Dear Almu, In the development version of Phaser currently available in nightly builds of Phenix (and soon in an upcoming stable release of Phenix, as well as in CCP4), solutions that fail to pack, even though they have such high TFZ scores that they should normally have been convincing, are subjected to a pruning algorithm, where the local occupancies of residues along the chain are refined and ones that refine to low values are trimmed out. This will often sort out problems from loops, or even domains, that are in the wrong conformation. By default, potential solutions have to have a TFZ>8 to be subjected to this algorithm, but this threshold can be changed. Please give this a try and tell us how it works for you! If it doesn’t, there are other possible issues, generally coming down to having the wrong spacegroup, so it might be worth double-checking the choice of spacegroup. 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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

On 2 Jul 2015, at 13:55, Almudena Ponce Salvatierra wrote:

Hi everyone,

I am running Phaser (from Phenix) and while checking the .log file (it is still running) I realize that it found some solutions with a TFZ score over 7, but it won't take them I guess because the number of clashes is higher than allowed (>12, I guess they're not so many either).

My models are poor and for so I would like to check these solutions that for now Phaser will reject. However in the input I don't want to increase the allowed number of clashes because this will then affect all the other solutions and this will take forever...

So my question is: can I tell phaser somehow to write down/save the solutions for which the TFZ score will be higher than 7? Even though the clashes

Thanks a lot in advance

All the best,

Almu

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

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