SHELX C/D/E: Difference between revisions

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 A common 'user error' is to set MIND -3.5 even though the distances between heavy atoms are less than 3.5 Å.  For example, in a Fe<sub>4</sub>S<sub>4</sub> cluster the Fe...Fe distance is about 2.7 Å, so MIND -2 would be appropriate. A disulfide bond has a length of 2.03 Å so then MIND -1.5 could be used to resolve the sulfur atoms, however if DSUL is used for this purpose MIND -3.5 is required.
-If heavy atoms can lie on special positions (as is the case with an iodide soak in a space group with twofold axes) the rejection of atoms on special positions should be switched off by giving the second MIND parameter as -0.1 (as in the above thaumatin example).
+If heavy atoms can lie on special positions (as is the case with an iodide soak in a space group with twofold axes) the rejection of atoms on special positions should be switched off by giving the second MIND parameter as -0.1 .
 === Interpretation of results ===
@@ Line 178: / Line 178: @@
 (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]
   -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]
   -z  - substructure optimization, number of atoms not limited [off]
   -t values of 3.0 or more switch to more accurate but appreciably
   slower tracing algorithms, this is recommended when the resolution
@@ Line 225: / Line 300: @@
   and output only once CC>30 so poly-alanine tracing scores
   can be used to identify solutions as before.
   Please cite: I. Uson & G.M. Sheldrick (2018), "An introduction to
   experimental phasing of macromolecules illustrated by SHELX;
@@ Line 291: / Line 366: @@
 === How to tell SHELXE about NCS in a molecular replacement solution PDB file ===
-(communicated by Isabel Uson) Insert a line
+(communicated by Isabel Usón) Insert a line
   REMARK 299 NCS GROUP BEGIN
 before the ATOM (or HETATM) lines of each NCS group (e.g. chain), and insert the line
@@ Line 408: / Line 483: @@
 [[hkl2map]] can be downloaded from a website at EMBL Hamburg. XDSGUI can be downloaded from its [[xds:XDSGUI|XDSwiki article]].
+== See also ==
+[[Solve a small-molecule structure]]
 == References ==
@@ Line 423: / Line 502: @@
 Usón, I., Stevenson, C.E.M., Lawson, D.M. & Sheldrick, G.M. (2007). "Structure determination of the O-methyltransferase NovP using the `free lunch algorithm' as implemented in SHELXE", ''Acta Crystallogr''. '''D63''', 1069-1074 [''Implementation of the FLA in SHELXE''].<br>
-[http://scripts.iucr.org/cgi-bin/paper?sc5010 Sheldrick, G.M. (2008). "A short history of SHELX", ''Acta Crystallogr''. '''D64''', 112-122] [''Standard reference for all SHELX* programs''].<br>
+[http://scripts.iucr.org/cgi-bin/paper?sc5010 Sheldrick, G.M. (2008). "A short history of SHELX", ''Acta Crystallogr''. '''D64''', 112-122] [''Standard reference for all SHELX* programs''].
 [http://dx.doi.org/10.1107/S0907444909038360 Sheldrick, G.M. (2010). "Experimental phasing with SHELXC/D/E: combining chain tracing with density modification", ''Acta Cryst'' '''D66''', 479-485.]
 [https://doi.org/10.1107/S0907444913027534 A. Thorn and Sheldrick, G.M. (2013). Extending molecular-replacement solutions with SHELXE. ''Acta Cryst'' '''D69''', 2251-2256.]
 [https://journals.iucr.org/d/issues/2018/02/00/ba5271/ba5271.pdf Usón, I. & Sheldrick, G. M. (2018). An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features. ''Acta Cryst.'' '''D74''', 106-116.]
-<br>
-See also the [http://shelx.uni-goettingen.de/ SHELX homepage]
+[https://journals.iucr.org/d/issues/2024/01/00/qu5004/index.html Usón, I. & Sheldrick, G. M. (2024) Modes and model building in ''SHELXE. Acta Cryst D80, 4-15''.]
+<br>See also the [http://shelx.uni-goettingen.de/ SHELX homepage]
 <br>