[phenixbb] Problem during refinement

Terwilliger, Thomas Charles terwilliger at lanl.gov
Sat Jan 24 07:05:23 PST 2015

Hi Almudena,

I think we would need to know what the model and map look like before refinement.  I am guessing that perhaps the result from autosol was in itself not good, and then refinement could not do anything with it?  If instead the autosol result was good (a clear map, a model that looks like you expect) then this is indeed very surprising and we'd be more than happy to try and figure out what is going on.

All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Almudena Ponce Salvatierra [maps.farma at gmail.com]
Sent: Saturday, January 24, 2015 1:08 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] Problem during refinement

Dear all,

I have partially rebuilt my model after autosol and now I would like to submit it for refinement to Phenix refine.

However when I do so, even though the R factors go down when I have a look at the result, it just looks awful! All the model is placed out of the electron density map, plus the electron density map doesn't look anymore like a 3 A one, but just like sausages.

Why is this happening? The truth is I have no idea...

What I do is to provide Phenix refine with overall_best_refine_data.mtz (coming from autosol) as phases, x Ray data and x Ray r free data. Additionally, the starting model and the sequence.

Any suggestions are more than welcome.

Thanks a lot in advance.

Best wishes,


Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen

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