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Recent Changes
-233 Fixed some accidental HFIX instructions.
-232 Fixed rmsd value of fragment fit.
-231 Removed numpy dependency for fragment fit.
-230 Added "REM HFIX ..." to the list of restraints for fragments in residues.
-229 Fixed wrong atom name in some restraints.
-228 Fixed crash when solely "resi" occours in the res file.
-227 Fixd bug in restraints generation.
-226 New fragments PMe3 and tBu, thanks to Krzysztof Radacki.
-225 Fixed bug where fragments got wrong orientation.
-224 Fixed bug where certain fragments got really large with DFIX command.
-223 Fixed acetone restraints. Added test for inconsistent restraints with two atom pairs.
-222-1 Fixed damaged numpy in Windows installer.
-222 Fixed faulty 1,3 restraints in benzene.
-221 Separated restraints and fragment during transfer. The restraints are now always inserted after
UNIT. The new fragment is always located before HKLF. This has the advantage that it does not depend on
the position of the DSR command and the SAME instruction has always the better fragments
as reference. Also the often demanded sorting of the residue numbers should be in an inreasing order now.
I also discarded the fragment fit with SHELXL FRAG/FEND. This implies that DSR now relies
on the numpy package. If you have just auto-updated DSR for a long time,
you might have to reinstall DSR from the installer one time in order to get it running.
Non-Windows users have to make sure that numpy is installed in addition! The windows installer
includes the numpy package and should run just fine.
-220 Allowing space characters in fragment search. Fixed bug where cf3 group generation could fail.
-219 Adding "SIMU 0.04 0.08 1" to all restraints. This is necessary, because "SIMU_XYZ atoms"
only affects each residue in itself and not to atoms of residues near each other.
-218 Fixed Exception occouring when source atoms had lower-case names.
-217 Fixed linux packages.
-216 New fit procedure should be stable now. In windows, you need to install the installer
executable once! DSR needs numpy for the faster fit now. Without numpy, the old
fragment fit is used.
-215 Kabsch fit resulted in wrong translation of the fragment in some cases. This is fixed now.
-214 Fixed external restraints with Kabsch fit. All feature should work now.
-213 Added fragment fit with Kabsch algorithm instead of FRAG/FEND fit. This runs much faster
for large structures. This version might be unstable and not all features are suported,
but regular fragment fit with or without RESIdues and PARTs work.
-212 Fixed SFAC with exponential parameters. Teflat fragment added. Added Trifluorbenzene.
-211 More fragments: Dimethyl ammonium, tert-Butyl isocyanide, improved replace mode.
-210 Added check for DFIX/DANG if the d value is larger than the sigma (as it should be).
DSR now ignores fragments that do not contain atoms. Less output during fragment fit
(wR2 and Gof were useless). Fixed line endings in start script. This should fix
updates on Unix systems.
-209 Added 4,4'-Di-tert-butyl-2,2'-bipyridine and TEMPO fragments, users manual updated esp.
residues chapter, optimized restraints, fixed Acetonitrile restraints (why did nobody
noticed this?).
-208 Changed self-update process to be secured by checksums and ssl.
-207 When using residues, DSR will now introduce a SAME_name 'first atom' > 'last atom'
to the list of restraints. First/last atom means first and last atom from the
respective fragment. This will make distances in all residues more consisten but should
do no harm.
Restructured a lot. Acess to the text database is now clearer and the parser
easyer to read.
-206 Added Thiophen and 1,2,3,4-Tetrafluorobenzene.
-205 Added SO2. Added full SHELXL-2017/1 compatibility (Except for chain IDs). Fixed
restraints in acetonitrile.
-204 Added Methyl tert-butyl ether to the DB. Small fix for CF3 groups. Refractured
some code.
-203 Added logfile 'dsr-log.lst' to dsr output. Every last dsr run is now in the
'dsr-log.lst' file. Improved detection of already used restraints. The standard
deviations are now ignored for detection of duplicate restraints. This prevents
adding new restraints although they are alredy there but with different values.
