Dear Almu, Apparently, you have more than one search model. What worked very well for me was to superimpose these models and cut out the loops which are variable between the models. These loops may be different again in your protein and may be behind the clashes in Phaser. Without these troublesome loops, Phaser should be able to find the correct solution. You could also use all models at once, weighted by the sequence identity as explained in the Phaser manual. This might give superior results when your starting models are poor.
Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Almudena Ponce Salvatierra Gesendet: Donnerstag, 2. Juli 2015 14:56 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] accept MR solution even if the number of clashes is above the threshold 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
