HI!
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
mornings!!)
Best wishes,
Almudena.
2015-01-25 21:06 GMT+01:00 Terwilliger, Thomas Charles : 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: [email protected] [
[email protected]] on behalf of Georg Mlynek [
[email protected]]
Sent: Sunday, January 25, 2015 4:54 AM
To: [email protected]
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.
_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb --
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany