[phenixbb] accept MR solution even if the number of clashes is above the threshold

Randy Read rjr27 at cam.ac.uk
Thu Jul 2 06:16:36 PDT 2015

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: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                               www-structmed.cimr.cam.ac.uk

> On 2 Jul 2015, at 13:55, Almudena Ponce Salvatierra <maps.farma at GMAIL.COM> 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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