How to generate an anomalous map in PHENIX?
Hi, I am trying to make an anomalous map in the latest phenix. After refinement of a medium resolution structure (1.8A) with anomalous data (and signal) I used the ANOM and PHANOM columns in the map_coeffs.mtz file to generate a map. The map was created either in coot or via fft, but shows no anomalous peaks for a present Cl1 nor for SS bonds. It rather mimics a noisy protein map. Generation of an anomalous map in CNX using the same data (FOBS(+/-) and HL coeffs(calc) ) produces a nice map with the expected peaks. Am I misunderstanding the purpose of the ANOM/PHANOM columns or is this feature not implemented yet. Cheers Carsten
Hi Carsten, I'm not certain which file map_coeffs.mtz is (I don't recognize the labels ANOM and PHANOM and my AutoSol_run_1_/TEMP0/map_coeffs.mtz doesn't have these columns), but I if it is coming from a wizard think that none of the files produced by the wizards will give you the desired anomalous map. I hope that helps! Perhaps someone else will recognize these column labels... All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss On Jun 17, 2008, at 10:52 AM, Schubert, Carsten [PRDUS] wrote:
Hi,
I am trying to make an anomalous map in the latest phenix. After refinement of a medium resolution structure (1.8A) with anomalous data (and signal) I used the ANOM and PHANOM columns in the map_coeffs.mtz file to generate a map. The map was created either in coot or via fft, but shows no anomalous peaks for a present Cl1 nor for SS bonds. It rather mimics a noisy protein map. Generation of an anomalous map in CNX using the same data (FOBS(+/-) and HL coeffs(calc) ) produces a nice map with the expected peaks. Am I misunderstanding the purpose of the ANOM/PHANOM columns or is this feature not implemented yet.
Cheers
Carsten
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Hi Carsten,
Am I misunderstanding the purpose of the ANOM/PHANOM columns or is this feature not implemented yet.
This is for an anomalous difference map, i.e. (F(obs)+)-(F(obs)-) with F(calc) phases, weighted with FOM (refinement). Is this what you want? This is a fairly new feature. If the anomalous difference map doesn't show peaks where you expect them we'd have to check the algorithm generating the coefficients. Ralf
Hi Ralf, yes thats the map I'd wanted to make. I assume that these should be map coefficients with the phases already shifted by 90 degs, so a simple FFT should produce the map? If you guys could recheck the procedure and let me know if it works in your hands that would be great. A regular lysozyme dataset with anomalous differences should be enough to test this. Let me know if you need a test set, if not I may either have something here or could generate it over night Cheers, Carsten
-----Original Message----- From: [email protected] [mailto:[email protected]]On Behalf Of Ralf W. Grosse-Kunstleve Sent: Tuesday, June 17, 2008 2:27 PM To: [email protected] Subject: Re: [phenixbb] How to generate an anomalous map in PHENIX?
Hi Carsten,
Am I misunderstanding the purpose of the ANOM/PHANOM columns or is this feature not implemented yet.
This is for an anomalous difference map, i.e. (F(obs)+)-(F(obs)-) with F(calc) phases, weighted with FOM (refinement). Is this what you want?
This is a fairly new feature. If the anomalous difference map doesn't show peaks where you expect them we'd have to check the algorithm generating the coefficients.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Carsten, it is most likely a bug in phenix.refine. We need to fix it. Pavel. On 6/17/2008 9:52 AM, Schubert, Carsten [PRDUS] wrote:
Hi,
I am trying to make an anomalous map in the latest phenix. After refinement of a medium resolution structure (1.8A) with anomalous data (and signal) I used the ANOM and PHANOM columns in the map_coeffs.mtz file to generate a map. The map was created either in coot or via fft, but shows no anomalous peaks for a present Cl1 nor for SS bonds. It rather mimics a noisy protein map. Generation of an anomalous map in CNX using the same data (FOBS(+/-) and HL coeffs(calc) ) produces a nice map with the expected peaks. Am I misunderstanding the purpose of the ANOM/PHANOM columns or is this feature not implemented yet.
Cheers
Carsten
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participants (4)
-
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Schubert, Carsten [PRDUS] -
Tom Terwilliger