FAQ

Frequently Asked Questions

Installation

User Interface

Refinements


Installation


How can I reset all preferences?

Program settings are stored outside of the Profex directories. Deleting and re-installing Profex will not reset the preferences. Here is what you need to do in order to start with a fresh installation:

Windows:

  1. Close Profex
  2. Open the windows menu and enter the command „regedit.exe“
  3. Navigate to „HKEY_CURRENT_USER/Software/doebelin.org“
  4. Delete the entire folder „Profex2“

OS X:

  1. Close Profex
  2. Delete the file ~/Library/Preferences/org.doebelin.Profex2.plist
  3. Restart your computer

Note: If you don’t restart your computer, it will continue using a buffered version of the plist file and the settings will not be reset to default. Alternatively, you can enter the following command in a terminal in order to force updating the buffered file:

defaults read org.doebelin.Profex2.plist

Linux:

  1. Close Profex
  2. Delete the file ~/.config/doebelin.org/Profex2.conf

User Interface


I closed all dock windows. How can I open them again?

All dock windows (tool windows arranged around the plot area) can be opened from the „Windows“ menu.


How can I share refinement projects with other users?

The easiest way to share projects with other users is to share project backups:

On the source computer:

  1. In Profex click „Project –> Save project backup“ to create a *.zip file with all required scan, control, structure, and instrument files.
  2. The name of the created file will be shown in the „Refinement Protocol“ console.
  3. Share the *.zip file with the recipient.

On the recipient’s computer:

  1. Save the received *.zip file at the location where you want to process it.
  2. In Profex click „File –> Open Project Archive…“ to open the *.zip file.
  3. Run the refinement.

The *.zip file will be extracted and the file formats will be converted to the target platform’s text file format.


How can I share refinement projects between Windows and OS X / Linux platforms?

Opening a refinement project created on one platform (either Windows or OS X / Linux) on another platform (OS X / Linux or Windows) will cause an error message as soon as the refinement is started. This is due to the fact that both types of platforms use different characters for line endings in text files, and BGMN only accepts the format native to the platform it is used on.

To avoid these error messages, use the backup feature to share projects as described here. It automatically converts the files to the target platform.


The „Reference Structures“ list is empty

Here is a list of things to try if the reference structures menu is empty:

Favorites

  • Make sure the „Favorites“ button is unchecked („heart“ button next to the reference structures list).

Re-index the reference structures

  • Select „Tools –> Index Reference Structures“ to update the structures database (or click the „magnifying glass“ button).

Clear the hkl buffer file and re-index the structure files

  • Select „Edit –> Preferences –> BGMN –> Reference Structures“ and clicking „Clear Buffer“.
  • Close the preferences dialog.
  • Select „Tools –> Index Reference Structures“ to update the structures database (or click the „magnifying glass“ button).

Verify the location of the structure file repository

  • Select „Edit –> Preferences –> BGMN –> Repositories“ and verify that the structure file repository points to a valid location containing *.str files.

The „Add/Remove Phases“ dialog is empty

Here is a list of things to try if the „Add/Remove Phases dialog“ is empty:

Favorites

  • Make sure the „Favorites“ button is unchecked („heart“ button in the bottom-right corner).

Re-index the reference structures

  • Select „Tools –> Index Reference Structures“ to update the structures database (or click the „magnifying glass“ button).

Clear the hkl buffer file and re-index the structure files

  • Select „Edit –> Preferences –> BGMN –> Reference Structures“ and clicking „Clear Buffer“.
  • Close the preferences dialog.
  • Select „Tools –> Index Reference Structures“ to update the structures database (or click the „magnifying glass“ button).

Verify the location of the structure file repository

  • Select „Edit –> Preferences –> BGMN –> Repositories“ and verify that the structure file repository points to a valid location containing *.str files.

The „Add/Remove Phases“ dialog only shows checkboxes, but no text

All columns showing the file and phase names are minimized to the left side of the dialog. Resize the columns to show the names and selection checkboxes.


Refinements


What does the error message „insufficient angular range“ mean?

Coming soon…