profex – a graphical user interface for...
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Nicola Döbelin
RMS Foundation, Bettlach, Switzerland
Profex – A Graphical User Interface for BGMN
BGMN/Profex User Meeting 2019
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BGMN: Based on Text Files2
BGMNRaw data(*.xy)
Structure models(*.str)
Instrument config.(*.geq)
Wavelength(*.lam)
Control file (*.sav) Refined parameters
(*.lst)
Refined pattern(*.dia)
Peak parameters(*.par)
More optional output files
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BGMN Command Line Application3
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BGMN Command Line Application4
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Graphical User Interfaces for BGMN5
BGMN can be used from acommand shell. No user interfaceis required.
But much more convenientwith a user interface
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Profex – A Graphical User Interface for BGMN6
Developer: Nicola Döbelin (private)License: GPL v2 or later (open source)Founded in: 2003Platforms: Windows 7 / 8 / 8.1 / 10
Mac OS X 10.9 -10.14 (64bit)Linux
Rietveld Backends: BGMN, Fullprof.2kWebsite: http://www.profex-xrd.orgCurrent stable version: 4.0.0
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Profex – A Graphical User Interface for BGMN7
Version 4.0.0:- Released in August 2019- Bundled with BGMN- Includes >750 structure files
(~400 by BGMN team + ~350 by Profex)- Includes 35 instrument configurations- Many new features:
- Search/Match- Electron density maps- Reporting- …
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Installing Profex8
Profex program executable
BGMN suite
Device file repository
Structure file repository
Windows: Installer (*.exe) or portable bundle (*.zip)
OS X: Compressed disk image (*.dmg.zip)
Linux: Source code
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Installing Profex9
Profex program
executable
BGMN suite (inside
Profex application
bundle)
Device file repository
Structure file repository
Windows: Installer (*.exe) or portable bundle (*.zip)
OS X: Compressed disk image (*.dmg.zip)
Linux: Source code
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Profex: First Start Security Warnings10
«More Info» «Run anyway»
OS X:
Ctrl + Click on Profex “Open”
«Open»
Windows
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Profex: First Start11
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Profex: First Start12
3
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Profex: First Start13
Plot area(cannot be closed)
Dock windows(can be closed / stacked/ rearranged / detached)
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Profex: First Start14
Closed Dock Windows can be re-openedfrom the «Window» menu
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Profex: First Start15
Help Mouse and Keyboard Commands:
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Indexed Reference Structures16
ResetSelect
Reference hkl lines
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Step 1: Identify Phases17
Double-click
on strongest peak
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Step 2: Create Refinement Project1
8
1. Click «Add/Remove Phase»
2. Select correct instrument
configuration
3. Select identified phases
4. Click «OK»
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Step 2: Create Refinement Project19
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Step 3: Release parameters for refinement20
Open all structure files
Already released for refinement:- Unit cell A and C- Crystallite size (B1)- Scale factor with texture (GEWICHT=SPHAR4)
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Step 4: Run the refinement21
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Results22
Summary of results
Detailed results (*.lst file)
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Context Help23
Open «Window Context Help»
1. Place the cursor on a parameter (here: k2)2. Press «F1» key
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Release Micro-Strain for refinement24
1. Open the Apatite-OH.str file ( button)2. Place the cursor on the parameter «k2»3. Right mouse button to open context menu
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Release Micro-Strain for refinement25
1. Select «Refine isotropically»2. Run the refinement
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Releasing / Fixing Parameters for Refinement26
1. Place cursor on parameter2. Right mouse button3. Select status from menu
Alternatively:1. Place cursor on parameter2. Use «F5» and «F6» keys to change refinement status
FixIsotropically
with boundaries
Anisotropically(if supported)
…or…
Isotropicallywithout boundaries
F6 F6
F5 F5
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Example 2: Favorites / Phase quantification27
Double-clicking the strongest peak
will not identify the phase correctly
Problems:- Too many phases to chose from- Highest intensity ≠ strongest peak (highest integrated intensity)
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Example 2: Favorites / Phase quantification28
1. Check «phosphate» group2. Close dialog («OK»)
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Example 2: Favorites / Phase quantification29
«Favorites» button:
Check to limit the database to favorite phases only.Double-clicking peaks only searches among favorite phases.
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Example 2: Favorites / Phase quantification30
1. Scroll through the list of reference structures2. Try to find the best match3. Create refinement project Run
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Example 2: Favorites / Phase quantification31
More unidentified phases
Use double-click or scroll through thereference structures to identify them.
Solution:
- TCP-beta or TCP-beta-Mg
- Apatite-OH or Apatite-O
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Example 2: Favorites / Phase quantification32
1. Add/Remove phase:2. Leave this unchecked (we already have a control file)
3. Select identifiedphases
4. «OK»
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Example 2: Favorites / Phase quantification33
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Example 2: Favorites / Phase quantification34
Phase quantification isupdated automatically:
𝑠𝑢𝑚 = 𝐺𝐸𝑊𝐼𝐶𝐻𝑇 𝑄𝑃ℎ𝑎𝑠𝑒 =𝐺𝐸𝑊𝐼𝐶𝐻𝑇𝑃ℎ𝑎𝑠𝑒
𝑠𝑢𝑚
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Example 2: Favorites / Phase quantification35
Refinement statistics
Phase quantities
If necessary: Release / fix parameters in STR files Repeat refinement
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Example 2: Exporting Results36
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Example 2: Exporting Results37
Report in HTML format(opens in web browser)
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Example 2: Refined Chemical Composition38
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Example 2: Refined Chemical Composition39
Calculates the refined chemical composition based on:- Refined atomic sites (scattering factors, site occupancy factors)- Refined phase quantities
Not recommended as a chemical analysis,but useful to validate refinement results bycomparison with chemical analysis (ICP, XRF)
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Example 2: Refined Chemical Composition40
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Refined Chemical Composition41
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Up Next and Tomorrow: New Features in Profex 4
GUI changes
Search / Match
Peak detection
Interaction with QualX / Match!
Electron-density maps
Drawing crystal structures with Vesta / Mercury
Customizing report layouts
42