Re: [ccp4bb] Highest shell standards

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

Previous message:
Subject: Re: SHARP question
From: Schneider Sabine paxss2 {- at -} NOTTINGHAM {- dot -} AC {- dot -} UK
Date: 2007-03-26

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Subject: phaser in ccp46.0.2
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2007-03-26

Subject: Re: Highest shell standards
From: price {- at -} UCHICAGO {- dot -} EDU price {- at -} UCHICAGO {- dot -} EDU
Date: 2007-03-26

Isn't automatically included fabricated data for missing reflections
a really bad idea for anisotropic data where most reflections are
"missing" at high resolution? Shouldn't there be a big flashing red
flag alerting the user to what's been done?
Phoebe

At 01:22 PM 3/26/2007, Edward A. Berry wrote:
>Actually I was thinking of a somewhat earlier paper:
>
>Rayment,I. Molecular relacement method at low resolution:
>optimum strategy and intrinsic limitations as determined
>by calculations on icosahedral virus models.
>Acta Crystallogr. A 39, 102 116 (1983).
>
>But thanks for bringing the Caliandro et al. paper to my attention.
>Thanks also to Fred. Vellieux for his comments, and to Pete Dunton
>for explaining to me that while fft doesn't do fillin by default,
>the 2MFo-DFc map coefficients from refmac5 do have fillin values
>for the missing reflection, making model bias a problem when
>many missing residues are included.
>
>Now I understand Petrus's question.
>
>Ed
>
>Michel Fodje wrote:
>>You are probably referring to the following works:
>>Caliandro et al, Acta Cryst. D61 (2005) 556-565
>>and Caliandro et al, Acta Cryst. D61 (2005) 1080-1087
>>in which they used density modification to calculate phases for
>>unmeasured reflections, and used the phases to extend the resolution by
>>calculating rough estimates unmeasured amplitudes. Using this technique
>>they actually could improve the electron density.
>>If I'm not mistaken, George Sheldrick has implemented this "Free Lunch"
>>algorithm in SHELXE.
>>/Michel
>>On Fri, 2007-03-23 at 08:05 -0800, Edward Berry wrote:
>>
>>>If instead you allow the missing F's
>>>to "float", calculating them on each cycle from the previous map
>>>using the fillin option, someone has shown (don't have the
>>>reference handy at the moment) that the F's tend toward the true F's
>>>(in the case that they weren't really missing but omitted as part
>>>of the test).
>>>
>>>Ed

---------------------------------------------------------------------------------------------------------------------------
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/index.html
http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html

CCP4bb navigation

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

Previous message:
Subject: Re: SHARP question
From: Schneider Sabine paxss2 {- at -} NOTTINGHAM {- dot -} AC {- dot -} UK
Date: 2007-03-26

Next message:
Subject: phaser in ccp46.0.2
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2007-03-26