Several installer scripts fail and require the use of the below instructions to get their setup to return to a working order! The following specifically shows how to setup Fallout4.

Step1: Install Wine. Details of which are not covered herein. Refer to: https://wiki.winehq.org/Download

Step2: Install Steam. Details of which are not covered herein. Refer to: https://www.howtogeek.com/753511/how-to-download-and-install-steam-on-linux/

Step3: Install your game on Steam. For example install Fallout 4. See Note01.
-Run the game at least one time to ensure that Steam sets up a wine prefix for it. See Note02.
-Right click the game in Steam’s ‘Library’, selecting ‘Properties’. Then select the left menu item for ‘Compatibility’, and select the check box for ‘Force the use of a specific Steam Play compatibility tool’. Select the Proton version most similar to your wine version, e.g. if using any wine version 8, then you should select either of: GE-proton8x, Proton Experimental, or Proton 8x. You can use others, however you may be missing needed features if you choose an older Proton than your wine version.
-Right click the game in Steam’s ‘Library’, selecting ‘Properties’. Then select the left menu item for ‘General’, and select the ‘Launch Options’ dialog box. Enter the following command:
PROTON_DUMP_DEBUG_COMMANDS=1 %command%
-Run the game again to ensure that Steam sets up the custom wine prefix and the game can launch properly. This may take many minutes (sometime over 10) if you need to download many plugins for the wine prefix, so be patient.
-The previously entered command causes Steam’s proton to output the command line options for launching your game while also linking it to the Steam managed wine prefix. We will now capture a copy of this executable text file an use it as an easily modifiable base for executing our copy of ModOrganizer2 and linking it to Steam’s wine prefix.
-Navigate to your systems temp directory and search for a directory such as ‘proton_username’. Within this directory copy the ‘run’ file and paste a copy of it in your Steam game’s directory, such as within your Fallout 4 directory. Then rename the file something like ‘run_Fallout4’. This file should launch the Steam game successfully; test it now.
Using Fedora 38 and my username as an example, this file can be found within /tmp/proton_awesome/

Step4: Install winetricks. Details for install are not covered herein. System native or direct download and configure work just fine. Refer to your system store, or use command line install, or to directly install/configure see https://wiki.winehq.org/Winetricks

Step5: Install protontricks. Details for install are not covered herein. System native or flatpack installer work just fine. Refer to your system store, or use command line install, or to directly install/configure see https://github.com/Matoking/protontricks

Step6: Install ModOrganizer2.
-Download the zip file ‘Mod.Organizer-2.4.4.7z’ from https://github.com/ModOrganizer2/modorganizer/releases
-Extract it to a directory you intend to use it from. It can even be placed within the game directory you wish to use it with, however in this case to make it more organized it is recommended to make it a sudirectory; e.g.:
/path to your Steam games/Fallout 4/modorganizer2/
-DO NOT RUN it yet. If you do it will configure within your system wine default, and not the Steam wine prefix as in Note2. Running it now will mean you have to run it again later; it will not break your ModOrganizer2 and you do not have to uninstall/reinstall it if you made this mistake. Proceed to the next step.

Step7: Grant access for protontricks to access both Steam and ModOrganizer2 directories, if installed as a flatpack. Disregard this step if not a flatpack. Modify the terminal command lines below to match the directory of your Steam library and your ModOrganizer2 directory. From a terminal submit the commands:

flatpak override --user --filesystem=”/path_to_other_Steam_Library/” com.github.Matoking.protontricks

flatpak override --user --filesystem=”/path_to_ModOrganizer2/” com.github.Matoking.protontricks

Step8: Run protontricks.
-Select your Steam app, i.e. ‘Fallout 4’. Be patient, wait for the script to bring up the next window. This should link the next dialog to your Steam wine prefix.
-Select ‘Select the default wineprefix’
-Select ‘Run winecfg’
-From within the Wine configuration
-Under the ‘Application Settings’ tab, choose your default Windows version. I recommend choosing ‘Windows 11’.
-Under the ‘Graphics’ tab, set your screen resolution scaling by using the slider to change the dpi entry. Increasing the font size will increase the render size of wine applications for people with poor eyesight.
Under the ‘Audio’ tab, set your Speaker configuration. This is needed for anyone using other than 2.0 sound. It must match what your system audio is configured as or you will get either no sound or intermittent sound in game.
Under the ‘Staging’ tab, select the checkbox for ‘Enable VAAPI as backend for DXVA2 GPU decoding’ if the option is present for you. Then check the box for ‘Hide Wine version from applications’ if present. Press okay to accept, then exit the configuration dialog by repeatedly using the X in the top right corner of the window.

