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SHELX C/D/E: Difference between revisions
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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 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 | shelxc xx <t | ||
which would read the instructions from the file t and write the files xx.hkl (h,k,l,I,σ(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>,σ(F<sub>A</sub>),α for both SHELXD and SHELXE). The starting phases for density modification are estimated as (heavy atom phase + α) in the simplified approach used by SHELXE, α is calculated by SHELXC from the anomalous and dispersive differences. For SAD α 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. | which would read the instructions from the file t and write the files xx.hkl (h,k,l,I,σ(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>,σ(F<sub>A</sub>),α for both SHELXD and SHELXE). The starting phases for density modification are estimated as (heavy atom phase + α) in the simplified approach used by SHELXE, α is calculated by SHELXC from the anomalous and dispersive differences. For SAD α is 90º (I<sub>+</sub> > I<sub>–</sub>) or 270º (I<sub>+</sub> < I<sub>–</sub>), for SIR and RIP α is 0º or 180º and for SIRAS or MAD α 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> | <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> | ||
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In general the critical parameters for locating heavy atoms with SHELXD are: | In general the critical parameters for locating heavy atoms with SHELXD are: | ||
# The resolution cutoff. In the MAD case this is best determined by finding where the correlation coefficient between the signed anomalous differences for wavelengths with the highest anomalous signal (PEAK and HREM or PEAK and INFL) falls below about 30%. For SAD a less reliable guide is where delF/ | # The resolution cutoff. In the MAD case this is best determined by finding where the correlation coefficient between the signed anomalous differences for wavelengths with the highest anomalous signal (PEAK and HREM or PEAK and INFL) falls below about 30%. For SAD a less reliable guide is where delF/σ(ΔF) falls below about 1.2 (a value of 0.8 would indicate pure noise), and for S-SAD with CuKα the data can be truncated where I/σ for the native data falls below 30. If unmerged data are used, SHELXC calculates a correlation coefficient between two randomly selected subsets of the signed anomalous differences; this is a better indicator because it does not require that the intensity esds are on an absolute scale, but it does require a reasonable redundancy and again the data can be truncated where it drops to below 30% (the CCP4 program SCALA prints a similar statistic). | ||
# The estimated number of sites (FIND) should be within about 20% of the true number. For SeMet or S-SAD phasing there should be a sharp drop in the occupancy after the last true site. For iodide soaks, a good rule of thumb is to start with a number of iodide sites equal to the number of amino-acids in the asymmetric unit divided by 15. If after SHELXD occupancy refinement the occupancy of the last site is more than 0.2 it might be worth increasing this number, and vice versa. | # The estimated number of sites (FIND) should be within about 20% of the true number. For SeMet or S-SAD phasing there should be a sharp drop in the occupancy after the last true site. For iodide soaks, a good rule of thumb is to start with a number of iodide sites equal to the number of amino-acids in the asymmetric unit divided by 15. If after SHELXD occupancy refinement the occupancy of the last site is more than 0.2 it might be worth increasing this number, and vice versa. | ||
# 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 Fe4S4 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 Fe4S4 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. | ||