SHELX C/D/E: Difference between revisions

SHELX C/D/E (edit)

Revision as of 14:34, 5 March 2014

1,355 bytes added , 5 March 2014

shelxc: insert usage notes as written out by the program

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Bureaucrats

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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). If you are interested in beta-testing the new version of SHELXE that includes autotracing of protein backbones, please request the password and downloading instructions by sending an email to gsheldr[at]shelx.uni-ac.gwdg.de. 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.
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 '''SHELXC''' is designed to provide a simple and fast way of setting up the files for the programs '''SHELXD''' (heavy atom location) and '''SHELXE''' (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. These three programs may be run in batch mode or called from a GUI such as [[CCP4i]] or (better) [[hkl2map]]. SHELXC is much less versatile than the Bruker AXS XPREP program for this purpose, but if you are sure of the space group and there are no problems with the indexing or twinning and the f’ and f” parts of the scattering factors do not need to be refined, SHELXC should be adequate.
-SHELXC can read either HKL2000 format .sca files, or SHELX .hkl files (F<sup>2</sup> unless the -f switch is used to specify F), or .hkl files from XDS/XSCALE. To transfer data from CCP4 it is advisable to generate .sca files using 'output unmerged polish' from SCALA or to use the program mtz2sca written by Tim Grüne and supplied with SHELX.  The current version of SHELXC outputs extra useful diagnostic statistics if fed unmerged data.
+The starting phases for density modification are estimated as (heavy atom phase + &alpha;) in the simplified approach used by SHELXE, &alpha; is calculated by SHELXC from the anomalous and dispersive differences. For SAD &alpha; is 90º (I<sub>+</sub> > I<sub>–</sub>) or 270º (I<sub>+</sub> < I<sub>–</sub>), for SIR and RIP &alpha; is 0º or 180º and for SIRAS or MAD &alpha; may be anywhere in the range 0º to 360º.
+SHELXC reads a filename stem (denoted here by 'xx') on the command line
+plus some instructions from 'standard input'. It writes some statistics to
+'standard output' and prepares the three files needed to run SHELXD and
+SHELXE. SHELXC can be called from a GUI by a command line such as:
-SHELXC reads a filename stem on the command line plus some instructions from 'standard input'. It writes some statistics to 'standard output' and prepares the three files needed to run SHELXD and SHELXE. It can be called from a GUI using a single command line such as:
   shelxc xx <t
-which would read the instructions from the file t and write the files xx.hkl (h,k,l,I,&sigma;(I) in SHELX HKLF4 format for density modification by SHELXE), xx_fa.ins (cell, symmetry etc. for heavy atom location using SHELXD) and xx_fa.hkl (h,k,l,F<sub>A</sub>,&sigma;(F<sub>A</sub>),&alpha; for both SHELXD and SHELXE). The starting phases for density modification are estimated as (heavy atom phase + &alpha;) in the simplified approach used by SHELXE, &alpha; is calculated by SHELXC from the anomalous and dispersive differences. For SAD &alpha; is 90º (I<sub>+</sub> > I<sub>–</sub>) or 270º (I<sub>+</sub> < I<sub>–</sub>), for SIR and RIP &alpha; is 0º or 180º and for SIRAS or MAD &alpha; may be anywhere in the range 0º to 360º.
-<p>The above command line could be used under UNIX or Windows; under UNIX the commands to run SHELXC, SHELXD and SHELXE and the instructions for SHELXC may also be combined into a single script file as shown in the following examples. In these scripts, the instructions start on the line after '<<EOF' and are terminated by 'EOF'. The instructions may be given in any order; CELL (unit-cell), SPAG (space group in PDB notation, spaces are ignored) and FIND (followed by the number of heavy atoms) must be given; the optional instructions SFAC, MIND, NTRY, SHEL, ESEL and DSUL, if present, are copied to the SHELXD input file.<br><br>
+which would read the instructions from the file t, or (under most UNIX
-A beta-test version is currently [[SHELX_C/D/E#Obtaining_the_SHELX_programs|available]].
+systems) by a simple shell script that includes the instructions, e.g.
+ shelxc xx <<EOF
+ CELL 49.70 57.90 74.17 90 90 90
+ SPAG P212121
+ SAD elastase.sca
+ FIND 12
+ <<EOF
+ shelxd xx_fa
+ shelxe xx xx_fa -s0.37 -m20 -h -b
+ shelxe xx xx_fa -s0.37 -m20 -h -b -i
+which would also run shelxd to locate the sulfur atoms and shelxe (for
+both substructure enantiomers) to solve elastase by sulfur-SAD phasing.
+The reflection data may be in SHELX (.hkl), HKL2000 (.sca) or XDS
+XDS_ASCII.HKL format. Any names may be used for XDS reflection files,
+SHELXC recognises them by reading the first record.
+This script would read data from the .sca file and write the files
+xx.hkl (h,k,l,I,sig(I) in SHELX HKLF4 format for density modification
+by SHELXE or refinement with SHELXL), xx_fa.ins (cell, symmetry etc. for
+heavy atoms location  by SHELXD) and xx_fa.hkl (h,k,l,FA,sig(FA),alpha
+for both SHELXD and SHELXE). The starting phases for density
+modification are estimated as given above.
+For SIR or SIRAS, two input reflections files are specified by the
+keywords NAT and SIR or SIRA; for MAD at least two of the reflection files
+HREM, LREM, PEAK and INFL are required and NAT may also be given if higher
+resolution native data are available (e.g. SMet for SeMet MAD). Reflection
+data should be in SHELX .hkl or SCALEPACK .sca format; many other programs,
+including SCALA and XPREP, can output .sca format too. The keywords CELL,
+SPAG (space group) SPAG (space group) and FIND (number of heavy atoms) are
+always required, SFAC, MIND, NTRY, SHEL, ESEL and DSUL may be given and are
+written to the file xx_fa.ins for SHELXD. MAXM can be used to reserve
+memory in units of 1M reflections. For RIP phasing, NAT (or BEFORE) denotes
+the file before radiation damage and RIP (or AFTER) after radiation
+damage. For RIPAS the 'after' file must be called 'RIPA' and a keyword RIPW
+(default 0.6) gives the weight w to be assigned to the 'NAT' data in the
+estimation of the anomalous signal (a weight of 1-w is applied to the 'RIPA'
+data). DSCA (default 0.98) gives the factor to multiply the native data
+for SIR and SIRAS or the 'after' data for RIP after the data have been
+put on the same scale (this allows for the extra scattering power of the
+heavy atoms etc.); this can be critical for RIP phasing.
+ASCA (default 1.0) is a scale factor applied to the anomalous signal in a
+MAD experiment; to apply MAD to a small molecule, ASCA and DSCA should both
+be between 0 and 1, the best values have to be found by trial and error.
+Finally SMAD (without a number) sets the dispersive term to zero in a MAD
+experiment, equivalent to SAD using weighted mean anomalous differences
+from all the MAD datasets. This should always be tried whenever radiation
+damage is suspected.
+SHELXC also tests for and if necessary corrects the more common cases of
+inconsistent indexing when more than one dataset is involved. In addition,
+the mean value of |E^2-1| is calculated for each dataset to detect twinning.
 == SHELXD ==