SHELXL: Difference between revisions

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SHELXL (edit)

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add PDB2INS; add Lübben reference; remove outdated compilation hints for Mac

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 == Input files for SHELXL ==
-SHELXL usually requires two input files: an .ins file containing crystal data, instructions and atoms, and an .hkl file containing h, k, l, F<sup>2</sup> and &sigma;(F<sup>2</sup>) in fixed ‘HKLF 4’ format [alternatively F and &sigma;(F) may input; this requires the instruction ‘HKLF 3’]. The .ins file will usually be generated from a PDB format file using the ‘I’ option in SHELXPRO. This sets up the TITL...UNIT instructions followed by standard refinement instructions, restraints, instructions for generating hydrogen atoms (commented out until needed) and atoms in '''''crystal coordinates'''''. For residues other than the 20 standard amino-acids, suitable restraints (see below) must be added by hand (see below). The ‘I’ option in SHELXPRO provides a way of renumbering the residues; since SHELXL does not (currently) recognize chain identifiers, chains must be emulated by (for example) adding 1000, 2000 etc. to the residue numbers. SHELXPRO can also perform the reverse operation when preparing a PDB file for deposition (the ‘B’ option). After each refinement job, the output .res file is edited or renamed to a new .ins file that serves as the input for the next refinement job. The updating of the .res file to .ins may also be performed by ‘U’ option in SHELXPRO; do not use the "I" option and the .pdb file for this, because all the special instructions in the .ins file will be lost.<br>
+SHELXL usually requires two input files: an .ins file containing crystal data, instructions and atoms, and an .hkl file containing h, k, l, F<sup>2</sup> and &sigma;(F<sup>2</sup>) in fixed ‘HKLF 4’ format [alternatively F and &sigma;(F) may input; this requires the instruction ‘HKLF 3’].
+Until 2019, the following text held: ''The .ins file will usually be generated from a PDB format file using the ‘I’ option in SHELXPRO. This sets up the TITL...UNIT instructions followed by standard refinement instructions, restraints, instructions for generating hydrogen atoms (commented out until needed) and atoms in '''''crystal coordinates'''''. For residues other than the 20 standard amino-acids, suitable restraints (see below) must be added by hand (see below). The ‘I’ option in SHELXPRO provides a way of renumbering the residues; since SHELXL does not (currently) recognize chain identifiers, chains must be emulated by (for example) adding 1000, 2000 etc. to the residue numbers. SHELXPRO can also perform the reverse operation when preparing a PDB file for deposition (the ‘B’ option). After each refinement job, the output .res file is edited or renamed to a new .ins file that serves as the input for the next refinement job. The updating of the .res file to .ins may also be performed by ‘U’ option in SHELXPRO; do not use the "I" option and the .pdb file for this, because all the special instructions in the .ins file will be lost.''<br>
+Since 2019, the .ins file should be produced by PDB2INS (Lübben and Sheldrick, 2019).
 The .hkl file contains the reflection intensity data. It is not necessary to sort the data, eliminate systematic absences or merge equivalents, SHELXL can do this anyway. If it is desired to refine (using complex scattering factors) against separate F<sup>2</sup>-values for h,k,l and –h,-k,-l some care is needed; there are problems using data processing software (such as CCP4) that does not keep these measurements separate, and ‘MERG 2’ must be specified in the .ins file to prevent SHELXL from merging the Friedel opposites (and setting all f” values to zero). A further problem on continuing a refinement started with another program is to ensure consistent flagging of the free-R reflections. For this reason it is strongly recommended that Tim Gr&uuml;ne's program [[mtz2hkl]] is used for this conversion. The Bruker [[XPREP]] program provides general facilities for setting Rfree flags and for transferring and extending free-R flags consistently from one reflection file to another taking space group symmetry into account. When twinning or NCS are present, it is better to flag thin resolution shells, otherwise random reflections should be flagged.<br>
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 SHELXC/D/E and test data may be downloaded from the SHELX fileserver. Users should register online at  http://shelx.uni-ac.gwdg.de/SHELX/ .  Downloading instructions will then be emailed.  The programs are free to academics but a small license fee is required for 'for-profit' use.  <br>
-== Installing of the multiprocessor version on a Mac ==
+== References and other sources of information ==
-The mp version of SHELXL runs on all 16 processors of a Mac (two quad core with hyperthreading). In a test case, the refinement with total processor time of 70.7 seconds was finished within less than six seconds:-)
+Lübben, A.V. and Sheldrick, G.M. (2019). "PDB2INS: bridging the gap between small-molecule and macromolecular refinement", ''J. Appl. Cryst.''. '''52''', 669–673 [https://journals.iucr.org/j/issues/2019/03/00/fs5176/index.html open access] .<br>
-The following packages need to be installed before the compilation:
+Sheldrick, G.M. (2015). "Crystal structure refinement with SHELXL", ''Acta Crystallogr''. '''C71''', 3-8 [https://journals.iucr.org/c/issues/2015/01/00/fa3356/index.html open access] .<br>
-* XCode 312_2621_developerdvd.dmg   (downloaded from apple - 996 MB)
+Gruene, T. et ''al.'' (2014). "Refinement of Macromolecular Structures against Neutron Data with SHELXL-2013". ''J. Appl. Cryst.''. '''47''', 462-466 [''Reference for refinement against neutron data and for hydrogen restraints''].
-* Intel fortran compiler Professional 31 day evaluation version)
-*# m_cprof_p_11.0.059.dmg  (downloaded from intel - 343 MB)
-*# m_cprof_ifort_redist_p_11.0.059.dmg (downloaded from intel - 20,3 MB)
-the compilation works smoothly, but instead of -static flag, it is necessary to use a -static-intel flag. A 64 bit compilation is invoked with:
- ifort -axPT -openmp -ip -static-intel shelxh_omp.f shelxlv_omp.f -o shelxl_omp.64bit
-Update 6/2010: Problems exist with Xcode 3.2.2 . The workaround is to add the -use-asm flag. See http://software.intel.com/en-us/articles/intel-fortran-for-mac-os-x-incompatible-with-xcode-322/
-== References and other sources of information ==
 Sheldrick, G.M. (2008). "A short history of SHELX", ''Acta Crystallogr''. '''D64''', 112-122 [''Standard reference for all SHELX... programs''].<br>
-Gruene, T. et ''al.'' (2014). "Refinement of Macromolecular Structures against Neutron Data with SHELXL-2013". ''J. Appl. Cryst.''. '''47''', 462-466 [''Reference for refinement against neutron data and for hydrogen restraints''].
-Sheldrick, G.M. & Schneider, T.R. (1997). ''Methods Enzymol''. '''277''', 319-343 [''Macromolecular refinement with SHELXL''].
 The following additional sources of information may be found via the SHELX homepage (http://shelx.uni-ac.gwdg.de/SHELX):  "SHELX-97 Manual as PDF", "Mini-protein refinement tutorial". "P1-Lysozyme refinement tutorial", "Thomas Schneider's FAQs" and "FAQs: Macromolecules"