Thank you both,

Below are the first 3 lines of my script

select 3n7h
alter all, b=0.0
set_color color0, [0.30196078431372547,0.0,0.29411764705882354]

I introduced line 1 for the selection of the protein (similarly in the second 
script).
Is this line correct because it didn’t get rid of the problem?

> 
> 
>> On 24 Apr 2020, at 14:39, Tamas Hegedus <biohege...@gmail.com> wrote:
>> 
>> Use a selection in your commands in your scripts. Set the selection to one 
>> of your proteins in one of your script and the selection to the other one in 
>> the other script.
>> 
>> 
>> On 4/24/20 3:02 PM, George Tzotzos via PyMOL-users wrote:
>>> Below is a summary of a task I’m trying to implement in pymol
>>> 
>>> 1. Load 2 proteins
>>> 2. Align them (align prt1, prt2)
>>> 3. Use grid_slot to display the proteins side by side
>>> 4. Load two different scripts (one for each protein)
>>> 
>>> Step 4 is where I get stuck. Each script is applied to both proteins.
>>> 
>>> Is there a way to apply each script to one grid only?
>>> 
>>> Thanks in advance for any suggestions
>>> 
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>> 
>> 
>> 
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> 



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