ubject: Re: [ccp4bb] Phasing statistics
I have to say that I don't share James' enthusiasm for the FOM as a
useful statistic, even for experimental phases, and particularly not
in the SAD (and SIR) cases, which after all is what this thread is
supposed to be about. This is even without delv
I have to say that I don't share James' enthusiasm for the FOM as a
useful statistic, even for experimental phases, and particularly not
in the SAD (and SIR) cases, which after all is what this thread is
supposed to be about. This is even without delving further into the
murky issues of wildly in
l-space Rfactor of the _final_ model in the
> _original_ map?
>
> In the real world ;) I don't see that happening anytime soon
>
> all the best
>Martyn
>
> Martyn Symmons
> Cambridge
>
>
>
>
>
> ----- Original Message
> From: &qu
final_ model in the _original_
map?
In the real world ;) I don't see that happening anytime soon
all the best
Martyn
Martyn Symmons
Cambridge
- Original Message
From: "Soisson, Stephen M"
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, 13 April, 2010 19:09:12
Su
ve
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
James Holton
Sent: Tuesday, April 13, 2010 1:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Phasing statistics
Probably the only phasing stat that I pay any attention to these days is
the Fig
om: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
James Holton
Sent: Tuesday, April 13, 2010 1:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Phasing statistics
Probably the only phasing stat that I pay any attention to these days is
the Figure of Merit (FOM). This is because, the
Probably the only phasing stat that I pay any attention to these days is
the Figure of Merit (FOM). This is because, the _definition_ of FOM is
that it is the cosine of the phase error (or at least your best estimate
of it). FOM=1 is perfect phases and FOM=0 is random phases, and a
reasonable
I like the ideal of calling SHARP 'vintage'. ;-)
Indeed, it gets better by the time, but at the same time i like having
a sip or two all the time, and not wait for it to really mature!
Maybe Gerard can hint if major releases of SHARP are always coinciding
with good years in the valley of Borde
Well, Frank, your "membranous" by their science (not very frequently)
colleagues will say - first of all look on the properly calculated electron
density maps first of all - good map will be manifested by continuity, shape,
accordance to the secondary structure elements etc.
For us/them (memb
Hi Tassos,
On Mon, Apr 12, 2010 at 04:10:57PM +0200, Anastassis Perrakis wrote:
> As for Frank's argument, I fully agree low resolution cases are a
> different ball game
> (talking about ball games, I usually agree with Frank, he is much
> bigger than me, and its healthier to agree with him,
Frank-
Are you referring to our colleagues personal qualities, or the projects
on which they work? :)
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Frank von Delft
(I don't know the answer, btw, but our membranous colleagues surely
spen
Hi Dirk -
I am afraid I still don't agree and will try to defend my thesis a bit
further.
First, as eorge explained why in SHELXE these things are meaningless
anyway, so the answer to that referee is simple:
"SHELXE that was used for calculating phase probabilities; that
precludes reporti
As Tassos correctly says, the 'usual phasing statistics' are utterly
irrelevant to phasing a structure with SHELXE. SHELXC/D/E adopt a
minimalist approach, and input and calculate only what is needed to get a
map that is good enough to interpret. For example, in order to calculate
RCullis one w
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
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, 12
Hi Tassos,
my personal opinion is, that I would like to see the usual phasing
statistics. At least to me, they provide hints how well the structure
was determined, analogous to the R-factor/Free-R-factor providing hints
how well the structure was refined.
It would be good if SHELXE would pri
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
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, is
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 sol
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 equiva
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