Added two more ether conformers (zigzag and only one side angled).
-202 Greatly improved search results of "dsr -s name". A bug prevented to display
very similar names in the search results.
-201 Fixed bug in threefold disordered CF3 group. Fixed -target option. Q-peaks
with -target can now have duplicate names. Removed FLAT in alkanes.
-200-1 Added missing python27.dll in Windows package. Fixes "unknown error" in
ShelXle GUI (Thanks to Christoph Wölper).
-200 Startup speed improvements. Added possibility to define target position
of atoms as coordinates (-target option“).
-199 Added documentation how to control DSR with an external user interface.
Hexamethyl benzene fragment added. DSR inserts a comment about the origin
of the fragment into the res file.
-198 Fixed some error messages. Added Leucine and Lysine. Improved search behavior.
Improved sorting of fragment list. Added [SbF6]-. SFAC names are now case insensitive.
-197-1 2,6-Dichlorobenzene added.
-197 Fixed bug that prevents using more than nine free variables. Added
Dichloroethane and TMEDA fragments, RSS-Feed, unit tests, more search
-196 Improved C20, C60 and C70 fragments. Now they all have restraints and
optimized geometry. Fixed case sensitivity bug. Improved FLAT restraints.
Added CF3, CF6 and CF9 fragments as dummys to the database.
Improved unit tests.
-195 Slight speed improvement. Cleaner code (needs more cleaning). Fixed too
optimistic replace mode in 194. External restraints shouuld work again.
-194 Fixed ANSI escape codes appearing in ShelXle GUI. Improved updater.
-193 Added auto updater to DSR. Run "dsr -u" to update to the most recent version.
-192 Fixed strange characters in fragment list in Linux and other Small fixes.
-191 Prevent ** NEGATIVE OCCUPANCY FOR ATOM XX ** warning in case of wrong
free variable values before fit. Added Isopropanole. Optimized examples.
Updated user manual. Fixed minor problem in case no shelxl executable is
found during fit in ShelXle.
-190 Fixed TypeError when using split and cf6.
-189 Improved GRADE import. Fixed bug regarding calculated FLAT restraints.
-188 Fixed bug that produces "dsr: error: unrecognized arguments: [...]" if
SHELXL was located in a directory containing space characters.
Fixed bug where "FVAR 1" ended up as 1000000.
Added all natural amino acids. Improved FLAT restraints.
-187 No CF3 groups inside of residues allowed any more. Fixed exception when
DSR tries to delete a file.
MAC OS: Fixed broken startup script.
-186 Fixed bug in sorting of names list. Made outlier test for SADI a bit weaker.
Added Fluorobenzene. User manual update.
-185 Added COD to database. Fixed bug where cf3fit could delete the first atom
in the res file (Thanks to C. Maichle-Moessmer for reporting). Fixed
damaging of L.S. command with more than one parameter.
-184 PMDETA and DMAP fragments added, Fixed bug where cf3fit could not handle
isotropic atoms (Thanks to C. Maichle-Moessmer for reporting).
-183 New fragments, improved handling of relative paths for external restraints,
restore refinement cycles after DSR run.
-182 IMPORTANT! The default path for the user database is now the users home
directory! For example /home/username/dsr_user_db.txt in Linux and
C:/users/Username in windows Vista and later. The DSR_DB_DIr environment
variable is now deprecated.
This version of DSR is not compatible with the DSR GUI in ShelXle-1.0.758
and below!
ShelXle 758 expects the user database file in the DSR directory while later
versions will expect it in the users home directory.
The fragment names in the listing output are now mostly sorted correctly.
An unreadable SHELXL executable will not create an exeption any more.
-181 Fixed bug where external restraints produced "illegal instruction" error
in SHELXL. AFIX 9 and +dfixfile is now recognized by a unique id.
