从 PDB 获取结构并查看密度
TL;DR 找到感兴趣的结构，这里以目前数据库中分辨率最高（0.48 Å）的结构 5D8V 为例。 下载模型和密度 PDB format 的模型 Validation 2fo-fc coefficients 文件，解压得到 cif 格式文件 Validation fo-fc coefficients 文件，解压得到 cif 格式文件 得到 3 个文件： 5d8v.pdb 5d8v_validation_2fo...
De novo assemble RNA-seq sequence
Intro A research paper published on biorxiv determined a new coronavirus subgenus, I would like to figure out is there any changes on protease. However, the sequence data has not been publish. Fortunately, the similar sequence is ...
Xia2
[!NOTE] This methods is written maybe one year ago, it's published for memorandum only. Intro Xia2 is an expert system for automated reduction of X-ray diffraction data from macromolecular crystals. It's open-source and you can get its source code [**he...
图床解决方案：Cloudflare R2+PicGo+WebP Cloud
Intro 此前我的图床是基于 Cloudflare + Telegraph 这两位大善人的，我本以为他们会比我的博客活得更久，因此我默认这是一个长期的解决方案，足够可靠易用，最重要的是免费。 但最近 Telegram CEO 被捕，韩国也因为审查方面的原因和 Telegram 有冲突，可能受此影响，Telegraph 的图床服务已经不能上床新的图片，旧的图片尚且可以访问，但也不知道什么时候就会完蛋。 于是我开始寻找新的图床解决方案，我的期望是可靠易用，最好免费，Cloudflare R2+PicGo+WebP Cloud 就是这样的解决方案。 本文主要参考了*...
Linux Mint & Windows 双系统远程启动
Intro 我的小服务器上安装了双系统，先安装的 Windows 再 安装的 Linux Mint，由 GRUB 进行引导，默认引导到 Linux Mint。 如果您也是这样安装的话，可以通过一下方法远程切换系统。 从任意系统重启至 Linux Mint 因为 GRUB 默认引导至 Linux Mint，因此直接重启即可。 从 Linux Mint 引导至 Windows 我的 GRUB 的引导中，我的 Windows 序号为 2（从上往下从 0 开始计数）。 因此想重启到 Windows 有一个临时的设置，在下次重启时重启到某一序号，再下次重启时则失效。...
Keep aria2 running in the background on macOS
Intro This method introduces how to install aria2 and configure it, and how to set a startup. Then work with Alist. Install aria2 Install brew: /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" echo 'eval "$(/opt/homebr...
Color Protein Model by Sequence Conservation with ConSurf
ConSurf | Evolutionary conservation profiles of proteins, which analyze the sequence conservation of proteins and color the model by the result, it could be helpful if the proteins you studied are conserved on structure but vary on the sequence....
Build Models for cryo-EM Maps with ModelAngelo
Intro Building a model for a huge cryo-EM map may be annoying, especially when it's supercomplex. But now you can use ModelAngleo to build models for a cryo-EM map locally, without worry about data leakage. Usage Ensure you have met the computing requirements of ModelAngelo: m...
XDS Installation Issue on arm64 Mac
Recently I encountered an XDS installation error when processing a set of diffraction data, so I tried to reinstall the whole XDS-related software. When you try to install it according to the official guide, you can **install the X...
Deploy X-Ray Data Process Software on Linux
==This note is based on Linux Mint 21.3==, it should be also useful if you running a Ubuntu. XDS Related Software Reference：https://wiki.uni-konstanz.de/xds/index.php/Installation XDS package: wget https://xds.mr.mpg.de/XDS-INTEL64_Linux_x86_64.tar.gz --no-check-certificate Fo...