picking Rfree set

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David Garboczi

22 Jan 2008 22 Jan '08

4:19 p.m.

Does phenix.refine take NCS into account when picking the Rfree set? Thin shells, or other strategy... Dave --

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Ralf W. Grosse-Kunstleve

22 Jan 22 Jan

5:23 p.m.

...

Does phenix.refine take NCS into account when picking the Rfree set? Thin shells, or other strategy...

The short answer is no. We had long internal discussions about this without reaching a final conclusion. In the long run we may integrate alternative R-free set distributions in phenix.refine; in the meantime you have to use an external program (e.g. dataman or sftools). BTW 1: just to prove that we have thought about this subject, we have a simple tool for "visualizing" distributions of R-free flags: iotbx.r_free_flags_accumulation your.mtz It writes a file with x,y pairs which you can plot with e.g. Excel or any other 2D plotting program. BTW 2: The free reflections aren't as free as one may think. When using a maximum likelihood target (any program), the free reflections are used in the estimatation of the error model. This estimation becomes more tricky if the reflections are distributed in thin shells. I.e. if you go to thin shells you may in fact account to some degree for the NCS, but at the same time you compromise the error model estimation. Ralf

Peter Zwart

5:31 p.m.

btw3: the lattice symmetry is taken into account when choosing an free set in phenix.refine (unless specified otherwise). If all NCS rotational operators are approximately parallel to twin laws, you should be fine. P 2008/1/22, Ralf W. Grosse-Kunstleve :

...

...
Does phenix.refine take NCS into account when picking the Rfree set? Thin shells, or other strategy...

The short answer is no. We had long internal discussions about this without reaching a final conclusion. In the long run we may integrate alternative R-free set distributions in phenix.refine; in the meantime you have to use an external program (e.g. dataman or sftools). BTW 1: just to prove that we have thought about this subject, we have a simple tool for "visualizing" distributions of R-free flags: iotbx.r_free_flags_accumulation your.mtz It writes a file with x,y pairs which you can plot with e.g. Excel or any other 2D plotting program. BTW 2: The free reflections aren't as free as one may think. When using a maximum likelihood target (any program), the free reflections are used in the estimatation of the error model. This estimation becomes more tricky if the reflections are distributed in thin shells. I.e. if you go to thin shells you may in fact account to some degree for the NCS, but at the same time you compromise the error model estimation. Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

David Garboczi

5:48 p.m.

So, for instance, when addition of a ligand to a P212121 cell (1 mol) changes the symmetry to P21 (almost same cell, but 2 mol), the selection of the Rfree set from the P21 data by phenix.refine will take the higher almost symmetry into account? Dave

...

btw3: the lattice symmetry is taken into account when choosing an free set in phenix.refine (unless specified otherwise). If all NCS rotational operators are approximately parallel to twin laws, you should be fine.

P

2008/1/22, Ralf W. Grosse-Kunstleve :

...
...
Does phenix.refine take NCS into account when picking the Rfree set? Thin shells, or other strategy...

The short answer is no. We had long internal discussions about this without reaching a final conclusion. In the long run we may integrate alternative R-free set distributions in phenix.refine; in the meantime you have to use an external program (e.g. dataman or sftools). BTW 1: just to prove that we have thought about this subject, we have a simple tool for "visualizing" distributions of R-free flags: iotbx.r_free_flags_accumulation your.mtz It writes a file with x,y pairs which you can plot with e.g. Excel or any other 2D plotting program. BTW 2: The free reflections aren't as free as one may think. When using a maximum likelihood target (any program), the free reflections are used in the estimatation of the error model. This estimation becomes more tricky if the reflections are distributed in thin shells. I.e. if you go to thin shells you may in fact account to some degree for the NCS, but at the same time you compromise the error model estimation. Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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

-- David N. Garboczi, PhD Phone: 301-496-4773 Investigator, Structural Biology Section (SBS) Laboratory of Immunogenetics (LIG) National Institute of Allergy and Infectious Diseases (NIAID) National Institutes of Health (NIH) Twinbrook 2/Room 110 12441 Parklawn Drive Rockville, Maryland 20852-1742 Fax: 301-402-0284 Email: [email protected] The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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David Garboczi
Peter Zwart
Ralf W. Grosse-Kunstleve