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Scripts for fitting GLIC receptor to cryo-EM densities

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Scripts for project on GLIC fitting to cryo-EM densities

Last updated: Aug 15 2019

Contents

file use with description
align_tmd.tcl vmd align GLIC structure against its transmembrane domain
calc_rmsf.tcl vmd calculate RMSF of specified residues
chap_plot_together.py python plot multiple json files together from CHAP pore analysis
color_frames.tcl vmd color selection by each specified set of frames
decompose_matrix.py python decompose matrix extracted from align_tmd.tcl into rot, transl, etc.
density_chimera.py python, chimera generate synthetic density in chimera for each structure
distance_map_diff.py python plot heat map for one distance map minus another from nanoHUB output
fsc_delta.py python plot change in Fourier Shell Correlation curve from input xml files
genmap.cmd chimera called by density_chimera.py to generate synthetic density
genmask.cmd chimera generate mask for map from around a reference protein structure
natsort.py python import from other scripts for natural sort of file names
record_plane.cmd chimera open in chimera to generate movie of plane snapshot over varying z
rmsd_residue.tcl vmd compute RMSD for each residue backbone between two structures
tempy.py python example application of moving density with input rotation/translation
tempy_pdb.py python related to tempy.py; now take structure and move to orig map
transformations.py python called by decompose_matrix.py to decompose 4x4 move matrix
vmd_color_subunit.tcl vmd color each of five subunits in VMD for when chains not recognized
vmd_mask.tcl vmd quickly generate/view masked map in vmd; vmd can only write .dx map
write_nth_frame.tcl* vmd write every nth frame from trajectory as separate pdb file
xyz_constrict.tcl vmd get coords of constriction site (center of E223 alphaC of 5 subunits)

*Note: Located in misc repo

Contents of archive folder

For files that are not actively used in the project but may come into handy.

file use with description
contact_map.py python generate contact map (not distance map) on two PDBs to compare
density_gromaps.sh bash, gromaps create run file for gromaps to write densities from gromacs trajectory
rmsd_pairwise.tcl vmd compute all by all pairwise rmsd of protein residues

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