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SHELX C/D/E: Difference between revisions
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→Minimum distance between atoms (MIND): remove "(as in the above thaumatin example" because that does not exist
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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 list of SHELXE options ( Version | === Full list of SHELXE options ( Version 2021/1; defaults in brackets) === | ||
-aN - N cycles autotracing [off] | -aN - N cycles autotracing [off] | ||
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-n or -nN - apply N-fold NCS to traces [off] | -n or -nN - apply N-fold NCS to traces [off] | ||
-o or -oN - prune up to N residues to optimize CC for xx.pda [off] | -o or -oN - prune up to N residues to optimize CC for xx.pda [off] | ||
-O - trace side chains [off] | |||
-p or -pN - search for N DNA or RNA phosphates (-p = -p12) [off] | -p or -pN - search for N DNA or RNA phosphates (-p = -p12) [off] | ||
-qN - search for alpha-helices of length 6<N<15; -q sets -q7 [off] | -qN - search for alpha-helices of length 6<N<15; -q sets -q7 [off] | ||
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-sX - solvent fraction [-s0.45] | -sX - solvent fraction [-s0.45] | ||
-SX - radius of sphere of influence. Increase for low res [-S2.42] | -SX - radius of sphere of influence. Increase for low res [-S2.42] | ||
-tX - time for initial searches (- | -tX - time for initial searches (-t3 or more if difficult) [-t1.0] | ||
-uX - allocable memory in MB for fragment optimization [-u500] | -uX - allocable memory in MB for fragment optimization [-u500] | ||
-UX - abort if less than X% of initial CA stay within 0.7A [-U0] | -UX - abort if less than X% of initial CA stay within 0.7A [-U0] | ||
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-z - substructure optimization, number of atoms not limited [off] | -z - substructure optimization, number of atoms not limited [off] | ||
-t values of | -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 | ||
is poor or the initial phase information is weak. | is poor or the initial phase information is weak; -a10 is preferred. | ||
In case of side chain tracing with -O, sequence will be docked | |||
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; | |||
new autotracing features" Acta Cryst. D74, 106-116 | |||
(Open Access) if SHELXE proves useful. | |||
Meaning of additional output when using the -x option: | Meaning of additional output when using the -x option: | ||
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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''].<br> | |||
[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.] | ||
[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> | <br> | ||
See also the [http://shelx.uni-goettingen.de/ SHELX homepage] | See also the [http://shelx.uni-goettingen.de/ SHELX homepage] | ||
<br> | <br> | ||