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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]] ! | ||
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== Refinement of macromolecules with SHELXL == | == Refinement of macromolecules with SHELXL == | ||
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Despite this generality, it must be emphasized that SHELXL is not suitable for refinements at resolutions lower than about 2.0 Å because, unlike [[Refmac]] and [[PHENIX|phenix.refine]], it does not provide (side-chain) torsion angle restraints, and that a least-squares refinement program such as SHELXL will suffer more from model bias than a program based on maximumlikelihood. Also the Babinet bulk solvent model used in SHELXL is in need of improvement. Almost always the initial refinement will have been performed with another program and SHELXL will be used for the final refinement, perhaps involving extension to very high resolution, modeling of disorder, anisotropic refinement and the least-squares estimation of parameter errors. Thus the starting point for a SHELXL refinement will usually be a PDB format file from the previous refinement. Even when SHELXL has to be used for the refinement of a non-merohedrally twinned structure at lower resolution, the starting model is likely to be in the form of a PDB file from a molecular replacement solution.<br> | Despite this generality, it must be emphasized that SHELXL is not suitable for refinements at resolutions lower than about 2.0 Å because, unlike [[Refmac]] and [[PHENIX|phenix.refine]], it does not provide (side-chain) torsion angle restraints, and that a least-squares refinement program such as SHELXL will suffer more from model bias than a program based on maximumlikelihood. Also the Babinet bulk solvent model used in SHELXL is in need of improvement. Almost always the initial refinement will have been performed with another program and SHELXL will be used for the final refinement, perhaps involving extension to very high resolution, modeling of disorder, anisotropic refinement and the least-squares estimation of parameter errors. Thus the starting point for a SHELXL refinement will usually be a PDB format file from the previous refinement. Even when SHELXL has to be used for the refinement of a non-merohedrally twinned structure at lower resolution, the starting model is likely to be in the form of a PDB file from a molecular replacement solution.<br> | ||
== Input files for SHELXL == | == Input files for 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 [http://shelx.uni-ac.gwdg.de/~tg/mtz2x/mtz2hkl/mtz2hkl.php 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. | 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 [http://shelx.uni-ac.gwdg.de/~tg/mtz2x/mtz2hkl/mtz2hkl.php 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, a .pdb file with the new atom coordinates (unfortunately one has to add the space group to the CRYST1 record before Coot can read this 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. | SHELXL writes a updated parameter file with the extension .res in the same format as the input .ins file, a .pdb file with the new atom coordinates (unfortunately one has to add the space group to the CRYST1 record before Coot can read this 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 (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 C</b><br> | ||
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<b>CHIV_DAL 29 CA</b> | <b>CHIV_DAL 29 CA</b> | ||
(i.e. -1*fv(3)). | (i.e. -1*fv(3)).<br> | ||
== Least-squares refinement algebra == | == Least-squares refinement algebra == | ||