[phenixbb] [ccp4bb] anomalous phasing with HySS - phaser - Autobuild

Terwilliger, Thomas Charles terwilliger at lanl.gov
Fri Jun 26 05:38:38 PDT 2015

Hi Almudena,

Normally the best path in Phenix if you have found the sites is to run AutoSol with the sites, sequence file, and your anomalous data.  It will then calculate phases for the hand of the sites that you found and for the inverse hand and evaluate the maps for each. Then it will density modify and carry out model-building.

If you go right to AutoBuild you may have the wrong hand of the substructure.  Also the density modification may not be as good as AutoSol tests various possibilities for density modification.

Be sure to have a look at your maps...if they look like a macromolecule you definitely should be able to build it (depending on the resolution of your data).

Also be sure to run Xtriage and check on the space group and any unusual features of your data.

All the best,
Tom T

From: CCP4 bulletin board [CCP4BB at JISCMAIL.AC.UK] on behalf of Almudena Ponce Salvatierra [maps.farma at GMAIL.COM]
Sent: Friday, June 26, 2015 4:32 AM
Subject: [ccp4bb] anomalous phasing with HySS - phaser - Autobuild

Hi all,

I have SeMet data for which HySs locates 127 Selenium atoms with a CC of 0.31, which I think is decent.

Then I run Phaser to generate the first maps, and it gives a score of 25 and LLG of 190 or so...

The next step would be running Autobuild, however, the first models I realize it is building have R work and R free between 50 and 55%. So I guess it is just some random stuff there.

If the result from HySS and Phaser looks more or less good, why does AutoBuild show these numbers?? Any idea of what I could do to improve so?

Any ideas are welcome.

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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