[phenixbb] MR-SAD, SAD

Almudena Ponce Salvatierra maps.farma at gmail.com
Mon Jan 26 00:40:34 PST 2015


George gave me an idea actually... I did SAD phasing with Co sites and with
AutoSol I got a partial model, that I then edited. However, since you were
suggesting the phases should be better when you combine those from the
model with the experimental ones I ran Phaser-EP in SAD-MR mode. I have
provided the model I edited after AutoSol, my HA sites, and the data, and I
got a better map than even just with AutoSol!!! I mean, when I submit it to
Resolve, after phaser. :-)

Is it a good solution if the FOM is 0.49 and LLG is 36449.63 after Phaser?

Sooo thanks a lot for the inspiration! (it's not so easy on Monday

Best wishes,


2015-01-25 21:06 GMT+01:00 Terwilliger, Thomas Charles <terwilliger at lanl.gov

> Hi Georg,
> I would say probably neither a bug nor exactly "normal"...
> If everything were ideal, then an MR solution, even if very distant and
> contributing very little phase information, should improve the Phaser
> identification of the sub-structure.  Therefore as you imagine, including
> it should have improved the situation.  In real life there is a lot of
> noise in the system, so small changes can sometimes make the difference
> between finding sites and not. Also the default parameters for Phaser
> sub-structure identification are not exactly the same for MR-SAD and for
> extreme defaults in autosol.
> I am guessing that autosol, with extreme defaults, managed to find
> something that was partially correct, then the iteration of the
> substructure search (using density from the density-modified map and/or
> partial model that was built) resulted in additional sites, while MR-SAD
> did not happen to identify any convincing sites and autosol stopped.
> On your second question...the HL coefficients from MR-SAD are actually
> produced twice in the output MTZ file; once with information from the
> model  (HLA HLB etc) and once without information from the model. (HLanomA
> HLanomB etc). I think in general your intuition is right and the best map
> will come from including model information.  However if you would like to
> reduce model bias, you might want to exclude model information and use the
> HLanomA etc.  The map coefficients (FWT PHWT) in the
> overall_best_denmod_map_coeffs.mtz from MRSAD will include or not include
> the model information based on how you set the parameter
> use_hl_anom_in_denmod (default is False, use HL coeffs and include model
> information).
> I'll pass on the other requests!
> All the best,
> Tom T
> ________________________________________
> From: phenixbb-bounces at phenix-online.org [
> phenixbb-bounces at phenix-online.org] on behalf of Georg Mlynek [
> georg.mlynek at univie.ac.at]
> Sent: Sunday, January 25, 2015 4:54 AM
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] MR-SAD, SAD
> Dear phenix-developers,
> I have collected a high redundancy dataset on our bruker home-source to
> get good anomalous data to confirm if a ligandbound near the active site
> is really the one I think.
> 1. If I do MR with phaser-MR a solution is found easiliy. If I then
> continue with MR-SAD the program does not give me a solution.
> No file named overall_best.pdb is  present in the output directory.
> Warnings: FOM < 0.05 ... skipping solution 1
> However Autosol with extreme density modification and  Iterate
> substructure search is able to solve the structure.
> Is this a bug or normal.
> 2. A follow up on this: Will be the MTZ file (phases) produced from
> MR-SAD always better (compared to SAD or MR alone) because it will
> contain phases that combine the information from both the MR model and
> the SAD data. Or can there be cases where bad phases form either MR or
> SAD will mess up the other one.
> 3. There is a small bug in merging statistics. cc_ano is just writen out
> in the log output tab but not in the summary tab.
> 4. It would be nice, if xtriage could also print how many % of the
> reflections are Rfree flagged.
> Thanks in advance, best regards, Georg.
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Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
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