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I am trying to make the color of my wine apps match my GTK theme in Ubuntu 13.04. I have found a script that does just that but I don't know how to use it with play on Linux. The script can be found here. 

Hello,
It seems to depend on $WINEPREFIX being set, and regedit being available, so running it from a console inside the virtual drive you want should do:

Configure button > (select virtual drive) > Miscellaneous tab > Open a shell in this virtual drive button

I am trying to make the color of my wine apps match my GTK theme in Ubuntu 13.04. I have found a script that does just that but I don't know how to use it with play on Linux. The script can be found here. 
It would be awesome if there was a Faience theme for Windows XP/Wine, but there isn't, at least not that I know of. But if I could just get the colors to match I would be very happy. 
Thank you.

Do this at your own risk
PlayOnLinux forums is not responsible for any malicious effects or bugs related to this script.

Step 1:
download the script to your desktop
Note:  You may have to copy every line first, paste in gedit and then save as wine_colors_from_gtk.py

Step 2:
Launch Terminal (its a command prompt)

Step 3:
Type:  [code]cd /home/username/Desktop[/code]
Press Enter

Note:  username is where you put your login

Step 4:
Type:  [code]ls[/code]
Press Enter

You should see the script you downloaded:  wine_colors_from_gtk.py

Step 5:
Type:  [code]sudo chmod +x wine_colors_from_gtk.py[/code]
Press Enter

Terminal will ask for your password.  This command makes the script executable.

Step 6:
Now lets execute the script
Type: [code]./wine_colors_from_gtk.py[/code]
Press Enter

It should run a bunch of code or give you some errors.
If you get errors, there is a chance Python isn't installed, but if you have PlayOnLinux and Wine already, then it probably is.

I have not tried the script myself, so let us know if it works or not.

I have already ran the script, it only seems to affect the systems installation of wine. If I right click on a exe and run with "wine windows program loader" then I can see the changes. However it had no affect on any of the prefixes created with playonlinux.

Gotcha, try what Petch suggested

I just tried what Petch said, It sat for about 30sec before saying "command not found".

The thing I did read in the script was that it scrapes the GTK theme and then creates a temp reg file. If there was some way to get it to just create a reg file and place it in the home directory then I could just load that reg file into what ever virtual drives I want.

Any ideas? frankly I wish this was built into playonlinux, its such a basic feature.

I have a feeling its a temporary REG because if you change your theme in Linux, you can run the script again and Wine will update to match it.

The Readme.txt suggested this:
Run with a command like "python wine_colors_from_gtk.py"

Also the script was made back in 2011... there may be something newer by now

I have searched high and low and have found nothing similar aside from manually setting the colors in winecfg. I would love to know if there is a newer alternative. Also I would actually like to recommend implementing such a feature into playonlinux, do you know how I would go about doing that?

Hmm, it really seems like a Wine feature and not a PlayOnLinux feature.
PlayOnLinux uses the Window decoration of the Linux themes.
But good point!

There should be a suggestion box over at WineHQ.org
I don't mind the lame Windows decoration because I play most of my games full screen and you won't see it.