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SHELXL: Difference between revisions
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For the other [http://shelx.uni-ac.gwdg.de/SHELX/ SHELX] programs featured in this Wiki, see [[SHELX C/D/E]] ! | For the other [http://shelx.uni-ac.gwdg.de/SHELX/ SHELX] programs featured in this Wiki, see [[SHELX C/D/E]] ! | ||
<br> | |||
== Refinement of macromolecules with SHELXL == | == Refinement of macromolecules with SHELXL == | ||
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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 σ(F<sup>2</sup>) in fixed ‘HKLF 4’ format [alternatively F and σ(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 σ(F<sup>2</sup>) in fixed ‘HKLF 4’ format [alternatively F and σ(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> | ||
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 Grüne's program [ | 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 Grüne'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> | ||
== SHELXL Output files == | == SHELXL Output files == | ||
SHELXL writes a updated parameter file with the extension .res in the same format as the input .ins file, | SHELXL writes a updated parameter file with the extension .res in the same format as the input .ins file, and an output .fcf file containing phased reflection data in CIF format. This file can be used for depositing the reflection data with the PDB, and both the .res and the .fcf file can be read by Coot to enable the refined atoms and σ<sub>A</sub>-weighted maps to be displayed directly.<br> | ||
== Constraints and restraints == | == Constraints and restraints == | ||
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The PRODRG server: http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ is recommended for generating restraints in SHELX format for ligands etc; the "J" option in SHELXPRO can also be useful for this if a model is already available. File of DNA and RNA restraints are available from the SHELX download site.<br> | The PRODRG server: http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ is recommended for generating restraints in SHELX format for ligands etc; the "J" option in SHELXPRO can also be useful for this if a model is already available. File of DNA and RNA restraints are available from the SHELX download site.<br> | ||
== Chiral volumes == | == Chiral volumes == | ||
SHELXL defines a chiral volume as the volume of the 'unit-cell' that can be constructed using the three interatomic | SHELXL defines a chiral volume as the volume of the 'unit-cell' that can be constructed using the three interatomic vectors from the atom in question; this can be calculated as a determinant using orthogonal cartesian coordinates. SHELXL restricts chiral volumes to cases where an atom makes exactly three bonds to other non-hydrogen atoms; hydrogen atoms are ignored. The sign is determined by evaluating the determinant with the rows representing the three vectors in the order of their ASCII codes, and so is independent of the order of the atoms in the input file. This means that the alpha carbon in the 19 standard chiral L-amino-acids will always have a chiral volume of about +2.5 Å<sup>3</sup> (using the Cahn-Ingold-Prelog R and S convention would have required L-Cys to have the opposite sign). CB of Ile has a chiral volume of 2.495 but CB of Thr is -2.628. However the CHIV instruction in SHELXL also has other uses, e.g. | ||
vectors from the atom in question; this can be calculated as a determinant using orthogonal cartesian coordinates. SHELXL restricts chiral volumes to cases where an atom makes exactly three bonds to other non-hydrogen atoms; hydrogen atoms are | |||
ignored. The sign is determined by evaluating the determinant with the rows representing the three vectors in the order of their ASCII codes, and so is independent of the order of the atoms in the input file. This means that the alpha carbon in the 19 standard chiral L-amino-acids will always have a | |||
< | <b>CHIV_VAL C</b><br> | ||
< | <b>CHIV_VAL 2.516 CA</b><br> | ||
< | <b>CHIV_VAL -2.622 CB</b> | ||
This restrains the chiral volume of the carbonyl carbon to be zero (the default) with a default esd (0.1 | This restrains the chiral volume of the carbonyl carbon to be zero (the default) with a default esd (0.1 Å<sup>3</sup>), i.e. restrains it to be planar. CB is not chiral for valine, but the above restraint makes sure that CG1 and CG2 are named conventionally (the RSCB now use this idea to check the naming of H-atoms in -CH<sub>2</sub>- groups, which is one of the reasons why the hydrogens should be removed before depositing the structure (they are always recalculated anyway before use, e.g. by MolProbity). And if you wanted all the alpha-carbons for the alanines to have the same chiral volume but would like to refine its value, a SHELXL 'free-variable' can be used (here #3): | ||
<b>CHIV_ALA 31 CA</b> | |||
(i.e. 1*fv(3)); if there is a D-Ala in the structure as well: | (i.e. 1*fv(3)); if there is a D-Ala in the structure as well: | ||
<b>CHIV_DAL 29 CA</b> | |||
(i.e. -1*fv(3)).<br> | |||
== Least-squares refinement algebra == | == Least-squares refinement algebra == | ||
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== Obtaining the SHELX programs == | == Obtaining the SHELX programs == | ||
SHELXC/D/E and test data may be downloaded from the SHELX fileserver. | 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 == | |||
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:-) | |||
The following packages need to be installed before the compilation: | |||
* XCode 312_2621_developerdvd.dmg (downloaded from apple - 996 MB) | |||
* 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 == | == 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> | 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'']. | 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" | 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" | ||