addenda and errata\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoBIOLOGICAL
CRYSTALLOGRAPHY
ISSN: 1399-0047

Pushing the boundaries of molecular replacement with maximum likelihood. Erratum

aDepartment of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, England
*Correspondence e-mail: rjr27@cam.ac.uk

(Received 19 December 2002; accepted 3 January 2003)

In the calculations testing maximum-likelihood molecular-replacement methods reported in the paper by Read [(2001[Read, R. J. (2001). Acta Cryst. D57, 1373-1382.]). Acta Cryst. D57, 1373–1382 ] simulated data constructed to test isomorphous replacement methods in the presence of known errors were used inadvertently. The test calculations have been repeated using the measured data, and the results are given.

In the reported calculations testing maximum-likelihood molecular-replacement methods (Read, 2001[Read, R. J. (2001). Acta Cryst. D57, 1373-1382.]) on the structure of Streptomyces griseus trypsin (SGT), I inadvertently used simulated data computed from the final refined structure of SGT (Read & James, 1986[Read, R. J. & James, M. N. G. (1988). J. Mol. Biol. 200, 523-551.]). The simulated data had been constructed to test isomorphous replacement methods in the presence of known errors. The test calculations have been repeated using the measured data, and the results are given in new Tables 1[link] and 2[link]. The original conclusions are upheld, except that in a translation search with an orientation in error by 6.9°, the correct translation no longer has the highest likelihood score. However, when this translation search is repeated, increasing the assumed r.m.s. error of the molecular-replacement model from the default value of 1.4 to 2.0 Å to compensate for the effect of orientation error, the correct translation again has the highest likelihood score. As before, the discrimination from incorrect translations is poor with the most inaccurate orientation.

Table 1
Rotation function results for S griseus trypsin

Algorithm Resolution range (Å) Correct peak Orientation error (°)
Crowther 10.0–2.8 5.32 6.9
Crowther 10.0–3.5 5.62 3.4
Likelihood 14.7–2.8 7.39 0.6
†Peak height expressed in terms of r.m.s. deviations from the mean.
‡Compared with final orientation from molecular replacement after rigid-body refinement.

Table 2
Translation function results for S griseus trypsin

Orientation error (°) Correct peak Highest noise peak Mean of search R.m.s. from mean
6.9 −11.3 −5.3 −54.7 10.5
6.9 15.3 14.5 −5.1 4.3
3.4 77.3 30.7 −35.9 11.5
0.6 117.9 50.5 −27.0 11.6
†Scores are expressed in terms of log-likelihood gain.
‡Results from run in which r.m.s. error of 2 Å was assumed instead of default of 1.4 Å, to compensate for effect of orientation error.

References

First citationRead, R. J. (2001). Acta Cryst. D57, 1373–1382.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationRead, R. J. & James, M. N. G. (1988). J. Mol. Biol. 200, 523–551.  CrossRef CAS PubMed Web of Science Google Scholar

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Journal logoBIOLOGICAL
CRYSTALLOGRAPHY
ISSN: 1399-0047
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