A related question: is there a current example of using phaser to calculate SAD LLG maps from a refined model not refined with phenix.refine? In the past I have used the description posted here: http://www.phenix-online.org/pipermail/phenixbb/2008-July/012399.html However phaser syntax and keywords seem to have changed a bit as this no longer works. Also, have the derived FLLG and PHLLG columns been renamed ? thanks, Alastair Fyfe On 04/03/2014 09:13 AM, Nathaniel Echols wrote:

PS. Tom pointed out that the anomalous measurability in Xtriage depends on the sigmas, which is obviously a problem for synthetic data - you can generate fake sigmas with "add_sigmas=True", but the resulting statistics will be meaningless.

-Nat

On Thu, Apr 3, 2014 at 8:27 AM, Nathaniel Echols wrote:

...

I guess it depends on what you're looking for as the final output. It's easy to generate an MTZ file with anomalous Fcalc (this is in the GUI too, of course):

phenix.fmodel model.pdb high_resolution=2.0 type=real wavelength=0.9792

Extracting some kind of useful summary from the data might require a little extra scripting - although this may be the kind of thing we should just add to Xtriage (which only reports "anomalous measurability" right now).

-Nat

On Thu, Apr 3, 2014 at 7:20 AM, Jonathan Grimes wrote:

...

Given a refined protein structure, is there an straightforward way to calculate the anomalous differences as a function of resolution, at wavelength X.

many thanks jon

Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer DIAMOND Research Fellow

Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK

Email: [email protected], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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Hi, The syntax and behaviour have changed since 2008. Most of the time, people run LLG completion until Phaser finds no more sites, in which case the log-likelihood-gradient map is by definition close to flat at that point. So the default is not to write out the map coefficients. A special flag (LLGMAPS ON) has to be set to get the map coefficients, and then they go into a separate file. Here's a sample script to make an initial log-likelihood-gradient map for our MR-SAD tutorial: phenix.phaser << eof > LLGmap.log ROOT LLGmap TITLE MR_SAD starting from MR sol with goat alpha-lactalbumin model MODE EP_AUTO HKLIN lyso2001_scala1.mtz LLGCOMPLETE COMPLETE ON LLGCOMPLETE NCYC 0 LLGMAPS ON LLGCOMPLETE SCATTERER S PARTIAL PDB eptute_1.1.pdb IDENT 0.4 CRYSTAL four DATASET CuKa LABIN F+ = F_CuKa(+) SIG+ = SIGF_CuKa(+) F- = F_CuKa(-) SIG- = SIGF_CuKa(-) COMPOSITION PROTEIN SEQ hewl.pir NUMBER 1 WAVELENGTH 1.5418 eof You have to say "LLGCOMPLETE COMPLETE ON" to get the LLG map calculated, but "LLGCOMPLETE NCYC 0" to avoid any sites being added, and "LLGMAPS ON" to get the output LLG map, which has coefficients FLLG_S and PHLLG_S for this case (with "S" for the type of scatterer). However, we've tested various options as part of the work on ion identification (led by Nat Echols), and if you want to identify anomalous scatterers from a final model it's better to do iterative completion adding purely imaginary scatterers to a model of real scatterers. The refined occupancy gives you a measure of the f" (or f" times occupancy for a partially occupied anomalous scatterer) for the site identified by the imaginary scatterer location, and by doing iterative completion the inclusion of sites found in the initial cycles improves the signal-to-noise in later cycles. Here's a script that could be used for a final model: phenix.phaser << eof > MRSAD_imag.log ROOT MRSAD_imag TITLE MR_SAD adding purely imaginary scatterers to final model MODE EP_AUTO HKLIN lyso2001_scala1.mtz LLGCOMPLETE COMPLETE ON LLGCOMPLETE SCATTERER AX PARTIAL PDB HEWL.pdb IDENT 1.0 CRYSTAL four DATASET CuKa LABIN F+ = F_CuKa(+) SIG+ = SIGF_CuKa(+) F- = F_CuKa(-) SIG- = SIGF_CuKa(-) COMPOSITION PROTEIN SEQ hewl.pir NUMBER 1 WAVELENGTH 1.5418 eof Here what you want to look at is the set of sites (MRSAD_imag.1.pdb) with their occupancies, and not an LLG map (which isn't produced by this script). There are occasionally some spurious sites, especially if the anomalous signal is very weak, but it usually provides good evidence when a site falls on top of what you expect to be a metal ion. Best wishes, Randy On 3 Apr 2014, at 17:28, Alastair Fyfe wrote:

A related question: is there a current example of using phaser to calculate SAD LLG maps from a refined model not refined with phenix.refine? In the past I have used the description posted here: http://www.phenix-online.org/pipermail/phenixbb/2008-July/012399.html

However phaser syntax and keywords seem to have changed a bit as this no longer works. Also, have the derived FLLG and PHLLG columns been renamed ? thanks, Alastair Fyfe

On 04/03/2014 09:13 AM, Nathaniel Echols wrote:

...

PS. Tom pointed out that the anomalous measurability in Xtriage depends on the sigmas, which is obviously a problem for synthetic data - you can generate fake sigmas with "add_sigmas=True", but the resulting statistics will be meaningless.

-Nat

On Thu, Apr 3, 2014 at 8:27 AM, Nathaniel Echols wrote:

...

I guess it depends on what you're looking for as the final output. It's easy to generate an MTZ file with anomalous Fcalc (this is in the GUI too, of course):

phenix.fmodel model.pdb high_resolution=2.0 type=real wavelength=0.9792

Extracting some kind of useful summary from the data might require a little extra scripting - although this may be the kind of thing we should just add to Xtriage (which only reports "anomalous measurability" right now).

-Nat

On Thu, Apr 3, 2014 at 7:20 AM, Jonathan Grimes wrote:

...

Given a refined protein structure, is there an straightforward way to calculate the anomalous differences as a function of resolution, at wavelength X.

many thanks jon

Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer DIAMOND Research Fellow

Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK

Email: [email protected], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk