SHELX C/D/E: Difference between revisions

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SHELX C/D/E (edit)

Revision as of 14:18, 5 March 2014

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usage notes and options as written out by SHELXE Version 2014/1
(shelxc: insert usage notes as written out by the program)
(usage notes and options as written out by SHELXE Version 2014/1)
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== SHELXE ==
== SHELXE ==


=== Modes of operation  ===
=== Usage ===


SHELXE has following modes of action (xx and yy are filename stems):<br>
A typical SHELXE job for SAD, MAD, SIR or SIRAS phasing could be:


  shelxe xx [reads xx.hkl and xx.ins, phases from atoms]
  shelxe xx xx_fa -s0.5 -z -a3
shelxe xx yy [normal mode: reads xx.hkl, yy.hkl, yy.res]
shelxe xx yy zz.pdb [as above plus partial structure from zz.pdb]  [NEW!]
shelxe xx.phi [reads xx.phi, xx.hkl, xx.ins]
shelxe xx.phi yy.pdb [reads xx.phi, xx.hkl, xx.ins, partial structure yy.pdb]  [NEW!]
shelxe xx.fcf [reads only xx.fcf]
shelxe xx.phi yy [reads xx.phi, xx.hkl, xx.ins, yy.hkl]
shelxe xx.fcf yy [reads xx.fcf, yy.hkl, yy.res]


xx.hkl contains native data, yy.hkl contains F<sub>A</sub> and &alpha; and should have been created using SHELXC or XPREP. xx.phi has .phs format (h,k,l,F,fom,&phi; in free format) and can be made by renaming a .phs output file from SHELXE, but only the starting phases are read from it; if a .phi file is read, the cell and symmetry are read from xx.ins and the native F-values are read from xx.hkl. xx.fcf (from a SHELXL structure refinement) provides cell, symmetry and starting phases. The output phases are written to xx.phs, the log file is written to xx.lst and, if -b is set, improved substructure phases are output to xx.pha and revised heavy atoms to xx.hat.<br>
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.


The first six modes provide density modification starting from atoms and/or phases, the seventh is an inverse cross-Fourier for finding heavy atoms for a second derivative (yy) with the same origin as the first (xx), and the last mode is useful to confirm the heavy atom substructure from the final refined phases. This is useful as a post-mortem if SAD or MAD phasing fails but the structure could be solved by other means. For these last two modes, the phases for the inverse Fourier are (&phi;<sub>nat</sub> – &alpha;), where &phi;<sub>nat</sub> may be refined (-m etc.) and &alpha; is taken from yy.hkl. A few cycles of phase refinement may reduce the noise in such maps by improving the weights.<br>
-a sets the number of global autotracing cycles. -n imposes NCS
during tracing, e.g. -n6 for six-fold NCS or -n if the number of
copies is not known.
 
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. -O enables local rigid group optimization of the domains
defined in the .pda file. If -O and/or -o (-O acts before -o) are
used to improve a model in xx.pda, the revised model is output to
xx.pdo. To refine rigid group domains separately with -O, insert
'REMARK DOMAIN N' records into the .pda file to split the model
into domains, where N (default 1) is the rigid group number of
the following atoms (until the next 'REMARK DOMAIN N'). -ON makes
N simplex trials with starting positions within a cube (edge set
by -Z) around the positions in xx.pda. The first search (the only
one for -O or -O1) starts from the initial position. If the MR
model is large but does not fit well, -o should be included to
prune it before density modification.
 
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, -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).
 
=== Full list of SHELXE options (defaults in brackets) ===
 
-aN - N cycles autotracing [off]
-AX - maximum random initial rotation in deg. for -O [-A3.0]
-bX - B-value to weight anomalous map (xx.pha and xx.hat) [-b5.0]
-B or -B1 - refine one B-value for complete trace [off]
-B2 - refine one B-value per traced chain [off]
-B3 - refine one B-value per traced residue [on]
-cX - fraction of pixels in crossover region [-c0.4]
-dX - truncate reflection data to X Angstroms [off]
-eX - add missing 'free lunch' data up to X Angstroms [dmin+0.2]
-f  - read F rather than intensity from native .hkl file [off]
-FX - fract. weight for phases from previous global cycle [-F0.8]
-gX - solvent gamma flipping factor [-g1.1]
-GX - threshold for accepting new peptide when tracing [-G0.7]
-h or -hN - (N) heavy atoms also present in native structure [-h0]
-i  - invert space group and input (sub)structure or phases [off]
-IN - in global cycle 1 only, do N cycles DM (free lunch if -e set) [off]
-kX - minimum height/sigma for heavy atom sites in xx.hat [-k4.5]
-KN - keep starting fragment unchanged for N global cycles [off]
-K  - keep fragment unchanged throughout
-lN - reserve space for 1000000N reflections [-l2]
  -LN - minimum chain length (at least 3 chains are retained) [-L6}
-mN - N iterations of density modification per global cycle [-m20]
-n or -nN - apply N-fold NCS to traces [off]
-O or -ON - N random-start rigid-group domain searches [off]
-o or -oN - prune up to N residues to optimize CC for xx.pda [off]
-q  - search for alpha-helices [off]
-rX - FFT grid set to X times maximum indices [-r3.0]
-sX - solvent fraction [-s0.45]
-tX - time factor for helix and peptide search [-t1.0]
-uX - allocable memory in MB for fragment optimization [-u500]
-UX - abort if less than X% of initial CA stay within 0.7A [-U0]
-vX - density sharpening [default set by resol., 0 if .pda read]
-wX - add experimental phases with weight X each iteration [-w0.2]
-x  - diagnostics, requires PDB reference file xx.ent [off]
-yX - highest resol. in Ang. for calc. phases from xx.pda [-y1.8]
-zN - substructure optimization for a maximum of N atoms [off]
-z  - subucture optimization, number of atoms not limited [off]
-ZX - maximum shift in Ang. from initial position for -O [-Z1.0]


=== Phasing and density modification ===
=== Phasing and density modification ===
Kay
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