1,330
edits
SHELX C/D/E: Difference between revisions
→Full list of SHELXE options ( Version 2021/1; defaults in brackets)
(→References: add "see also" section, and link existing article) |
|||
| Line 178: | Line 178: | ||
(or xx_i.hat). | (or xx_i.hat). | ||
=== Full | === Full SHELXE help output === | ||
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | |||
+ SHELXE - PHASING AND DENSITY MODIFICATION - Version 2023/1 + | |||
+ Copyright (c) George M. Sheldrick and Isabel Uson 2001-23 + | |||
+ Started at 18:30:57 on 24 Jan 2024 + | |||
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | |||
A typical SHELXE job for SAD, MAD, SIR or SIRAS phasing could be: | |||
shelxe xx xx_fa -s0.5 -z -a10 -O | |||
where xx.hkl contains native data and xx_fa.hkl, which should have | |||
been created by SHELXC or XPREP, contains FA and alpha. The heavy | |||
atoms are read from xx_fa.res, which can be generated by SHELXD or | |||
ANODE. 'xx' and 'xx_fa' may be replaced by any strings that make | |||
legal file names. If these heavy atom are present in the native | |||
structure (e.g. for sulfur-SAD but not SIRAS for an iodide soak) | |||
-h is required (or e.g. -h8 to use only the first 8). -z optimizes | |||
the substructure at the start of the phasing. -z9 limits the number | |||
of heavy atoms to 9. If -z is specified without a number, | |||
no limit is imposed. Normally the heavy atom enantiomorph is not | |||
known, so SHELXE should also be run with the -i switch to invert | |||
the heavy atoms and if necessary the space group; this writes | |||
files xx_i.phs instead of xx.phs etc., so may be run in parallel. | |||
-a sets the number of global autotracing cycles. -a not followed | |||
by a number sets 30 cycles or three cycles after a CC of 30 has been | |||
exceeded, whichever' is less. -n generates NCS operators from heavy | |||
atom positions, e.g. -n6 for six-fold NCS or -n if the number of | |||
copies is not known. -n imposes NCS during tracing.' if NCS is | |||
defined in a pda file -n may not be used. -p traces a DNA or RNA | |||
backbone, -p10 would restrict this search to 10 phosphates. | |||
To start from a MR model without other phase information, the PDB | |||
file from MR should be renamed xx.pda and input to SHELXE, e.g. | |||
shelxe xx.pda -s0.5 -a20 | |||
The number of tracing cycles is usually more here to reduce model | |||
bias. If the MR model is large but does not fit well, -o | |||
should be included to prune it before density modification, the | |||
revised model is then writen to xx.pdo. | |||
Tracing from an MR model requires a favorable combination of model | |||
quality, solvent content and data resolution. If e.g. SAD phase | |||
information is available, even if it is too weak for phasing on | |||
its own, the two approaches may be combined: | |||
shelxe xx.pda xx_fa -s0.5 -a10 -h -z | |||
The phases from the MR model are used to generate the heavy atom | |||
substructure. This is used to derive experimental phases that are | |||
then combined with the phases from the MR model (MRSAD). The -h, | |||
-o and -z flags are often needed for this mode. | |||
If approximate phases are available, SHELXE may be used to refine | |||
them and make a poly-Ala trace: | |||
shelxe xx.zzz -s0.5 -a3 | |||
where zzz is phi (phs file format), fcf (from SHELXL) or hlc | |||
(Hendrickson-Lattman coefficients, e.g. from SHARP or BP3). | |||
In all cases, native data are read from xx.hkl in SHELX format, | |||
and the density modified phases are output to xx.phs (or xx_i.phs | |||
if -i was set). The listing file is xx.lst (or xx_i.lst). If | |||
xx_fa.hkl is read, substructure phases are output to xx.pha (or | |||
xx_i.pha) and the revised substructure is written to xx.hat | |||
(or xx_i.hat).' If -o is used to improve a model in xx.pda, the | |||
revised model is output to xx.pdo. | |||
Full list of SHELXE options (defaults in brackets): | |||
================================================== | |||
-aN - N cycles autotracing [off] | -aN - N cycles autotracing [off] | ||
-bX - B-value to weight anomalous map (xx.pha and xx.hat) [-b5.0] | -bX - B-value to weight anomalous map (xx.pha and xx.hat) [-b5.0] | ||
| Line 218: | Line 293: | ||
-zN - substructure optimization for a maximum of N atoms [off] | -zN - substructure optimization for a maximum of N atoms [off] | ||
-z - substructure optimization, number of atoms not limited [off] | -z - substructure optimization, number of atoms not limited [off] | ||
-t values of 3.0 or more switch to more accurate but appreciably | -t values of 3.0 or more switch to more accurate but appreciably | ||
slower tracing algorithms, this is recommended when the resolution | slower tracing algorithms, this is recommended when the resolution | ||
| Line 225: | Line 300: | ||
and output only once CC>30 so poly-alanine tracing scores | and output only once CC>30 so poly-alanine tracing scores | ||
can be used to identify solutions as before. | can be used to identify solutions as before. | ||
Please cite: I. Uson & G.M. Sheldrick (2018), "An introduction to | Please cite: I. Uson & G.M. Sheldrick (2018), "An introduction to | ||
experimental phasing of macromolecules illustrated by SHELX; | experimental phasing of macromolecules illustrated by SHELX; | ||