SHELX C/D/E: Difference between revisions

3,460 bytes added ,  24 January
(→‎References: add "see also" section, and link existing article)
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(or xx_i.hat).
(or xx_i.hat).


=== Full list of SHELXE options ( Version 2021/1; defaults in brackets) ===
=== 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]
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  -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
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  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;
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