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New: Macro to export DLS data to SEDFIT

28 October 2015 No Comment

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New macro for zetaisizerNew macro available to support DLS data analysis in external software

Over the last years, the Zetasizer has become the most popular light scattering system in biophysical characterization labs around the globe. One of the key components of its success is the easy-to-use Zetasizer DTS software.  When the raw light scattering data (i.e. the correlation function) is analyzed to find the size distribution, this problem is mathematically very similar to the analysis of Analytical Ultracentrifugation (AUC) data sets. Some of our customers have used the advanced fitting algorithms from SEDFIT to gain further insights into their experiments. SEDFIT is a software for the analysis of analytical ultracentrifugation and other hydrodynamic data, written at the National Institutes of Health and distributed without charge for research use (free download). The SEDFIT/SEDPHAT modeling environment has many features that traditional dynamic light scattering (DLS) instrument software doesn’t have – besides the discrete species models also improved distribution analyses, and most importantly, global modeling and global multi-method modeling in SEDPHAT.

How can Zetasizer DLS data be used in SedFit? In order to analyze dynamic light scattering data from the Zetasizer ( a “.dts” file) they must be converted to be readable with SEDFIT. In order to import & use data in SEDFIT the correlation function needs to be presented in column format. This can be achieved by three different methods.

  • Use the macros extracted from Macors-from-blog (zip file) [[preferred]]
  • Use the new MakeDLSDAT-v1-0 macro (download, then change extension to .zmac)
  • Use the Record-Exporter-v1-1 macro (exports correlation function in ASCII which can then be converted, change extension to .zmac)
  • Use the Excel Correlation Data Import_v5+ spreadsheet, compatible with prior versions (least preferred for this purpose)

We’ll start with the easiest and add the two more involved schemes (which may work for other purposes, and for older software versions) towards the end.

Method 1: MakeDLSDAT macro

 

Install-new-macro-option-zetasizer-menu

To install the macro:
Download the MakeDLSDAT-v1-0 file,  change extension to “.zmac” and copy the MakeDLSDAT-v1-0.zmac to the folder
… My Documents\Malvern Instruments\Zetasizer\Macros\ExtraMacros

Start the Malvern Zetasizer software. Go to Tools
–> Options
–> Macros
–> Install new Macro
navigate to the ExtraMacros folder and install the MakeDLSDAT-v1-0 macro
Restart the Malvern Zetasizer software to complete the macro installation.

To use the macro:
Open the dts data file, select(=highlight) the record you want to export, right-click
–> Macros
–> MakeDLSDAT-v1-0
– then navigate to desired folder and enter the name of the file. The macro will produce a file with the extension .dlsdat for use with Sedfit.

To analyze your data with SEDFIT:
This is taken from Peter Schuck’s tutorial, slightly modified)

  1. Open Sedfit . Go to DATA, Load DLS data. Choose your *.DLSDAT file.
  2. Set limits.
    LEFT side, position cursor on the green line. CNTL double click. Or: Drag and confirm.
    RIGHT side, position cursor on green line. CNTL double click. (Ideally include as much data as possible. It may turn out that some of your data, at the extremes is not free from artifacts in which case you will want to adjust the fitting limits to other values.) If you are happy with the quality of your data, do not adjust the green bar fitting limits.
    In any event, set the green bars if you want to avoid bad data at the extrema. Use most of the data if possible.
  3. Model: Dynamic Light Scattering – discrete Stokes Radii. Set viscosity (automatic popup window)
  4. Parameters: Check component 1, I, and R. Set “I” at 0.5. Set R at 5.
  5. Hit Run and then FIT.
  6. Go back to the parameters box and check component 2. I, R. Set I at 0.5 and R at 10. Hit run and then fit.
  7. Go back to the parameters box and check component 3. Repeat the process with the checks and the fitting. Repeat the process with component 4……
  8. After you have added in all the components, continue to hit the fit button until the radii, the rmsd and the fractions no longer change.
  9. You should find that the resolution and final data are beautiful. File is My Docs\Analyzing DLS ……

Method 2: Record-Exporter macro

 

Download and install the Record-Exporter-v1-1 macro just like in Method 1,  rename the extension from “.txt” to “.zmac” and install the macro from within the Zetasizer software. To use, right-click on the record right-click
–> Macros
–> Record-Exporter-v1-1
– then navigate to desired folder and enter the name of the file. The macro will produce a file with the extension .txt for use with Sedfit conversion facility.

Screenshot-convert-DLS-to-dlsdat-SEDFIT-format

Start SEDFIT and select Options

–> DLS Tools
–> Convert DLS data to SEDFIT format
–> 2 column ASCII g2-1

 

 

Then select the data file just saved from excel and press Save, next provide a filename for the converted file and save it in dlsdat format, default name is 00001.dlsdat Press Save. A popup window with name MAKE DLS DATA appears asking for the temperature (default 25C) OK, followed by time (default 1 sec) OK, followed by refractive index (default 1.33) , followed by absolute viscosity of solvent in Poise (default 0.01002) followed by scattering angle (default 173) followed by wave length (default 632.8nm)

For actual analysis with SEDFIT go to Data – Load DLS data and load the file with extension dlsdat, just as described above in the analysis section of Method 1.

Method 3: Excel

Excel-warning-click-Enable-content

 

First export the correlation function of the desired record in column format. This can be achieved via an Excel macro built into the Correlation Data Import_v5+ spreadsheet. Download and open the file. When open, all content has to be enabled as well as macros (i.e. click OK, OK in Excel). Open the Zetasizer data file and select the desired record in the size or summary workspace. Then tab to Excel, click the grey Run button, followed by the grey “Import Correlation Data” button and press the “Quit” button to end the macro. The correlation function delay times and values (G2 – 1) are now in the spreadsheet in columns A and B. Highlight the actual values, typically from A3 to B170, copy (Ctrl-C). Open a new spreadsheet, paste (Ctrl-V) into A1 then save the spreadsheet as a text file {select file type test (MS-DOS) (*.txt)} and remember the name. Once the text file is created, then follow the steps of Method 2 to convert into Sedfit format and subsequent analysis. For more details and additional Excel macros check this recent blog.

Good luck with your advanced dynamic light scattering data analysis!

Previously

If you have any questions, please email me at ulf.nobbmann@malvern.com. Thanks! While opinions expressed are generally those of the author, some parts may have been modified by our editorial team.