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.


What does the error message „No import filter found for file ….raw“ mean?

Several different file formats use the same extension *.raw (Rigaku, Bruker, Stoe). Attempting to open a raw file with an import filter for a different type of raw file will issue this error message.

When opening raw data files, make sure that the file format in the file dialog is set to the correct type of raw file („Bruker raw scan“, „Rigaku raw scan“, or „Stoe raw scan“).


Refinements


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

Short answer

The measured scan exceeds the angular range, in which the peak profile was calculated from the instrument configuration file. Clip your measured data using the keywords „WMIN“ (minimum angle) and „WMAX“ (maximum angle) in the refinement control file (*.sav) to limit the angular range of your scan to the range specified in your instrument configuration.

Example

Suppose the peak profile was calculated from 4 to 150° 2θ, but your scan was measured from 3 to 80° 2θ. This will trigger the error message, because the peak profile was not computed for the range from 3 to 4° 2θ. Add the following line to your refinement control file (*.sav):

WMIN=4

Then repeat the refinement. Now the measured range from 3 o 4° 2θ will be ignored and the error message should no longer occur.

Long answer

Open your instrument configuration file (*.sav) as follows:

Profex prior to version 3.14: Select „Edit –> Edit FPA Configuration…“, then navigate to your refinement project and open the file <instrument>.sav. „<instrument>“ is the name of the instrument you selected when creating the refinement project.

Profex version 3.14 and newer: Select „Edit –> Edit current FPA configuration“.

The instrument configuration file will be opened in a special editor. Scroll down to the last section, until you find a block that looks like this:

%-----------------------------------------------------------------------------------------------
% Parameters for the simulation of the profile function
%-----------------------------------------------------------------------------------------------

% angular positions for the MonteCarlo simulation (°2theta)
zweiTheta[1]=4
zweiTheta[2]=8
zweiTheta[3]=13
zweiTheta[4]=20
zweiTheta[5]=30
zweiTheta[6]=42
zweiTheta[7]=56
zweiTheta[8]=76
zweiTheta[9]=90
zweiTheta[10]=105
zweiTheta[11]=120
zweiTheta[12]=135
zweiTheta[13]=150

% angular range (°2theta)
WMIN=4
WMAX=150

This shows the 2θ positions at which the profile is simulated (zweiTheta[n]), and the range in which the profile is interpolated (WMIN and WMAX). In this example, the peak profile was modelled in the range from 4 to 150° 2θ. Outside of this range, the profile is unknown. Hence, if a measured scan starting below 4° 2θ, or ending beyond 150° 2θ, is attempted to be refined, the error message „insufficient angular range“ will be shown. There are two different ways to avoid the error message:

  • Clip your measured data in order to ignore the measured ranges not covered by the instrument configuration file using the keywords WMIN and WMAX in the refinement control file (example 2).
  • Extend your instrument configuration file to cover at least the range you measured (example 3).

For a demonstration of the two solutions, we assume that the instrument was configured in the range from 4 to 150° 2θ, and we are attempting to refine a dataset measured from 3 to 80° 2θ.

Clipping the measured scan

We need to clip the measured data below 4° 2θ, because it is outside of the valid range. In your refinement control file (*.sav), add the following lines:

WMIN=4
WMAX=150

Then repeat the refinement.

Extending the instrument configuration

We need to extend the range in the instrument configuration file from 4 to 3° 2θ. Open your instrument configuration file using the function „Edit –> Edit current FPA configuration…“ (or „Edit –> Edit FPA Configuration…“ in Profex versions prior to 3.14) and extend the angular range as follows:

%-----------------------------------------------------------------------------------------------
% Parameters for the simulation of the profile function
%-----------------------------------------------------------------------------------------------

% angular positions for the MonteCarlo simulation (°2theta)
zweiTheta[1]=3
zweiTheta[2]=4
zweiTheta[3]=8
...
zweiTheta[13]=135
zweiTheta[14]=150

% angular range (°2theta)
WMIN=3
WMAX=150

Then click „Run calculations“ to start the profile computation. Once it is complete, repeat the refinement. If it runs without error messages, and you want to keep the extended instrument configuration, copy all files <instrument>.* from your project directory to the devices repository.

Note: In Profex prior to version 3.14, the „Edit FPA Configuration…“ dialog will open in the devices repository. It is important to navigate to the current refinement project first, and open the instrument configuration file found there. Once this version of the instrument configuration file works as expected, copy all <instrument>.* files from there to the devices repository to make it available to all future refinement projects.


My fit looks good, but χ2 is still high. What should I do?

Absolute χ2 values are not always a good indicator for the quality of a fit. They are strongly influenced by the signal-to-noise ratio. In high intensity datasets it is generally more difficult to reach a χ2 value close to 1.0, whereas it is easily reached in noisy datasets. For example, the following fit resulted in χ2 = 43.05:

On the other hand, the following fit resulted in χ2 = 1.08:

Both fits are excellent and cannot be improved any further, despite vast differences in χ2.

The evolution of χ2 during a refinement is a good indicator when comparing different refinement strategies. But absolute values can be misleading. Sometimes it is better to trust your eyes and assess the quality of fit based on the difference curve.