Input Data for "Assembly and Analysis of Cell-Scale Membrane Envelopes"

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 command: `tar -zcvf protocellmodeling.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*xtc" --exclude="*gro" --exclude="*trr" --exclude="*js" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*xst" --exclude="*edr" --exclude="*state_prev.cpt" --exclude="*.o[0-9]*" cgDracula`, which intentionally excludes large files. The full 4.8TB dataset that includes trajectories is available upon request. The data is split into multiple subdirectories and largely undocumented, however here are the highlights: The <strong>Analysis</strong> subdirectory is where the analysis in the paper lives. All other directories are related to building or running systems. <strong>getsources.py</strong> in the main directory is the script that downloads the initial structure from MemProtMD. <strong>transform.py</strong> builds the initial protein models from MemProtMD. <strong>vesiclebuilder.py</strong> builds the lipid ball. <strong>protpatchplacer.py</strong> sets up the ultra-coarse grained simulation, which is in the <strong>supercg</strong> directory. <strong>movepatches.py</strong> takes the results from the ultra-coarse grained simulation, and builds the protein ball. <strong>gendx.tcl</strong> generates the density maps from the protein ball. This is used in <strong>lipids/picklipids.py</strong>, which cuts out the pieces of the lipid that need to be removed. The water is added to the system with <strong>addwater/quicksolvate.sh</strong> The system is ionized by <strong>ionize.py</strong> And a topology is written by <strong>writetop.py</strong>本数据集包含某学术论文手稿的输入结构，以及精选的输出数据与结构。本目录结构为用于生成模拟数据与开展分析的完整目录集的精简副本。为适配50GB的Zenodo存储限额，我们通过以下tar命令构建该副本：`tar -zcvf protocellmodeling.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*xtc" --exclude="*gro" --exclude="*trr" --exclude="*js" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*xst" --exclude="*edr" --exclude="*state_prev.cpt" --exclude="*.o[0-9]*" cgDracula`，该命令有意排除了各类大型文件。包含分子模拟轨迹的完整4.8TB数据集可按需申请获取。本数据分为多个子目录，且大多未附说明文档，核心内容如下：<strong>分析（Analysis）</strong>子目录为论文中所用分析代码与结果的存放位置；其余目录均与系统构建或运行相关。主目录下的<strong>getsources.py</strong>为从MemProtMD下载初始结构的脚本；<strong>transform.py</strong>用于基于MemProtMD构建初始蛋白质模型；<strong>vesiclebuilder.py</strong>用于构建脂质囊泡；<strong>protpatchplacer.py</strong>用于配置超粗粒度模拟（ultra-coarse grained simulation），相关代码位于<strong>supercg</strong>子目录中；<strong>movepatches.py</strong>可读取超粗粒度模拟的结果，并构建蛋白质球；<strong>gendx.tcl</strong>可从蛋白质球生成密度图，该功能被<strong>lipids/picklipids.py</strong>调用，用于裁剪需移除的脂质片段。系统的加水步骤由<strong>addwater/quicksolvate.sh</strong>完成；系统的离子化操作由<strong>ionize.py</strong>实现；拓扑文件则通过<strong>writetop.py</strong>生成。