[phenixbb] MR-SAD, SAD

Terwilliger, Thomas Charles terwilliger at lanl.gov
Mon Jan 26 17:14:04 PST 2015

Hi Georg,

Randy told me about the 100 in the expected RMSD field...not exactly anything that we had anticipated!  We'll put in a check to make sure that the number there is "reasonable".

The idea of using "rebuild_in_place" in autosol with MR-SAD is an interesting one.  Autosol is not set up to do that very conveniently, unfortunately.  I suppose that the best thing to do would be to just run autosol without building, then take the model you input to autosol and  overall_best_refine_data.mtz (data with HLAnom phase information) and  overall_best_denmod_map_coeffs.mtz (map file) and feed them all to autobuild.

All the best,
Tom T

From: Georg Mlynek [georg.mlynek at univie.ac.at]
Sent: Monday, January 26, 2015 3:12 PM
To: Randy Read; Terwilliger, Thomas Charles
Cc: phenixbb at phenix-online.org; developers at phenix-online.org
Subject: Re: [phenixbb] MR-SAD, SAD

Dear Tom,

1. Your answer " I would say probably neither a bug nor exactly "normal"..." was completely right. I was putting 100 in the Expected RMSD field, because I am so used that phaser asks about variance. So it was a user mistake.(thanks Randy)

2. I was running MR-SAD again and it works perfect. However if I tick Autobuild model in the Autosol gui, the MR-model is rebuild and the oligomeric arrangement is changed. If I untick,  no model pdb is written. Is there somewhere a parameter hidden which would do the same like in autobuild Rebuild in place =False?

Thanks again, best regards, Georg.

On 01/26/2015 10:44 AM, Randy Read wrote:

Dear Georg,

I agree with what Tom says in general about MR-SAD not necessarily always being better than ab initio substructure determination, particularly if the MR model is marginal in quality.  In your case it depends on what you mean by saying that an MR solution was found easily.  Usually when there’s a good signal in the MR search, the model is good enough to prime substructure determination with MR-SAD.  You could send me the MR and MR-SAD log files off-line, and I could check whether there was any problem in the way that these were run.

Best wishes,

Randy Read

Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research    Tel: +44 1223 336500
Wellcome Trust/MRC Building                         Fax: +44 1223 336827
Hills Road                                                            E-mail: rjr27 at cam.ac.uk<mailto:rjr27 at cam.ac.uk>
Cambridge CB2 0XY, U.K.                               www-structmed.cimr.cam.ac.uk

On 25 Jan 2015, at 20:06, Terwilliger, Thomas Charles <terwilliger at lanl.gov><mailto:terwilliger at lanl.gov> wrote:

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<mailto:phenixbb-bounces at phenix-online.org> [phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>] on behalf of Georg Mlynek [georg.mlynek at univie.ac.at<mailto:georg.mlynek at univie.ac.at>]
Sent: Sunday, January 25, 2015 4:54 AM
To: phenixbb at phenix-online.org<mailto: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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phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>

Mlynek Georg
University of Vienna
Department of Computational and Structural Biology Max F. Perutz Laboratories
Campus Vienna Biocenter 5 level -2
1030 Vienna Austria

e-mail: georg.mlynek at univie.ac.at<mailto:georg.mlynek at univie.ac.at>
mobil: +43 660 42 195 07
office: +43-1-4277-52263
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