Yes, the Rfreeflag column should be of type I, see e.g. "Output:" section of http://www.ccp4.ac.uk/dist/html/freerflag.html And this is what ccp4i expects, see $CCP4/etc/types.def But not all programs will check it. In fact, the type changed from W to I in 1995, back in the days when free R was still new and exciting. Cheers Martyn -----Original Message----- From: CCP4 bulletin board on behalf of iulek Sent: Sun 5/18/2008 12:48 PM To: [log in to unmask] Subject: [ccp4bb] [Re: [ccp4bb] warp/arp 7.0.1 to really use the Free R flag] - Summary Hi, Concerning this point, it turned out that some scripts of mine (for some historical good reasons) attribute "R" as column type for my r-free-flag column. Changing it to "I" (which I think is more ccp4 standard) solved the problem. According to what I talked to Anastassis, that must be a requirement from ccp4i. For several other programs there was no problem (although I must recognize that I make a very limited use of the ccp4 interface, ccp4i). Anyway, I will attach more to the conventions, now. Jorge -------- Original Message -------- Subject: {Spam?} Re: [ccp4bb] warp/arp 7.0.1 to really use the Free R flag Date: Tue, 29 Apr 2008 11:01:41 +0200 From: Anastassis Perrakis <[log in to unmask]> To: [log in to unmask] CC: [log in to unmask] References: <[log in to unmask]> Dear Jorge, I was unable to reproduce the error you report with 7.0.1. I selected an MTZ file, then chose 'use' FreeR flag and I run the job. I get: #CCP4I VERSION CCP4Interface 1.4.4.2 #CCP4I SCRIPT LOG arp_solvent #CCP4I DATE 29 Apr 2008 10:56:28 #CCP4I USER Tassos ... mtz labels taken: FP SIGFP FreeR_flag ... FreeR will be used for monitoring and sigmaa calculations ... Starting model: After refmac, R = 0.162 (Rfree = 0.170) Could you please try to do the same with first building the standard example (psp) and then adding waters? It might be a problem with your mtz file. Tassos On Apr 28, 2008, at 15:22, [log in to unmask] wrote: > Hi all, > > We recently installed arp/warp 7.0.1 under ccp4i (CCP4_6.0.2). > The installation went fine. We just wanted to add water molecules to > the current model. We toggle to "use" in the box > > "For refmac5 refinement do -use- the Free R flag" > > Also, we choose the due flag in the box > > Determine the free R label for reflections to be escluded from > refinement -FreeR_flag-" > > When we ask the program to run, it does, but without using the > Free R-flag; it says "FreeR will not be used" in the log file and > the R-free is reported as 0.000. Curiously, the box where the free R > label is becomes blank. > We googled and searched archive lists (both warp and CCP4). > What the problem might be ? > > Jorge