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DSR

Small molecule refinement tool

Disordered Structure Refinement (DSR)

The refinement of highly disordered solvents and moieties with SHELXL is an often slow or even difficult task. Therefore these voids frequently are "squeezed out" of the X-ray data. This practice is often not necessary. To help with the routine work of refining disordered solvents the program DSR was developed in Python.

 

 scheme

 

The program-package consists of a simple text-database with fragments of molecules and the DSR program itself. It acts as a preprocessor for SHELXL res-files. The user inserts a special command in the SHELXL .res file and the DSR program reads this information to place a molecular fragment with the desired atoms on the position of the target atoms or Q-peaks, respectively. Bond restraints are applied from the database to the fragment. DFIX restraints can be generated automatically, if desired. Ready to use fragments with senseful restraints can be imported from http://grade.globalphasing.org

Please report bugs or annoying problems to daniel.kratzert@ac.uni-freiburg.de. I can only fix bugs that are known to me. Also wishes for new fragments or program features are very welcome!

You may cite DSR (or FragmentDB) as

D. Kratzert, I. Krossing, J. Appl. Cryst. 2018, 51, 928-934. doi: 10.1107/S1600576718004508 (direct download)

D. Kratzert, J.J. Holstein, I. Krossing, J. Appl. Cryst. 2015, 48, 933-938. doi:10.1107/S1600576715005580 (download)

 

DSR GUI

You find a graphical user interface for DSR in ShelXle. Just select three source and three target atoms each and you can transfer the desired fragment into your structure. The edit window makes it easy to modify/create fragments. See a Youtube video how it works. You can of course always also use DSR on the command line.

Known bugs

In ShelXle, you might encounter the appearance of black or colored boxes instead of atom labels. This is a known bug in ShelXle. Sadly, I can not do anything against it. You can let the labels appear again if you change the label size by turning the mouse wheel.

 

User Manual:     DSR-manual.pdf

 

Version 216 has a new and faster way of fitting the fragment into the crystal structure. In order to use it in windows, you have to install the DSR-setup-xxx.exe file once (it needs the numpy package). Otherwise, the slow FRAG/FEND fit is used.

stable version:

Windows: DSR-setup-218.exe 28.11.2018
Linux: DSR-218-0.noarch.rpm
28.11.2018
  dsr-218.deb 28.11.2018
  DSR-218.tar.gz 28.11.2018
Mac: DSR-218.dmg
29.11.2018
All systems: previous versions    
Source code:      Github development platform  

 

 

 



 

 

Recent Changes:

changelog.txt

  

  • You prefer Olex2? Then you might want to use the FragmentDB plugin. It is a port of DSR to Olex2.
  • You just need a parser for SHELX files? Then you might be interested in my ShelXFile project.

 

Virus Scanners

Some antivirus scanners don't seem to like DSR. If you have problems installing DSR, please let me know. Most antivirus vendors allow the correction of false-positive virus detections.

 

Contribute 

Do you like to contribute? You are very welcome! Fork my code at Github (github.com/dkratzert/DSR) and send me pull requests, patches, feature requests, ideas ... Do not hesitate to ask how the code of DSR works! You don't have to be the best programmer in the world. You just need some Python knowledge.

 

Diskussion

You want to talk about DSR or FragmentDB? Join Slack about DSR.

 

Some molecular fragments are taken from the "Idealized Molecular Geometry Library" of Ilia A. Guzei 
(I. A. Guzei, J. Appl. Cryst. 2014, 47, 806-809).

DSR uses the following Python libraries:  

Fredrik Johansson et.al. mpmath: a Python library for arbitrary-precision floating-point arithmetic (version 0.18), December 2013, http://mpmath.org/.

A. Hagberg, D. Schult, P. Swart, NetworkX: package for the creation, manipulation, and study of complex networks (version 1.8.1) 2013http://networkx.github.io/

License

DSR is free software and licensed under the beerware license.