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SHELX C/D/E: Difference between revisions
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→Full list of SHELXE options ( Version 2021/1; defaults in brackets)
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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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-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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-x - diagnostics, requires PDB reference file xx.ent [off] | -x - diagnostics, requires PDB reference file xx.ent [off] | ||
-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 - 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 | |||
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: | Meaning of additional output when using the -x option: | ||