Beta-test versions are also available from time to time. The default setting when -e is not specified is to fill in missing low and medium resolution data but not to extrapolate to higher resolution than actually measured to switch off this filling in, use -e The starting phases for density modification are estimated as given above. The next number is times the number of CA found divided by the number expected for the whole structure. Alternatively one could try to find the individual sulfurs with: First fill the application form at http:
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[phenixbb] Problems with phasing a protein (aa)
For low resolution data, the use of more than 20 refinement cycles is normally counter-productive. SHELXC also tests for and if necessary corrects the more common cases of inconsistent indexing when more than one dataset is involved. The protein selx are written to jia. However in the case of SIR, both have the same contrast but one gives the inverted protein structure.
The presence of one or two reflections with very low esds can lead to unreasonably high e of the CC for wrong solutions. Heavy atom soaks truncated to low resolution often give spuriously high CC values, but these ‘solutions’ can be recognized as false by their low CC weak values.
[phenixbb] Problems with phasing a protein (1300aa)
In this example kindly donated by Zbigniew Dauter; Li et al. If the MR model is large but does not fit well, -o should be included to prune it before density modification. In the case of SAD both heavy atom enantiomers then give the correct structure, for SIR the result is an uninterpretable double image.
Tracing from an MR model requires a favorable combination of model quality, solvent content and data resolution. The number of tracing cycles is usually more here to reduce model bias.
RIP radiation damage induced phasing can be regarded as a sort of isomorphous replacement where the ‘after’ dataset has lost a few atoms that are particularly susceptible to radiation damage. SAD phase information is available, even if it is too weak for phasing on its own, the two approaches may be combined:. This can dramatically improve the final phase quality. The pseudo-free CC which is also reported in the hkl2map plot of contrast against cycle number is also a good indication as to when the phase refinement has converged.
The phases from the MR model are used to generate the heavy atom substructure. The username and password for accessing these may be obtained from GS. D59 uses 1. If the best CC is plotted against the resolution, a local maximum when also observed for the CC weak values may indicate a correct solution. In International Tables for CrystallographyVol. The first nine numbers in the row after locating a strand or in the ‘Global chain diagnostics’ are the percentages of CA within In fact, many structures have been solved unintentionally with a helping hand from RIP!
Cc reads a filename stem denoted here by ‘xx’ on the command line plus some instructions from ‘standard input’. The contrast is also the same for both if the heavy-atom substructure is centrosymmetric there is a server to find out.
The tenth number is the percentage further than 0. It is available as “Open Access” at http: They are announced by George Sheldrick and are available from the beta-test directory.
Fe distance is about 2.
The listing file is xx. P4 1 to P4 3which should be taken into account when moving to other programs! Navigation Main Page Recent changes Help. Normally this is a good way of finding where the noise begins, but for RIP if you want to recycle the negative peaks these lines should be removed.
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. The critical parameter is the scale factor applied to the ‘after’ data after both datasets have been brought onto a common scale.
The starting phases for density modification are estimated as given above. If these heavy atom are present in the native structure e.
It should be noted that in a pure RIP experiment, both hands of the radiation damage substructure will give the same figures of merit, but one will lead to an electron density map that is a mirror image of the true map the helices will go the wrong way round.