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

<blockquote> <p>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:<br><br>For <a href="../api/records/10800570/draft/files/bmc_shell_vs_sheet.tar.gz/content" target="_blank" rel="noopener noreferrer">bmc_shell_vs_sheet.tar.gz:</a><br><code>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" &nbsp;--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" &nbsp; --exclude="structures" --exclude="test-sim" --exclude="test-sim-flatten-constantarea" --exclude="*.dx"</code><br><br>For <a href="../api/records/10800570/draft/files/bmcflattenmdff.tar.gz/content" target="_blank" rel="noopener noreferrer">bmcflattenmdff.tar.gz</a>:<br><code>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</code><br><br>The bmc_shell_vs_sheet has the folder test-sim-curved for shell simulation while test-sim-flatten-noconstantratio for sheet simulation.<br>Pore analysis for shell can be found in hole2 and for sheet in hole-flatten<br>Analysis has been done with various *py *sh and *tcl files<br>For visualizing trajectories in VMD&nbsp; "<strong>load*.tcl</strong>" scripts were used.<br><br>The bmcflattenmdff contains all the scripts needed for converting the shell topology to sheet.</p> </blockquote>