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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. | 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 | 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 === | === Interpretation of results === | ||
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(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): | 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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=== How to tell SHELXE about NCS in a molecular replacement solution PDB file === | === How to tell SHELXE about NCS in a molecular replacement solution PDB file === | ||
(communicated by Isabel | (communicated by Isabel Usón) Insert a line | ||
REMARK 299 NCS GROUP BEGIN | REMARK 299 NCS GROUP BEGIN | ||
before the ATOM (or HETATM) lines of each NCS group (e.g. chain), and insert the line | before the ATOM (or HETATM) lines of each NCS group (e.g. chain), and insert the line | ||
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[[hkl2map]] can be downloaded from a website at EMBL Hamburg. XDSGUI can be downloaded from its [[xds:XDSGUI|XDSwiki article]]. | [[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 == | == References == | ||
If these programs prove useful, you may wish to cite (and read!):<br> | If these programs prove useful, you may wish to cite (and read!):<br> | ||
Sheldrick, G.M., Hauptman, H.A., Weeks, C.M., Miller, R. & Usón, I. (2001). "Ab initio phasing". In ''International Tables for Crystallography'', Vol. F, Eds. Rossmann, M.G. & Arnold, E., IUCr and Kluwer Academic Publishers, Dordrecht pp. 333-351 [''Full background to the dual-space recycling used in SHELXD''].<br> | Sheldrick, G.M., Hauptman, H.A., Weeks, C.M., Miller, R. & Usón, I. (2001). "Ab initio phasing". In ''International Tables for Crystallography'', Vol. F, Eds. Rossmann, M.G. & Arnold, E., IUCr and Kluwer Academic Publishers, Dordrecht pp. 333-351 [''Full background to the dual-space recycling used in SHELXD''].<br> | ||
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Nanao, M.H., Sheldrick, G.M. & Ravelli, R.B.G. (2005). "Improving radiation-damage substructures for RIP", ''Acta Crystallogr''. '''D61''', 1227-1237 [''Practical details of RIP phasing with SHELXC/D/E''].<br> | Nanao, M.H., Sheldrick, G.M. & Ravelli, R.B.G. (2005). "Improving radiation-damage substructures for RIP", ''Acta Crystallogr''. '''D61''', 1227-1237 [''Practical details of RIP phasing with SHELXC/D/E''].<br> | ||
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'']. | |||
[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.] | [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://doi.org/10.1107/S0907444913027534 A. Thorn and Sheldrick, G.M. (2013). Extending molecular-replacement solutions with SHELXE. ''Acta Cryst'' '''D69''', 2251-2256.] | ||
<br> | |||
See also the [http://shelx.uni-goettingen.de/ SHELX homepage] | [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.] | ||
[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> | <br> | ||