add LAMMPS .grid3d import #181
Conversation
…meraX-alphataubio into alphataubio-grid
…meraX-alphataubio into alphataubio-grid
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@tomgoddard ready for review and merge, no rush |
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I would need LAMMPS grid data to test this. I'm also wondering what the hundreds of lines of changes to md_crds/src/read_lammps.py were for. Is that change related to reading grids? |
i put so i just edited
its indirectly related. at the same time, i refactored my lammps data and dump reading code to be flexible to various number and ordering of columns so that i could use it to read a molecule into chimerax together with its esp grid. new refactored version is a lot more resilient to most cases with additional error checking. |
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Thanks for providing the nitrite.grid3d example data. I displayed it in ChimeraX using your pull request code. It look like just spherical shells centered at the 0,0,0 corner of the map. Is that what it is supposed to look like? Also all values are negative in this map. Is that typical of the LAMMPs maps you expect? If so ChimeraX won't display them in a useful way because it caps the surface at the map box faces as if the data outside the map is 0. To avoid that for maps where negative values are the norm the reader should turn off map box cap display for the map. I would need to see some realistic LAMMPS example data before I would merge this pull request in ChimeraX. |
Overview
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) can output grid data using the
dump gridcommand. This implementation allows ChimeraX to read and visualize these grid files, similar to how it handles MRC map files.Files
bundles/map_data/src/lammps/__init__.pybundles/map_data/src/lammps/lammps_format.pybundles/map_data/src/lammps/lammps_grid.pybundles/md_crds/src/read_lammps.pyTesting
bundles/map_data/tests/data/nitrite.grid3dminimal examplebundles/map_data/tests/test_map_data.pyadded test_lammps_grid3d()Usage Example
From the ChimeraX command line:
Additional Notes