External restraints with a rigid group produced an invalid RESI None None
-180 Moving version format to integer. Final export format for the ShelXle GUI.
Faster start in Windows. Many small fixes. Improved error messages.
In replace mode, really delete lines instead of producing blank lines.
User manual updates.
-1.7.7 New output format for DSRGui. New command line option for rigid group.
-1.7.6 Huge improvement in SADI consistency checker. Some new fragments NBt4+
NMe4+ C20. Small fixes.
-1.7.5 Also move fluorine atoms in direction of principal ellipsoid axis with
SPLIT option and CF6.
-1.7.4 Added check if SADI atom pair distances are consistent with each other.
Added Anthracene and 9,10-Dibromoanthracene.
Better formating of DFIX/DANG list with dfix option turned on.
Fixed bug with occ=0.25
Addedd C60 (with restraints) and C70 (without restraints, use dfix option).
Some more unit tests.
-1.7.3 Small fix regarding FVAR with CF6 fragment.
-1.7.2 Added [2.2.2]-cryptand to database. Tanks to Dejan Premuzic! Added Ability
to compute principal axes vectors of an ellipsoid. Added "split" option
to split CF6 group. Several other fixes.
-1.7.1-1 Fixed missing in Windows installer.
-1.7.1 Fixed typos in CF3 restraints. Improved residue handling with CF3 groups.
Known bugs: res files without FVAR (e.g. after shelxs or shelxt) cause a
-1.7.0 New feature: Ability to model disordered CF3 groups (1, 2 and 3 positions).
Fixed CF6 restraints.
-1.6.4 removed dependency of DFIX and PART in DSR, better warning for unsuccessful
shelxl runs.
-1.6.3 Improved FLAT restraints. Fixed Pyridine and Acetonitrile restraints.
Perfluoro adamantole added.
-1.6.2 Improved atom deleter in replace mode.
Finally, a brand new dmg image for Mac OS X.
-1.6.1 New feature: replace mode will replace all atoms in PART 0 that are 1.2 A
near the fitting fragment. Please tell me if 1.2 A is too far.
New fragment 18-Crown-6 (thanks to Dejan Premu�ic), New fragment Mesitylene.
Bug fixed that introduced
restraints again, even if they were already there (thanks to Olaf Petersen).
Better warning for bad residues. Several small fixes. ACTA card is restored
as it was before now.
Triphenylphosphane added to database. Fixed replacing of residues.
-1.6.0 Completely changed DFIX/DANG/FLAT routines. Connectivity list is now
calculated by DSR and not from .lst file (SHELXL).
FLAT also includes neighbouring ring atoms. Exported res files now include
DFIX/DANG/FLAT restraints. Please report bugs in this release.
-1.5.15 Database updates, Fixed missing U values in exported res files, during import
the name comes from the pdb file now.
-1.5.14 Bug fixes, nicer export, warning about missing database, database updates,
manual updates.
-1.5.13 Improved error logging. Implemented Support for negative atomic number for
atom type. Fixed some typos in the database.
-1.5.12 Fixed bug in replace mode.
-1.5.11 Ignore lines starting with # in the DB. Python3 compatible again. Lower
case resi fixed. Exceptions get logged.
Several improvements for external restraints.
-1.5.10 External restraints without residues are now supported. Small fixes.
-1.5.9 DSR now warns if data to paramter ratio is getting bad. small fixes.
-1.5.8 Support for both types of SFAC. Search result of -s also with line number.
More tests.
-1.5.7 DSR now creates a backup file before fragment fit in a separate directory.
Exported fragment res files now include database restraints.
-1.5.6 Program renamed to "Disordered Structure Refinement (DSR)" Small fixes.
Warning about inacurate restraints.
-1.5.5 Unit tests. Small fixes.
-1.5.4 Code cleanup and deletion from adjacent hydrogen atoms improved.
-1.5.3 Recognition of dsr command improved.
