Hi Ian,
The initial question was about which procedures to convert intensities
to amplitudes are deemed acceptable. I was proposing the Sivia & David
(1994) method as an alternative to the French & Wilson (1978) method.
You were objecting against this and came up with data simulations which
w
traints?
Again, apologies for the long delay, and for the essay!
Cheers
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> Sent: 06 October 2008 21:17
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Reading the old liter
ly for
low average intensity (<= 1 sigma). The Bayesian-corrected
intensities are not needed in practice for refinement (but may be
better for other purposes such as twinning tests) because the
likelihood function can handle the uncorrected negative & zero
intensities.Cheers-- Ian
e better for other
purposes such as twinning tests) because the likelihood function can
handle the uncorrected negative & zero intensities.
Cheers
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Frank von Delft
>
I mentioned previously phenix.refine tosses your weak data if IMEAN,
SIGIMEAN are chosen during refinement.
phenix.refine does not automatically remove the data based on sigma
(it does it by user's request only). phenix.refine removes only
negative or zero values for Iobs (Fobs).
That is
Hi Pete,
just a remark:
On 9/25/2008 4:00 PM, Dunten, Pete W. wrote:
I mentioned previously phenix.refine tosses your weak data if IMEAN,
SIGIMEAN are chosen during refinement.
phenix.refine does not automatically remove the data based on sigma (it
does it by user's request only). pheni
Can one make it? If so, what's the keyword? Because I couldn't it in
the online docs.
Cheers
phx
Peter Zwart wrote:
phenix.refine also might not (by default) use missing data in map calculation.
AFAIK, refmac fills in missing data with DFc. Phenix doesn't (maybe
this changed now).
When your h
phenix.refine also might not (by default) use missing data in map calculation.
AFAIK, refmac fills in missing data with DFc. Phenix doesn't (maybe
this changed now).
When your high resolution shells are incomplete (like when using the
anisotropy server to perform elliptical data truncation, or etc
Another factor may be that phenix.refine does not make a full use of
experimental phase information in its calculation of the error
parameters - I've been discussing this with Peter, Randy and Ralph. I
don't know that this is the cause, but I see inferior results when
recycling buccaneer with
This goes back to my previous idea about using the Bayesian estimates
( & sig()) of I & sig(I) in the refinement instead of the measured
ones. This would remove any objection to using negative observed
intensities, though it's hard to see what exactly the objection is.
Basically you're just moving
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