Location of Scaffold, Scaffold Elements and Scaffold PTM Program Settings and Key Files

This article describes where to find configuration and key files, which are often required to troubleshoot technical problems related to Protome Software programs. It is often necessary to gain access to hidden folders to find these files. Most operating systems make certain files/directories invisible to the user by default. The following article lists steps to make hidden folders visible by OS, and lists the directories for these files. 

View Hidden Folders by OS

Windows 7

  1. From the Start menu select the Control Panel
  2. Click on Folder Options and select the View tab
  3. Under the Hidden Folders section click Show hidden files, folders and drives and select Apply

Windows 8.1

  1. Click on the Folders icon in the lower left corner of the screen
  2. Select the View tab in the top left of the folders dialog box
  3. Click the check box for Hidden Items

Windows 10

  1. Click on the Folders icon
  2. Select the view tab and click Options
  3. From the Options dialog box click the View tab and select the Show hidden files, folder and drive button and click OK

Mac OS X

  1. To show hidden folder in OS X you must run a terminal command. Open the terminal: Finder > Utilities > Terminal
  2. Paste the following command into the terminal: defaults write com.apple.finder AppleShowAllFiles YES and press Return
  3. Hold the Option/Alt key and right click on the Finder icon, select relaunch
  4. Finder should relaunch and hidden folders should now be visible
  5. If you would like to disable hidden folders reopen the terminal and run the following command: defaults write com.apple.finder AppleShowAllFiles NO and press Return. Once you relaunch Finder they should be invisible again


In general, for Linux/UNIX systems, hidden files and folders are prepended with a period, eg, ~/.ssh (where encryption keys are stored). You can make these visible in the GUI (on Ubuntu, for example) by going to View > Show Hidden Files or by running a command like this: ls -a

Directory / Path for the Scaffold program_settings_S4.sfp file

Note, To follow paths hidden folders must be made visible


C:\Users\<username>\AppData\Roaming\Proteome Software\Scaffold\parameters

Mac OS X

From the Go dropdown menu: Home/Library/Application Support/Scaffold/parameters



Once you have navigated to to the Parameters folder find the program_settings_S4.sfp file. It is possible that during use this file has become corrupted and must be backed up. To do so rename to file program_settings_S4_back.sfp. This will force Scaffold to write an new file and should allow Scaffold to boot properly. Keep in mind that if you do this you will have to enter your Network settings again.

Scaffold Elements and Scaffold PTM

Scaffold Elements uses a similar file path, however the *_params.stp file is not contained within a parameters folder.

"C:\Users\Jacob\<username>\Roaming\Proteome Software\Elements\Elements_params.stp"


"C:\Users\Jacob\AppData\Roaming\Proteome Software\ScaffoldPTM\ScaffoldPTM_params.stp"

Directory / Path for Scaffold, Scaffold Elements and Scaffold PTM License Key Files

These are the locations of key files for Proteome Software products in if the default file option is selected. These examples are for Scaffold keys, there should be separate folders for corresponding to each product you have installed.


C:\ProgramData\Proteome Software\<program_name>\registeredKey.lkeynew

Mac OS X/ macOS

Home > Library/Application Support/<program_name>/registeredKey.lkeynew





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