Disordered Structure Refinement

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Graphical user interface of DSR in ShelXle. Dsr shelxle.png
Graphical user interface of DSR in ShelXle.

The Disordered Structure Refinement [1] [2] program (DSR), written by Daniel Kratzert, is designed to simplify the modeling of molecular disorder in crystal structures using SHELXL [3] [4] [5] by George M. Sheldrick. It has a database of approximately 120 standard solvent molecules and molecular moieties. These can be inserted into the crystal structure with little effort, while at the same time chemically meaningful binding and angular restraints [6] are set. DSR was developed because the previous description of disorder in crystal structures with SHELXL was very lengthy and error-prone. Instead of editing large text files manually and defining restraints manually, this process is automated with DSR.

Contents

Application

DSR can be started in a command line. The call has the basic form:

dsr [option] (SHELXL file)

DSR is controlled with a special command in the corresponding SHELXL file. This has the following syntax:

REM DSR PUT/REPLACE "fragment" WITH (atoms) ON (atoms or q-peaks) PART 1 OCC -21 =   RESI DFIX

The DSR command must always start with REM so that SHELXL does not recognize this line as its own command. Which atom of the molecule fragment from the database corresponds to which atom or q-peak in the crystal structure is specified in the list following WITH and ON.

By running

dsr -r file.res

the fragment fit is performed and the restraints transferred.

Graphical user interface

Since 2016 ShelXle has a graphical interface to DSR. Most commands of the command line version can be executed there.

In order to transfer a fragment into a structure, three atoms / q-peaks have to be selected in ShelXle and in the DSR GUI each to specify the position of the fragment. The 3D view of the fragment then shows a preview of the subsequent fragment fit.

Programming

DSR is only programmed in Python. Therefore, it runs in any Python-supported operating system.

It is under the free Beerware license and can be downloaded free of charge and changed as desired.

References

  1. ↑ Kratzert, Daniel; Krossing, Ingo (3 May 2018). "Recent improvements in DSR" . Journal of Applied Crystallography. 51 (3): 928–934. doi:10.1107/S1600576718004508. ISSN   1600-5767 . Retrieved 17 August 2018.
  2. ↑ Daniel Kratzert; Julian J. Holstein; Ingo Krossing (2015-06-01), "DSR: enhanced modelling and refinement of disordered structures with SHELXL", Journal of Applied Crystallography (in German), vol. 48, no. 3, pp. 933–938, doi:10.1107/s1600576715005580, ISSN   1600-5767, PMC   4453980 , PMID   26089767 , retrieved 2017-02-07
  3. ↑ "The SHELX homepage" (in German). Retrieved 2017-02-07.
  4. ↑ George M. Sheldrick (2008-01-01), "A short history of SHELX", Acta Crystallographica Section A: Foundations of Crystallography (in German), vol. 64, no. 1, pp. 112–122, Bibcode:2008AcCrA..64..112S, doi: 10.1107/s0108767307043930 , ISSN   0108-7673, PMID   18156677
  5. ↑ George M. Sheldrick (2015-01-01), "Crystal structure refinement with SHELXL", Acta Crystallographica Section C: Structural Chemistry (in German), vol. 71, no. 1, pp. 3–8, doi:10.1107/s2053229614024218, ISSN   2053-2296, PMC   4294323 , PMID   25567568
  6. ↑ Gerard J. Kleywegt (2007-01-01), "Crystallographic refinement of ligand complexes", Acta Crystallographica Section D: Biological Crystallography (in German), vol. 63, no. 1, pp. 94–100, doi:10.1107/s0907444906022657, ISSN   0907-4449, PMC   2483469 , PMID   17164531
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