I would like to render water sites generated by WaterMap using CPK or ball-and-stick rather than using the WaterMap analysis interface and I would then like to color the sites by free energy using the same color scheme used by the WaterMap analysis interface. I would like to do this so that I can show my colleagues WaterMap results using Maestro Scenes. Is this possible?

Yes. Follow these steps to generate a new custom color scheme that will be accessible from the color scheme toolbar button (painters palette icon).

1. Copy files from the installation into your user resources area:
   
   cp -r $SCHRODINGER/maestro-vversion/data/res/schemes $HOME/.schrodinger/maestroNN/
cp $SCHRODINGER/maestro-vversion/data/res/scheme.res $HOME/.schrodinger/maestroNN/
cp $SCHRODINGER/mmshare-vversion/data/colors.res $HOME/.schrodinger/maestroNN/
   
2. Add the following to the bottom of the scheme.res file:
   
   # *** Color by WaterMap free energy
watermap_free-energy
WaterMap Free Energy
watermap_free-energy.sch

3. Replace lines 161-174 in the file $HOME/.schrodinger/maestro92/colors.res with the following:
   
   161 255 0 0 user65
162 235 20 0 user66
163 215 40 0 user67
164 195 60 0 user68
165 175 80 0 user69
166 155 100 0 user70
167 135 120 0 user71
168 115 140 0 user72
169 95 160 0 user73
170 75 180 0 user74
171 55 200 0 user75
172 35 220 0 user76
173 15 240 0 user77
174 0 255 0 user78

4. Create a new file in $HOME/.schrodinger/maestro92/schemes/ called watermap_free-energy.sch. The contents of that file should be the following, with a tab character replacing <TAB>:
   
   # Color atom by WaterMap Free Energy
# Color ASL definition Description
#
user65 <TAB> atom.r_watermap_free_energy >=5.5 <TAB> >=5.5
user66 <TAB> atom.r_watermap_free_energy 5.0 - 5.5 <TAB> 5.0 ~ 5.5
user67 <TAB> atom.r_watermap_free_energy 4.5 - 5.0 <TAB> 4.5 ~ 5.0
user68 <TAB> atom.r_watermap_free_energy 4.0 - 4.5 <TAB> 4.0 ~ 4.5
user69 <TAB> atom.r_watermap_free_energy 3.5 - 4.0 <TAB> 3.5 ~ 4.0
user70 <TAB> atom.r_watermap_free_energy 3.0 - 3.5 <TAB> 3.0 ~ 3.5
user71 <TAB> atom.r_watermap_free_energy 2.5 - 3.0 <TAB> 2.5 ~ 3.0
user72 <TAB> atom.r_watermap_free_energy 2.0 - 2.5 <TAB> 2.0 ~ 2.5
user73 <TAB> atom.r_watermap_free_energy 1.5 - 2.0 <TAB> 1.5 ~ 2.0
user74 <TAB> atom.r_watermap_free_energy 1.0 - 1.5 <TAB> 1.0 ~ 1.5
user75 <TAB> atom.r_watermap_free_energy 0.5 - 1.0 <TAB> 0.5 ~ 1.0
user76 <TAB> atom.r_watermap_free_energy 0.0 - 0.5 <TAB> 0.0 ~ 0.5
user77 <TAB> atom.r_watermap_free_energy -0.5 - 0.0 <TAB> -0.5 ~ 0.0
user78 <TAB> atom.r_watermap_free_energy <=-0.5 <TAB> <=-0.5
#
#################################################
# The following word "DESCRIPTION" serves as a key
# for the scheme description to be displayed.
DESCRIPTION
This scheme will color WaterMap waters by the free energy calculated
by Watermap. Red corresponds to highly unstable waters (free energy
greater than 5.5 kcal/mol) and green corresponds to stable waters
(free energy less than -0.5 kcal/mol).

5. Restart Maestro.
6. Display in the Maestro Workspace the WaterMap hydration sites (first entry in the WaterMap output file).
7. Double-click the CPK or the ball-and-stick molecular representation toolbar button.
8. Select 'WaterMap Free Energy' from the color scheme toolbar button (painter's palette).

Keywords: WaterMap, color scheme

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