dkratzert / dsr

Refinement of disordered structures with SHELXL

DSR

The program DSR consists of a text database with fragments of molecules and the DSR program. 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 put a molecule or fragment with the desired atoms on the position of the target atoms or q-peaks in the unit cell. Bond restraints can be either applied from the database to the molecule or automatically generated.

• The homepage

I apologize for the messy code. This was my first bigger project...

You have either a command line version:

C:\Users\daniel>dsr
----------------------------------------------------- D S R - v238 -------------------------------------
Disordered Structure Refinement (DSR)

Example DSR .res file command line:
REM DSR PUT/REPLACE "Fragment" WITH C1 C2 C3 ON Q1 Q2 Q3 PART 1 OCC -21 =
  RESI DFIX
---------------------------------------------------------------------------------------------------------
   PUT:     Just put the fragment source atoms here.
   REPLACE: Replace atoms of PART 0 in 1.3 A distance around target atoms.
---------------------------------------------------------------------------------------------------------

optional arguments:
  -h, --help            show this help message and exit
  -r "res file" ["res file" ...]
                        res file with DSR command
  -re "res file" ["res file" ...]
                        res file with DSR command (write restraints to external file)
  -e "fragment"         export fragment as .res/.png file
  -c "fragment"         export fragment to clipboard
  -t                    inverts the current fragment
  -i "tgz file"         import a fragment from GRADE (needs .tgz file)
  -l                    list names of all database entries
  -s "string"           search the database for a name
  -g                    keep group rigid (no restraints)
  -u                    Update DSR to the most current version
  -n                    do not refine after fragment transfer

Or a graphical user interface in ShelXle:

dsr's Issues

Choose esd for restraints prior to fragment fit

• let user choose the esd prior to the fragment fit
• Should I apply this to one fragment explicitly? e.g. SADI 0.001 C1_2 C2_2 ...
  • Or alternatively as option to apply to all or a single fragment

Import of GRADE2 fails

DSR version: 237
Python version: 3.11.0 (main, Oct 24 2022, 18:26:48) [MSC v.1933 64 bit (AMD64)]
Commandline: Namespace(res_file='', external_restr=False, export_fragment='', export_clip='', invert=False, import_grade='.\QPD.gradeserver_all.tgz', list_db=False, search_string='', rigid_group=False, selfupdate=False, export_all=False, list_db_csv=False, search_extern=False, head_for_gui='', shelxl_ex=False, no_refine=False, target=[])
Platform: Windows 10, Windows LAPTOP-PJSBHG2Q 10 10.0.22621 AMD64 Intel64 Family 6 Model 142 Stepping 12, GenuineIntel
2023-06-13 15:44:48
Traceback (most recent call last):
File "C:\Program Files (x86)\DSR\dsr.py", line 485, in
main()
File "C:\Program Files (x86)\DSR\dsr.py", line 463, in main
dsr = DSR(options)
^^^^^^^^^^^^
File "C:\Program Files (x86)\DSR\dsr.py", line 150, in init
mog.write_user_database()
File "C:\Program Files (x86)\DSR\dbfile.py", line 1123, in write_user_database
imported_entry = self.bild_grade_db_entry()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files (x86)\DSR\dbfile.py", line 1102, in bild_grade_db_entry
'comments' : self.get_comments(),
^^^^^^^^^^^^^^^^^^^
File "C:\Program Files (x86)\DSR\dbfile.py", line 1016, in get_comments
name = 'REM Name: ' + self.get_name_from_pdbfile()
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TypeError: can only concatenate str (not "NoneType") to str