Step9: Duplicate the ‘run’ file that you copied previously in Step3. Rename this file to something like ‘run_ModOrganizer2’.
-Right-click the file and open it with a text editor. There are many highly important lines in here, they work to link an executable file to the Steam managed wine prefix. Find the “DEF_CMD=” line. This is usually the second line. You will change the path to match the path for where you unzipped ModOrganizer2. Then you will replace the executable name with modorganizer2’s. e.g.: similar to, and remember it is case sensitive!
DEF_CMD=("/home/awesome_user/myDisks/SteamLibrary/steamapps/common/Fallout 4/modorganizer2/ModOrganizer.exe")

Step10: Extract any manually installed per-requisites for the mods you have or will install. For example, in Fallout it is common to need the F4SE, refer to https://www.nexusmods.com/fallout4/mods/42147?tab=files
-Extract the file manually placing the ‘scripts’ subdirectory within the /steamapps/common/Fallout 4/Data/ directory. Then place the f3se dll files and exe file in the /steamapps/common/Fallout 4/Data/ directory.

Step11: Run ModOrganizer2 using the ‘run_ModOrganizer2’ link setup in Step9. This should prompt you to setup the instance for your game. I recommend using a global instance and accepting the default directories, as they will be within the ModOrganizer2 directory by default.
-Link your NexusMods account.
-When prompted ignore permanently the ‘Mod Manager Downloads’ functionality, as this does not work at all in Linux (to my knowledge).
-Download a Mod into the NexusMods subdirectory ‘/downloads/’
-Refresh your mods in ModOrganizer2, then in the right pane, select the ‘Downloads’ tab. This should show your newly downloaded file. Right click the file that has a red triangle next to it and select ‘Query Info’. This will hash the file, re-query Nexusmods.com and attain file version information for it.
-Now you can install the file by right-click ‘Install’. When it asks you what NAME to give the install I HIGHLY RECOMMEND that you scroll through the options and select the name that is the same as the zip file.
-This will show the file in the left pane of ModOrganizer2. Select the checkbox to enable it.
-Now use the selector in the top right of ModOrganizer2 to choose to launch either: Fallout4 launcher, Fallout4, or F4SE. If you have any scripts that require F4SE (or similar) this is what you should choose to run the game. If the game opens at the wrong resolution, then just close and relaunch the launcher to select the proper settings.
-Other items of note are:
-The ModOrganizer2 right hand pane, ‘Plugins’ tab has the option to sort. This usually works but you may have to manually deconflict files in the left hand pane to ensure that your mods work. Pre-requisites must be loaded at the top of the list, when sorted by priority, prior to the plugin(s) that needs them. When two or more mods affect the same file, whichever is loaded last (at the bottom of load order) wins and is used in game. Loose files always win against files that are packages up. Also highlighting a file that has a conflict in the left pane will show you with color coding which files it either loses out to, or wins over. It is also possible to enable a plugin in the left hand pane, and yet disable it completely from use in the right hand pane. Both must be checked for it to be available in game.

That’s it, I hope this saves someone from the grief I had to put up with in figuring out how to make it work! ;)
Let me know if I missed any major steps in this write-up, or otherwise botched something. Always launch your game from this ‘run_ModOrganizer2’ link and you should have no problems, outside of Steam game updates breaking your favorite mods and being forced to update them! See Note03 and Note04.



Note01: For a best experience your game should be installed to a physical hard disk that is the fastest possible, e.g. solid state drive. You should also hardlink your drive/partition so that it always is mounted at OS startup preventing issues when Steam is launched. You should use a partition manager, such as ‘GNOME Disks’, to setup that partition to be mounted at login by the default user, or using such mounting options as ‘gid=1000,uid=1000’ and using a Label which is easy to read/meaningful. Refer to https://askubuntu.com/questions/113733/how-to-mount-a-ntfs-partition-in-etc-fstab

Note02: This is an important understanding issue; Steam sets up and runs a different, self managed wine prefix from your system default wine prefix. This is why most people have issues running ModOrganizer2 on Linux, because when you simply open ModOrganizer2 then by default it uses the systems wine prefix, WHICH IS NOT THE SAME as that used by your Steam game. Thus the ModOrganizer2 cannot affect the Steam game. We will fix this by creating a launcher configuration file that links the ModOrganizer2 to the Steam wine prefix, allowing us to apply mods, then launch the game!

Note03: Yes it is possible to prevent updates to your Steam games (freezing the game files), thus preventing updates from forcing you to get all new plugins to match. That is not covered here!

Note04: Yes it is possible to manually strip out all the pertinent files from your finally setup mods, then replace all these files into the original game compressed files in order to dramatically speed up loading of the game. This is not covered here. Also, if you do it, NEVER again validate your game files or Steam will erase all your hard work!