-1.5.2 Fixed incorrect handling of lower-case residues.
-1.5.1 Fixed handling of atom names like C0W0. Exception handling for missing dsr
command fixed.
-1.5.0 New option "-s" to search for fragments in the database. Improved file formating.
-1.4.6 Fixed negative part numbers.
-1.4.5 Introduced the ability to invert the fragment (-t option). Simplified
startup script for windows. Splitted export to clipboard (-c option) and
to res/png file (-e option) in two options.
-1.4.4 small db updates, small fix in error handling.
-1.4.3 very long lines of restraints were not correctly wrapped.
-1.4.2 serious bug with wrong naming scheme of fragment atoms fixed.
-1.4.1 serious bug with wrapped lines in the database header fixed.
-1.4.0 Big database update (Many thanks to Ilia A. Guzei providing molecular
fragments). The automatic generation
of DFIX/DANG and FLAT restraints with the "DFIX" DSR-command is now implemented.
Success and fail reports about the restraint generation would be highly
Separate files with restraints e.g. in a +FILENAME.dfx file are now implemented
(system command line option -re). Full fragment names are now listed with
"dsr -l". The output of -l
now automatically fits to the command line width.
More meaningful comments about the import from a GRADE fragment are now
included during the import
and export. Multiple lines of REM in the database are now supported.
The molecules of the paper about "X-ray analysis on the nanogram to microgram
scale using porous complexes"
from Inokuma, Y. et al. Nature 495, 461�466 (2013) are included!
-1.3.2 FRAG in the database entrys was accidentally case sensitive. A missing
residue in the database entry was not properly checked.
-1.3.1 A lot of improvements: DFIX command now possible without RESI command.
line wrap of long command
lines and lines of restraints now fully working. Export to clipboard of
experimental coordinates now
working correctly. Networkx added to distribution.
-1.3.0 First implementation of automatic generated DFIX restraints.
-1.2.13 Restraints for same residue classes are now inserted only once. Port to Python-3.3
-1.2.12 Small fixes and new Linux packages.
-1.2.11 Supports now multiple lines of FVAR. DSR command line in res file is now
correctly wrapped
during processing with DSR bevor exceeding 80 characters.
-1.2.10 Much improved error handling for shelxl. In case of shelx errors the original
res file is restored now. The B array size is now set according to the number of atoms.
-1.2.9 Minor improvement in export. Better esds in the database.
-1.2.8 Fixed bug where sometimes atom names were case sensitive.
-1.2.7 A few improvements in the database. Small bugfixes.
-1.2.6 Olex2 macro was not working. Export inside Olex2 still does not work in 64bit windows.
Will be fixed later.
-1.2.5 Fixed bug where db content was printed to screen instead of the db name when no restraints
are in a db entry.
-1.2.4 export of a fragment now copies also to the clipboard. This can be used with the "match"
functionality of Olex2.
-1.2.3 better GRADE import directly from the .tgz file. Lots of small imporovements.
-1.2.2 small fixes
-1.2.1 nicer output
-1.2.0 Support for Grade import, more fragments, better output listing from "dsr -l", better error
handling. Please uninstall the previous version (<= 1.1.3 ) completely bevore installing
Version > 1.2.0
-1.1.2 fix for lowercase atom names
-1.1.1 Small corrections in the Windows setup process.
-1.1.0 Step by step example in the manual and example files in the package.
-1.0.6 files with no AFIX are now handled correctly
-1.0.5 small fix to handle the AFIX 9 after an AFIX mn correctly.
-1.0.4 DSR was not able to find xl.exe.
-1.0.3 Linux package now with unix line endings.
-1.0.2 new dsr makros for Olex2 (custom.xld)
-1.0.1 better for Olex2
-1.0.0 full support for residues in target atom notation e.g. C12_1. DSR finds a unique residue
number if no number is given, warns if residue number already in use und finds a uniq.
Adjacent hydrogen atoms are deleted in replace mode.