Visualize docking grids

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Written by Jiankun Lyu, 20180309

1) Convert grids into a format that Chimera can read in

cd /your/dock/path/dockfiles

1.1) The VDW grid

python /mnt/nfs/home/jklyu/zzz.script/pymol_movie/create_VDW_DX.py

The output should be vdw_energies_repulsive.dx, vdw_energies_attractive.dx and vdw.dx.

1.2) The electrostatics grid

python /mnt/nfs/home/jklyu/zzz.script/pymol_movie/phi_to_dx.py trim.electrostatics.phi trim.electrostatics.dx

The output should be trim.electrostatics.dx.

1.3) The desolvation grid

python /mnt/nfs/home/jklyu/zzz.script/pymol_movie/create_LigDeSolv_DX.py

The output should be ligdesolv.dx


2) Visualize grids in Chimera

2.1) Open the Chimera

2.2) Go to Tools --> Volume Data --> Volume Viewer

2.3) File --> Open map

2.4) select .dx files you want to visualize


Thanks Reed Stein and Trent Balius for writing those scripts.