Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar commands:For bmc_shell_vs_sheet.tar.gz:tar -zcvf bmc_shell_vs_sheet.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*log" --exclude="*xsc" --exclude="*coor" --exclude="*vel" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*ppm" --exclude="*png" --exclude="*pdf" --exclude="*catchy*" --exclude="*svg" --exclude="*restart*" --exclude="*history" --exclude="core.*" --exclude="FFTW_NAMD*" --exclude="*avi" --exclude="*mp4" --exclude="*pcad*" --exclude="*pcaa*" --exclude="*ammn*" --exclude="*amnp*" --exclude="*amsa*" --exclude="*dtnt*" --exclude="*mthl*" --exclude="*ntrt*" --exclude="*.inp" --exclude="*.sph" --exclude="structures" --exclude="test-sim" --exclude="test-sim-flatten-constantarea" --exclude="*.dx"For bmcflattenmdff.tar.gz:tar --exclude="emdensitymap" --exclude="emstructures" --exclude="forSaad" --exclude="*dcd" --exclude="*ppm" --exclude="*mp4" --exclude="*png" --exclude="*old" --exclude="*BAK" --exclude="*txt" --exclude="animations" --exclude="apbs*" -zcvf bmcflattenmdff.tar.gzThe bmc_shell_vs_sheet has the folder test-sim-curved for shell simulation while test-sim-flatten-noconstantratio for sheet simulation.Pore analysis for shell can be found in hole2 and for sheet in hole-flattenAnalysis has been done with various *py *sh and *tcl filesFor visualizing trajectories in VMD "load*.tcl" scripts were used.The bmcflattenmdff contains all the scripts needed for converting the shell topology to sheet.本数据集包含某投稿手稿所需的输入结构、精选输出数据及其对应结构文件。本目录结构为生成模拟数据与分析结果所用完整目录的精简副本。为适配Zenodo平台50GB的上传限额，我们通过以下tar打包指令完成压缩： 1. 针对bmc_shell_vs_sheet.tar.gz： tar -zcvf bmc_shell_vs_sheet.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*log" --exclude="*xsc" --exclude="*coor" --exclude="*vel" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*ppm" --exclude="*png" --exclude="*pdf" --exclude="*catchy*" --exclude="*svg" --exclude="*restart*" --exclude="*history" --exclude="core.*" --exclude="FFTW_NAMD*" --exclude="*avi" --exclude="*mp4" --exclude="*pcad*" --exclude="*pcaa*" --exclude="*ammn*" --exclude="*amnp*" --exclude="*amsa*" --exclude="*dtnt*" --exclude="*mthl*" --exclude="*ntrt*" --exclude="*.inp" --exclude="*.sph" --exclude="structures" --exclude="test-sim" --exclude="test-sim-flatten-constantarea" --exclude="*.dx" 2. 针对bmcflattenmdff.tar.gz： tar --exclude="emdensitymap" --exclude="emstructures" --exclude="forSaad" --exclude="*dcd" --exclude="*ppm" --exclude="*mp4" --exclude="*png" --exclude="*old" --exclude="*BAK" --exclude="*txt" --exclude="animations" --exclude="apbs*" -zcvf bmcflattenmdff.tar.gz 其中，bmc_shell_vs_sheet目录包含用于壳层模拟的test-sim-curved文件夹，以及用于片层模拟的test-sim-flatten-noconstantratio文件夹。壳层结构的孔隙分析结果存放于hole2目录，片层结构的孔隙分析结果则存放于hole-flatten目录；所有分析均通过各类*.py、*.sh及*.tcl脚本完成。针对VMD软件中的轨迹可视化，我们使用了load*.tcl脚本文件。bmcflattenmdff压缩包包含将壳层拓扑结构转换为片层拓扑结构所需的全部脚本文件。