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SHELX C/D/E: Difference between revisions
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In fact, many structures have been solved unintentionally with a helping hand from RIP! In a MAD experiment, provided that the 'inflection point' dataset is collected last from the same crystal, the radiation damage has the effect of making f' for the MAD element at this wavelength even more negative than usual, enhancing the dispersive part of the MAD signal. This is especially true of bromine MAD on bromouracil derivatives, because the radiation near the bromine absorption edge appears to be particularly effective at breaking the bromine-carbon bonds irreversibly. Of course if the inflection data are collected first the RIP and dispersive component of the MAD signal will tend to cancel one another, causing the MAD analysis to fail, although SAD may still be able to solve the structure (also a common scenario). | In fact, many structures have been solved unintentionally with a helping hand from RIP! In a MAD experiment, provided that the 'inflection point' dataset is collected last from the same crystal, the radiation damage has the effect of making f' for the MAD element at this wavelength even more negative than usual, enhancing the dispersive part of the MAD signal. This is especially true of bromine MAD on bromouracil derivatives, because the radiation near the bromine absorption edge appears to be particularly effective at breaking the bromine-carbon bonds irreversibly. Of course if the inflection data are collected first the RIP and dispersive component of the MAD signal will tend to cancel one another, causing the MAD analysis to fail, although SAD may still be able to solve the structure (also a common scenario). | ||
RIP (without using anomalous scattering) or RIPAS (like SIRAS, assuming that the anomalous atoms are also those most sensitive to radiation damage) can be capable of solving difficult structures. A typical procedure on a third generation synchrotron beamline is to collect the 'before' dataset with an attenuator in the beam, then to fry the crystal for a couple of minutes with the unattenuated beam, and finally to collect an 'after' dataset with the attenuator in. In the SHELXC instructions, the 'before' data are called 'NAT' or 'BEFORE' and the 'after' data are called 'RIP' or 'AFTER'. The critical parameter is the scale factor applied to the 'after' data after both datasets have been brought onto a common scale. This is set by the SHELXC instruction 'DSCA' and should usually be in the range 0. | RIP (without using anomalous scattering) or RIPAS (like SIRAS, assuming that the anomalous atoms are also those most sensitive to radiation damage) can be capable of solving difficult structures. A typical procedure on a third generation synchrotron beamline is to collect the 'before' dataset with an attenuator in the beam, then to fry the crystal for a couple of minutes with the unattenuated beam, and finally to collect an 'after' dataset with the attenuator in. In the SHELXC instructions, the 'before' data are called 'NAT' or 'BEFORE' and the 'after' data are called 'RIP' or 'AFTER'. The critical parameter is the scale factor applied to the 'after' data after both datasets have been brought onto a common scale. This is set by the SHELXC instruction 'DSCA' and should usually be in the range 0.9 to 1.05. This scale factor may also be used for SIR and SIRAS, where it is applied to the native data, but it appears to be less critical than for RIP. For RIPAS, the 'after' data should be called 'RIPA' and the 'RIPW' instruction specifies the weight w (default 0.6) for the anomalous contribution from the 'before' dataset (a weight 1–w is applied to the 'after' data). | ||
In RIP or RIPAS phase determination is usually necessary to recycle the 'heavy atom' sites by renaming the output .hat (or _i.hat) file as .res and rerunning SHELXE. It is advisable to edit this file so as to retain the stronger negative sites, these may well correspond to the new positions of displaced atoms. SHELXE can read negative occupancies but SHELXD can only search for positive atoms. | In RIP or RIPAS phase determination is usually necessary to recycle the 'heavy atom' sites by renaming the output .hat (or _i.hat) file as .res and rerunning SHELXE. It is advisable to edit this file so as to retain the stronger negative sites, these may well correspond to the new positions of displaced atoms. SHELXE can read negative occupancies but SHELXD can only search for positive atoms. | ||