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SHELX C/D/E: Difference between revisions
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SHELXC, SHELXD and SHELXE are stand-alone executables that do not require environment variables or parameter files etc., so all that is needed to install them is to put them in a directory that is in the ‘path’ (e.g. /usr/local/bin or ~/bin under Linux). There is a detailed description of these programs in the paper: <i>"Experimental phasing with SHELXC/D/E: combining chain tracing with density modification"</i>. Sheldrick, G.M. (2010). <i>Acta Cryst.</i> <b>D66</b>, 479-485. It is | SHELXC, SHELXD and SHELXE are stand-alone executables that do not require environment variables or parameter files etc., so all that is needed to install them is to put them in a directory that is in the ‘path’ (e.g. /usr/local/bin or ~/bin under Linux). There is a detailed description of these programs in the paper: <i>"Experimental phasing with SHELXC/D/E: combining chain tracing with density modification"</i>. Sheldrick, G.M. (2010). <i>Acta Cryst.</i> <b>D66</b>, 479-485. It is | ||
available as "Open Access" at http://dx.doi.org/10.1107/S0907444909038360 and should be cited whenever these programs are used. | available as "Open Access" at http://dx.doi.org/10.1107/S0907444909038360 and should be cited whenever these programs are used. | ||
[[hkl2map]] is a graphical user interface that makes it easy to use these programs. | |||
[[xds:xdsgui|XDSGUI]] is a graphical user interface for XDS that also makes it easy to use these programs. | |||
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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 (as in the above thaumatin example). | ||
=== Interpretation of results === | === Interpretation of results === | ||
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(or xx_i.hat). | (or xx_i.hat). | ||
=== Full list of SHELXE options (defaults in brackets) === | === Full list of SHELXE options ( Version 2021/1; 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] | ||
-B1 - anti-parallel beta sheet, -B2 parallel and -B3 both [off] | |||
-cX - fraction of pixels in crossover region [-c0.4] | -cX - fraction of pixels in crossover region [-c0.4] | ||
-dX - truncate reflection data to X Angstroms [off] | -dX - truncate reflection data to X Angstroms [off] | ||
-D - fuse disulfides before looking for NCS [off] | |||
-eX - add missing 'free lunch' data up to X Angstroms [dmin+0.2] | -eX - add missing 'free lunch' data up to X Angstroms [dmin+0.2] | ||
-f - read F rather than intensity from native .hkl file [off] | -f - read F rather than intensity from native .hkl file [off] | ||
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-h or -hN - (N) heavy atoms also present in native structure [-h0] | -h or -hN - (N) heavy atoms also present in native structure [-h0] | ||
-i - invert space group and input (sub)structure or phases [off] | -i - invert space group and input (sub)structure or phases [off] | ||
-IN - in | -IN - in cycle 1 only, do N cycles DM (free lunch if -e) [off] | ||
-kX - minimum height/sigma for heavy atom sites in xx.hat [-k4.5] | -kX - minimum height/sigma for heavy atom sites in xx.hat [-k4.5] | ||
-KN - keep starting fragment unchanged for N global cycles [off] | -KN - keep starting fragment unchanged for N global cycles [off] | ||
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-mN - N iterations of density modification per global cycle [-m20] | -mN - N iterations of density modification per global cycle [-m20] | ||
-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] | |||
-qN - search for alpha-helices of length 6<N<15; -q sets -q7 [off] | |||
-Q - search for 12-helix,' extended by sliding (overrides -q) [off] | |||
-rX - FFT grid set to X times maximum indices [-r3.0] | -rX - FFT grid set to X times maximum indices [-r3.0] | ||
-sX - solvent fraction [-s0.45] | -sX - solvent fraction [-s0.45] | ||
-tX - time | -SX - radius of sphere of influence. Increase for low res [-S2.42] | ||
-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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-yX - highest resol. in Ang. for calc. phases from xx.pda [-y1.8] | -yX - highest resol. in Ang. for calc. phases from xx.pda [-y1.8] | ||
-zN - substructure optimization for a maximum of N atoms [off] | -zN - substructure optimization for a maximum of N atoms [off] | ||
-z - | -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 | |||
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: | |||
MPE and wMPE are given as two numbers, the one after the '/' is for centric reflections only. | |||
The first nine numbers in the row after locating a strand or in the 'Global chain diagnostics' are the percentages of CA within 0-0.1, 0.1-0.2, 0.2-0.3Å etc from the nearest CA in the reference structure. The tenth number is the percentage further than 0.9Å from the nearest CA. | |||
The next number is 100 times the number of CA found divided by the number expected for the whole structure. The last number is the mean distance of a CA atom from the nearest CA in the reference structure, whereby distances greater than 2.5Å are replaced by 2.5. One should always look at the second number from the right; for a good trace it should be as low as possible. If you are expanding from a MR solution the program also tells you the percentages of starting atoms retained. | |||
=== Phasing and density modification === | === Phasing and density modification === | ||
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for a solved structure (25 to 50%). The solution with the best CC is | for a solved structure (25 to 50%). The solution with the best CC is | ||
written to name.pdb and its phases to name.phs for input to e.g. Coot. | written to name.pdb and its phases to name.phs for input to e.g. Coot. | ||
=== How to tell SHELXE about NCS in a molecular replacement solution PDB file === | |||
(communicated by Isabel Uson) 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 | |||
REMARK 299 NCS GROUP END | |||
after the last of these. The -n option is not needed then. The output of SHELXE should tell you about the fact that it understood the NCS specification. | |||
== RIP with SHELXC/D/E == | == RIP with SHELXC/D/E == | ||
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== SAD/MAD with automatic backbone building == | == SAD/MAD with automatic backbone building == | ||
shelxe | shelxe exp1 exp1_fa -a -q -h -s0.6 -m20 -b | ||
will use exp1.hkl, exp1_fa.hkl, exp1.ins (as above) and will try 3 cycles of backbone building. | will use exp1.hkl, exp1_fa.hkl, exp1.ins (as above) and will try 3 cycles of backbone building. | ||
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== Obtaining the SHELX programs == | == Obtaining the SHELX programs == | ||
SHELXC/D/E and test data may be downloaded from the SHELX fileserver | SHELXC/D/E are distributed with [https://www.ccp4.ac.uk/ CCP4]. | ||
The programs and test data may also be downloaded from the [http://shelx.uni-goettingen.de/bin/ SHELX fileserver]. First fill the application form at http://shelx.uni-goettingen.de/register.php Password and downloading instructions will then be emailed to the address given on the form. The programs are free to academics but a small license fee is required for 'for-profit' use. | |||
Beta-test versions are also available from time to time. They are announced by George Sheldrick and are available from the beta-test directory. The username and password for accessing these may be obtained from GS. | Beta-test versions are also available from time to time. They are announced by George Sheldrick and are available from the beta-test directory. The username and password for accessing these may be obtained from GS. | ||
[[hkl2map]] can be downloaded from a website at EMBL Hamburg. XDSGUI can be downloaded from its [[xds:XDSGUI|XDSwiki article]]. | |||
== References == | == References == | ||
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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. (2008). "A short history of SHELX", ''Acta Crystallogr''. '''D64''', 112-122 [''Standard reference for all SHELX | [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> | ||
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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Uson, 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> | Uson, 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> | ||
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.] | |||
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<br> | <br> | ||
See also the | See also the [http://shelx.uni-goettingen.de/ SHELX homepage] | ||
<br> | <br> | ||