Talk:Apbsplugin

From PyMOLWiki
Jump to: navigation, search

Example 1

Taken from User:Mglerner#APBS_Plugin_FAQ

Does not seem to work?

reinitialize 
fetch 1rx1, async=0
fetch 1rx2, async=0

set grid_mode,1
align 1rx1, 1rx2

show_as cartoon, 1rx1 or 1rx2

##  Run APBS on protein #1, 1rx1 
### Plugin > APBS Tools2 > ... Under "selection to use" type "(polymer) and 1rx1"
### Rename the map set_name pymol-generated, 1rx1_map. -> "Run Grid" -> "Run APBS"
##  Run APBS on protein #2, 1rx2; 
### Plugin > APBS Tools2 > ... Under "selection to use" type "(polymer) and 1rx2"
### Rename the map set_name pymol-generated, 1rx2_map.  -> "Run Grid" -> "Run APBS"
##  Use APBS to show the surfaces make sure you choose 1rx1_map for 1rx1 and 1rx2_map for 1rx2
### Click "Update" if those map names are not present. ...

### Assign grid slots just to be sure the right maps and proteins are in the right places 
#set grid_slot, 1, 1rx1 
#set grid_slot, 1, 1rx1_map 
#set grid_slot, 1, e_lvl_0_1
#set grid_slot, 2, 1rx2 
#set grid_slot, 2, 1rx2_map 
#set grid_slot, 2, e_lvl_1_1