Re: [ccp4bb] About solvent flattening

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

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Subject: Re: Recommendations for (linux) crystallography workstation, server?
From: Paul Smith paul {- at -} PALADINSCIENTIFIC {- dot -} COM
Date: 2010-06-04

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Subject: Re: Recommendations for (linux) crystallography workstation, server?
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2010-06-04

Subject: Re: About solvent flattening
From: Ian Tickle ianjt05 {- at -} GMAIL {- dot -} COM
Date: 2010-06-04

On Fri, Jun 4, 2010 at 2:28 AM, wrote:

> I was using ccp4-6.0.2. I was using the following scripts:

> sigmaa HKLIN test.mtz HKLOUT test-sigmaa.mtz << eof
> title tt
> labin FP=FP SIGFP=SIGFP FC=FP_atm PHIC=PHIC
> labout DELFWT=DELFWT FWT=FWT WCMB=WCMB
> symmetry P1211
> END
> eof

I get the same results, i.e. some FOMs (about 6%) have gone negative,
and about 75% are exactly zero, whether I use the 6.0.2 version or the
current one. This message in the output is pertinent:

Correlation between E**2's is non-positive -- SIGMAA set to 0.05

Also this table (final iteration of optimization of sigma-A) is telling:

Iteration Number 10 on SIGMAA
OLD NEW MEAN
D Limits SIGMAA Shift SIGMAA W
39.89 -- 8.74 0.00000 0.00000 0.00000 0.00000
8.74 -- 6.25 -0.59308 -0.00638 -0.59946 -0.45201
6.25 -- 5.13 0.66855 0.00000 0.66855 0.54835
5.13 -- 4.45 -0.61159 -0.00813 -0.61972 -0.49740
4.45 -- 3.99 0.71063 0.00000 0.71063 0.58634
3.99 -- 3.64 0.55934 0.00000 0.55934 0.43656
3.64 -- 3.37 0.00000 0.00000 0.00000 0.00000
3.37 -- 3.16 0.42551 0.00000 0.42551 0.32230
3.16 -- 2.98 0.00000 0.00000 0.00000 0.00000
2.98 -- 2.83 0.00000 0.00000 0.00000 0.00000
2.83 -- 2.69 0.00000 0.00000 0.00000 0.00000
2.69 -- 2.58 0.00000 0.00000 0.00000 0.00000
2.58 -- 2.48 0.00000 0.00000 0.00000 0.00000
2.48 -- 2.39 0.00000 0.00000 0.00000 0.00000
2.39 -- 2.31 0.00000 0.00000 0.00000 0.00000
2.31 -- 2.24 0.00000 0.00000 0.00000 0.00000
2.24 -- 2.17 0.00000 0.00000 0.00000 0.00000
2.17 -- 2.11 0.00000 0.00000 0.00000 0.00000
2.11 -- 2.05 0.00000 0.00000 0.00000 0.00000
2.05 -- 2.00 0.00000 0.00000 0.00000 0.00000

Refinement of SIGMAA has not converged -- using current values
Overall MEAN W is 0.05260

DATA for SIGMAA PLOT

STHOL**2 LN(SIGMAA)
0.008000 -0.402640
0.014211 -0.341601
0.017326 -0.580991
0.023544 -0.854478

ln(SigmaA) vs sthol**2 should give straight line with
slope = -26.3189*(mean square coordinate error) and intercept =
0.5*ln(sigmap/sigman).

> Is that possible that the negative FOM is due to the large discrepancy
> between FP and FC? Thanks for your kindly help!

Yes I think that's it: the Fo/Fc agreement is essentially random at
high resolution, so the sigma-A plot data only goes up to ~ 6.5 Ang
and is meaningless, i.e. this is a case of the method being
inappropriate rather than a program bug. Perhaps others who have
experience of using this program in this situation can comment, my
experience is only cases where agreement is good.

Cheers

-- Ian

CCP4bb navigation

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

Previous message:
Subject: Re: Recommendations for (linux) crystallography workstation, server?
From: Paul Smith paul {- at -} PALADINSCIENTIFIC {- dot -} COM
Date: 2010-06-04

Next message:
Subject: Re: Recommendations for (linux) crystallography workstation, server?
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2010-06-04