I noticed that Refmac has done the 1vs0 thing correct for ages, which is very useful because mix-ups between the work set and test set used to be quite common in the reflection files at the pdb (Refmac saved me a lot of extra work with this). Dealing with this problem is very simple as the smallest set is typically the test set.
Phenix however needs to deal with the CCP4 type reflection binning. Now the size of the sets cannot be used which means that you have find a smarter solution. So I wonder how this is implemented. Does Phenix use the (reasonable) assumption that the test set is labeled 1.00 or 0.00? Or does it also check the sets with other labels? Cheers, Robbie Sent from my Windows Phone ________________________________ From: Garib N Murshudov Sent: 2013-01-25 10:46 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refmac5 vs phenix refine mixed up Dear Tim In principle if a user defines freer flag then refmac knows about that (unless freer flag is 0 then refmac assumes that it is default). In this case (if freer defined by user) then it is not altered. regards Garib On 25 Jan 2013, at 09:14, Tim Gruene wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Pavel, dear Garib, > > how do you figure out automatically the correct flag? (I hope both > phenix and refmac will allow to manual overwrite the software's decision) > > Cheers, > Tim > > On 01/24/2013 07:47 PM, Pavel Afonine wrote: >> Hi, >> >> It would be nice if default setting was the same in different >> suites. >> >> >> it's a nice idea of course, but I feel it is impractical as it >> would require changing a lot of software, both modern and legacy. >> However, given array of flags it is algorithmically trivial to >> figure out what is test and work flags. That's what phenix.refine >> have been doing since its beginning (2005). And my understanding >> is that Refmac does this too. As always, there are corner cases >> here, but it's better than nothing. Plus, programs (at least >> phenix.refine, can't speak for others) tell which flag was >> actually used, and they provide option to define the flag value to >> use. >> >> Pavel >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFRAkzvUxlJ7aRr7hoRAlVfAKClRD4/JLNDcOab1HjBroQYXND3bQCfegA9 > UiHvuKXg2/b3LqlbPWQpKmY= > =Awum > -----END PGP SIGNATURE----- Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
