Dear Gabriel,
since you are already using autoSHARP: why not giving it the MR model
as input too? This way you will combine the model and the experimental
phasing.
This combination can not only be done in autoSHARP (for SAD, MAD,
SIR(AS) and MIR(AS)), but also in SHARP directly for any phasing
scenario you could think of. See eg.
https://www.globalphasing.com/sharp/manual/chapter4.html#ExternalPhaseInformation
If you need additional help, please contact us (or the SHARP
discussion list).
Cheers
Clemens
On Mon, Oct 13, 2014 at 12:48:18PM -0500, Gabriel Salzman wrote:
> Hello,
>
> I am wondering if anyone has experience or advice for my current situation:
>
> I have a native dataset of a ~50kD protein complex at 2.4angstroms. One of the members of the complex (~10kD) was able to be found easily by molecular replacement. The space group was determined as P65. I was able to use phenix.mr_rosetta to generate a partial model of the other member of the complex (~half of this 40kD protein). When I do molecular replacement for these two members of the complex in PHASER, the TFZ score is ~20-30. Therefore, I am confident that this partial model is accurate.
>
> I recently soaked some complex crystals in a variety of heavy atoms to obtain experimental phase information. My best signal is from an iodide soak. These crystals diffracted to 3 angstroms and I can see a very weak but significant anomalous signal to 5-4.5 angstroms. I have used autoSHARP to determine that I have one site of ~99% occupancy and 4 other sites of <50% occupancy. I am inclined to think these other sites are not true. My density modified map seems to me to be better if I only include the single high-occupancy site in the phase determination. Even with this weak experimental phase information, my map is not good enough to see the substantial density from the piece of my protein that was not included in the MR model.
>
> I have also tried phenix.phaser_EP with mediocre results.
>
> I apologize for the long question, and I would greatly appreciate any suggestions for how to combine all of these data into a workable map so I can build out the rest of the structure.
>
> Thanks,
> Gabriel
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