Hiya Frank Well my take on it would be that they did a certain experiment - which includes phasing datasets - and we have an expectation to see all the steps reported. Good structures are not the 'be all' and 'end all'. Reporting data is not merely to convince readers that this is not a 'made up' structure. It is like in mathematics when you don't just report the correct answer but your 'show your workings' as my old maths teacher used to say. So maybe phasing statistics are pretty important in that respect.
And it would be good to have datasets with experimental phases deposited. I should've done this with my 1e3h years ago as the experimental phases (which, as I recall, you were a friendly advisor on ;) were included in the refinement target (CNS mlhl). SeMet phases are usually good - but ones from other heavy atoms it might be nice to see too. There used to be a heavy atom database for such like things - not sure of the current status of that. see you all the best Martyn Martyn Symmons Cambridge ________________________________ From: Frank von Delft <frank.vonde...@sgc.ox.ac.uk> To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 12 April, 2010 12:24:50 Subject: Re: [ccp4bb] Phasing statistics I fully agree, for high quality data. What though if the data are not impeccable and the structure necessarily ropey? E.g. 4A phases and anisotropic diffraction. By what metrics do we then judge the results? (I don't know the answer, btw, but our membranous colleagues surely spend quite a bit of time with that question...) phx. On 12/04/2010 12:10, Anastassis Perrakis wrote: Hi - > > > >A year or so ago, I have asked as a referee somebody to provide >for a paper the statistics for their heavy atom derivative dataset, > >and for the phasing statistics. For some good reasons, they were >unable to do that, and they (politely) asked me >'what would it change if you knew these, isn't the structure we >present impeccable?'. Well, I think they were right. >Their structure was surely correct, surely high quality. After >that incident and giving it some thought, >I fail to see why should one report e.g. PP or Rcullis, or why >will I care what they were if the structure has a convincing Rfree and >is properly validated. >If someone wants to cheat at the end of the day, its easy to >provide two numbers, but its hard to provide a good validated model >that agrees with the data. >(and, yes, you can also make up the data, but we have been >there, haven't we?!?) > > >So, my question to that referee, likely being a ccp4bb >aficionado that is reading this email, or to anyone else really, is: > > >"What would it help to judge the quality of the structure or the >paper if you know PP, Rcullis and FOM?" > > >Best - > > >A. > > >PS Especially since you used SHELXE for phasing these statistics >are utterly irrelevant, and possibly you could advice the referee to >read a bit about how SHELXE works ... or go to one of the nice courses >that George teaches ... > > >On Apr 12, 2010, at 10:37, Eleanor Dodson wrote: > >You can feed the SHELX sites into phaser_er or CRANK both of >>which will >>>>give this sort of information. >> >>>>Or mlphare if you know how to set it up.. >> >>>>Eleanor >> >> >>>>Harmer, Nicholas wrote: >> >>Dear CCP4ers, >>> >> >>> >>I've been asked by a referee to provide the >>>phasing statistics for a SAD dataset that I used to solve a recent >>>structure. Whilst I have been able to find a figure-of-merit for the >>>data after phasing, I can't work out how to get any other statistics >>>(e.g. phasing power or an equivalent or Rcullis). Does anyone know a >>>good route to obtaining useful statistics to put in the paper for SAD >>>data? >>> >> >>> >>The structure solution was carried out >>>using SHELX C/D/E and then ARP/wARP. >>> >> >>> >>Thanks in advance, >>> >> >>> >>Nic Harmer >>> >> >>> >>===================== >>> >>Dr. Nic Harmer >>> >>School of Biosciences >>> >>University of Exeter >>> >>tel: +44 1392 725179 >>> >> >>> > >P please don't print this e-mail unless you really need to >Anastassis (Tassos) Perrakis, Principal >Investigator / Staff Member >Department of Biochemistry (B8) >Netherlands Cancer Institute, >Dept. B8, 1066 CX Amsterdam, The Netherlands >Tel: +31 20 512 1951 Fax: +31 20 512 >1954 Mobile / SMS: +31 6 28 597791 > > > > >
