Last updated: Aug 15 2019
| 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
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 |