{"id":15347380,"url":"https://github.com/vtlim/glic","last_synced_at":"2026-04-24T17:05:12.476Z","repository":{"id":182914668,"uuid":"194664685","full_name":"vtlim/GLIC","owner":"vtlim","description":"Scripts for fitting GLIC receptor to cryo-EM 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|\n|-----------------------|-------------------|-----------------------------------------------------------------------|\n| `align_tmd.tcl`       | vmd               | align GLIC structure against its transmembrane domain                 |\n| `calc_rmsf.tcl`       | vmd               | calculate RMSF of specified residues                                  |\n|`chap_plot_together.py`| python            | plot multiple json files together from CHAP pore analysis             |\n| `color_frames.tcl`    | vmd               | color selection by each specified set of frames                       |\n| `decompose_matrix.py` | python            | decompose matrix extracted from `align_tmd.tcl` into rot, transl, etc.|\n| `density_chimera.py`  | python, chimera   | generate synthetic density in chimera for each structure              |\n| `distance_map_diff.py`| python            | plot heat map for one distance map minus another from nanoHUB output  |\n| `fsc_delta.py`        | python            | plot change in Fourier Shell Correlation curve from input xml files   | \n| `genmap.cmd`          | chimera           | called by `density_chimera.py` to generate synthetic density          |\n| `genmask.cmd`         | chimera           | generate mask for map from around a reference protein structure       |\n| `natsort.py`          | python            | import from other scripts for natural sort of file names              |\n| `record_plane.cmd`    | chimera           | open in chimera to generate movie of plane snapshot over varying z    |\n| `rmsd_residue.tcl`    | vmd               | compute RMSD for each residue backbone between two structures         |\n| `tempy.py`            | python            | example application of moving density with input rotation/translation | \n| `tempy_pdb.py`        | python            | related to `tempy.py`; now take *structure* and move to orig map      | \n| `transformations.py`  | python            | called by `decompose_matrix.py` to decompose 4x4 move matrix          | \n| `vmd_color_subunit.tcl` | vmd             | color each of five subunits in VMD for when chains not recognized     |\n| `vmd_mask.tcl`          | vmd             | quickly generate/view masked map in vmd; vmd can only write .dx map   |\n| `write_nth_frame.tcl`\\* | vmd             | write every nth frame from trajectory as separate pdb file            |\n| `xyz_constrict.tcl`     | vmd             | get coords of constriction site (center of E223 alphaC of 5 subunits) |\n\n\\*Note: Located in [misc repo](https://github.com/vtlim/misc)\n\n\n## Contents of archive folder\n\nFor files that are not actively used in the project but may come into handy.\n\n| file                  | use with          | description                                                           |\n|-----------------------|-------------------|-----------------------------------------------------------------------|\n| `contact_map.py`      | python            | generate contact map (not distance map) on two PDBs to compare        |\n| `density_gromaps.sh`  | bash, gromaps     | create run file for gromaps to write densities from gromacs trajectory|\n| `rmsd_pairwise.tcl`   | vmd               | compute all by all pairwise rmsd of protein residues\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvtlim%2Fglic","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvtlim%2Fglic","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvtlim%2Fglic/lists"}