Re: [ccp4bb] Phasing statistics

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: applying B factor and scale correction to an MTZ
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-04-12

Next message:
Subject: Re: Phasing statistics
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2010-04-12

Subject: Re: Phasing statistics
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2010-04-12

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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: applying B factor and scale correction to an MTZ
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-04-12

Next message:
Subject: Re: Phasing statistics
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2010-04-12