1,334
edits
SHELX C/D/E: Difference between revisions
Jump to navigation
Jump to search
→Phasing and density modification: link to pirate
m (→SHELXC) |
(→Phasing and density modification: link to pirate) |
||
| Line 63: | Line 63: | ||
The -b switch in SHELXE causes updated heavy atom positions to be written to the file name.hat (or name_i.hat). This file can be copied or renamed to the .res file (which should be saved first!) and used to recycle the heavy atoms. The graphics program [[Coot]] should be able to deduce the space group name from the symmetry operators in this file, and so a very convenient way to obtain a map after running SHELXE is to start [[Coot]], read in 'coordinates' from the .hat or _i.hat file, and then input the phases from the .phs or _i.phs files and the phases of the heavy atom substructure from the .pha or _i.pha files. It is normally necessary to increase the σ level of the latter map (by hitting '+' several times). This procedure even works correctly when the space group has been inverted by SHELXE! <br> | The -b switch in SHELXE causes updated heavy atom positions to be written to the file name.hat (or name_i.hat). This file can be copied or renamed to the .res file (which should be saved first!) and used to recycle the heavy atoms. The graphics program [[Coot]] should be able to deduce the space group name from the symmetry operators in this file, and so a very convenient way to obtain a map after running SHELXE is to start [[Coot]], read in 'coordinates' from the .hat or _i.hat file, and then input the phases from the .phs or _i.phs files and the phases of the heavy atom substructure from the .pha or _i.pha files. It is normally necessary to increase the σ level of the latter map (by hitting '+' several times). This procedure even works correctly when the space group has been inverted by SHELXE! <br> | ||
Good quality MAD data, a high solvent content and/or high resolution for the native data can lead to maps of high quality that can be autotraced (e.g. with wARP) immediately. The .phs files contain h, k, l, F, fom, φ and σ(F) in free format and can be read directly into [[Coot]] or converted to CCP4 .mtz format using [[f2mtz]], e.g. for further density modification exploiting NCS using the CCP4 program [[Pirate]]. Note that if the inverted heavy atom enantiomorph is the correct one, the corresponding phases are in the *_i.phs file and SHELXE may have inverted the space group (e.g. P4<sub>1</sub> to P4<sub>3</sub>), which should be taken into account when moving to other programs!<br> | Good quality MAD data, a high solvent content and/or high resolution for the native data can lead to maps of high quality that can be autotraced (e.g. with wARP) immediately. The .phs files contain h, k, l, F, fom, φ and σ(F) in free format and can be read directly into [[Coot]] or converted to CCP4 .mtz format using [[f2mtz]], e.g. for further density modification exploiting NCS using the CCP4 program [[ccp4dev:Automated phase improvement with Pirate|Pirate]]. Note that if the inverted heavy atom enantiomorph is the correct one, the corresponding phases are in the *_i.phs file and SHELXE may have inverted the space group (e.g. P4<sub>1</sub> to P4<sub>3</sub>), which should be taken into account when moving to other programs!<br> | ||
=== The free lunch algorithm (FLA) === | === The free lunch algorithm (FLA) === | ||