Re: [ccp4bb] R free flag missing after ARP/wARP?

[Victor Lamzin]

Dear Lu, The MTZ file produced at the end of the ARP/wARP protein model building is created by Refmac and contains the following: 1. New columns created for the built model: (FC, PHIC, FC_ALL, PHIC_ALL, FWT, PHWT, DELFWT, PHDELWT, FOM, FC_ALL_LS, PHIC_ALL_LS) 2. Columns from the input data file that were used for the refinement - structure factor amplitudes and their estimated standard deviations scaled to those calculated from the model. If Rfree flag was used, the FREE column is also copied to the output MTZ file. Since you chose not to use Rfree for model building, the Rfree flag was not copied to the output. Historically, the default for ARP/wARP protein model building is not to use Rfree. Some years ago we did observe a number of cases where setting a part of the data aside for cross-validation resulted in lower observation-to-parameter ratio and poorer model building. We also thought that the auto-traced model (if built) could itself serve as a validation criterion. In contrast, for ARP/wARP building the solvent structure only, the use of Rfree is a default. Over the recent years much has improved, notably Refmac's likelihood targets. I am sure that in many cases the use of Rfree could now be advantageous for protein model building. We will try to repeat extensive benchmarking with different ARP/wARP protocols, so that many default parameters could be improved. With best regards, Victor On 20/10/2014 04:41, luzuok wrote: Dear all,     I was using ARP/wARP in ccp4i, the input mtz file certainly has free R flag, but the output mzt file doesn't have the free R flag label?  I chose " do not use the Free R flag" in the ARP/wARP GUI. Can anyone tell me what's wrong with this?  best reagrds! Lu Zuokun -- 卢作焜 南开大学新生物站A202