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.