Visualize docking grids: Difference between revisions
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(Created page with "Written by Jiankun Lyu, 20180309 1) Convert grids into a format that Chimera can read in 1.1) The vdw grid 1.2) The electrostatic grid 1.3) The desolvation grid 2) Visual...") |
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1) Convert grids into a format that Chimera can read in | 1) Convert grids into a format that Chimera can read in | ||
cd /your/dock/path/dockfiles | |||
1.2) The | 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 | 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) 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. | |||
[[Category:Grids]] | |||
[[Category:Visualization]] | |||
Latest revision as of 00:26, 25 May 2024
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.