：# extends includes/layout.pug block content #recent-posts.recent-posts include includes/rec。解决办法：在网站根目录下打开git bash ，输入命令：npm install –save hexo-renderer-jade hexo-generator-feed hexo-generator-sitemap hexo-bro ...</div></div></div><div class="recent-post-item"><div class="recent-post-info no-cover"><a class="article-title" href="/posts/4a17b156.html" title="Hello World">Hello World</a><div class="article-meta-wrap"><span class="post-meta-date"><i class="far fa-calendar-alt"></i><span class="article-meta-label">发表于</span><time datetime="2024-03-11T09:07:46.583Z" title="发表于 2024-03-11 17:07:46">2024-03-11</time></span></div><div class="content">This is a test.
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