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Lepore, Bryan

5 Oct 2010 5 Oct '10

8:36 p.m.

how might one start to go about getting phenix to automatically write out the value of sigma_A vs. resolution? e.g. when making maps, to get that nice table in Randy Read's SIGMAA program output of ln(sigma_A) vs. resolution. -bryan

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Pavel Afonine

6 Oct 6 Oct

1:47 a.m.

Hi Bryan,

how might one start to go about getting phenix to automatically write out the value of sigma_A vs. resolution?

e.g. when making maps, to get that nice table in Randy Read's SIGMAA program output of ln(sigma_A) vs. resolution.

easy -:) Simply nobody asked for this so far so it's not there. I will add it within next few weeks and let you know once it is available. It's not computed at the moment (we use different parametrization) but I can reformulate it to get what you want. May I ask you why you need it? Thanks! Pavel.

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crystallogrphy

10:48 a.m.

Hi, Pavel: I actually also need this function: sigma vs resolution, because I want to determine what is the real resolution of my crystal data. Randy Read and Axel Brunger had a paper talking about it. On Wed, Oct 6, 2010 at 12:47 AM, Pavel Afonine wrote:

Hi Bryan,

how might one start to go about getting phenix to automatically write out

...
the value of sigma_A vs. resolution?

e.g. when making maps, to get that nice table in Randy Read's SIGMAA program output of ln(sigma_A) vs. resolution.

easy -:) Simply nobody asked for this so far so it's not there. I will add it within next few weeks and let you know once it is available. It's not computed at the moment (we use different parametrization) but I can reformulate it to get what you want.

May I ask you why you need it?

Thanks! Pavel.

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Pavel Afonine

11:10 a.m.

Hi, isn't it better to use all data in refinement and expect that the ML target will down-weight those reflections that needs to? And if you have one single reflection at 1A resolution, while the data extends complete up to 2A resolution, you would use it up to 2A anyway? Anyway, I hope Randy might comment on this... Regardless, as I wrote yesterday I will add this functionality as soon as I get a chance. Pavel. On 10/6/10 6:48 AM, crystallogrphy wrote:

Hi, Pavel: I actually also need this function: sigma vs resolution, because I want to determine what is the real resolution of my crystal data. Randy Read and Axel Brunger had a paper talking about it.

On Wed, Oct 6, 2010 at 12:47 AM, Pavel Afonine mailto:[email protected]> wrote:

Hi Bryan,

how might one start to go about getting phenix to automatically write out the value of sigma_A vs. resolution?

e.g. when making maps, to get that nice table in Randy Read's SIGMAA program output of ln(sigma_A) vs. resolution.

easy -:) Simply nobody asked for this so far so it's not there. I will add it within next few weeks and let you know once it is available. It's not computed at the moment (we use different parametrization) but I can reformulate it to get what you want.

May I ask you why you need it?

Thanks! Pavel.

_______________________________________________ phenixbb mailing list [email protected] mailto:[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 Read

11:36 a.m.

Hi, The application we're talking about here is using a model that hasn't seen all the data in refinement to decide how far there's real signal in the data that were measured. We used that for the structure of 1bos (carbohydrate complex with Shiga-like toxin B-subunit), where the data should have been cut off at about 3.5A according to normal I/sigma criteria. However, by including weak data to 2.8A (helped in no small measure by 20-fold NCS), we were able to get very clear density for the bound carbohydrate. We validated the use of the weak data by taking the molecular replacement model before refinement and computing a SigmaA curve against all the data. The SigmaA values were significantly above zero up to 2.8A (indicating a correlation with the observed data, and since we hadn't done any refinement against those data this confirms that there's really some useful signal there), but dropping off dramatically at higher resolution. Axel has done similar things with even lower resolution structures where they really don't want to give up any information. Something like this could be done with cross-validation data after refinement, but the SigmaA determination is much more reliable with more reflections, so if it can be done using all the data before refinement, the results will be clearer. Regards, Randy Read On 6 Oct 2010, at 15:10, Pavel Afonine wrote:

Hi,

isn't it better to use all data in refinement and expect that the ML target will down-weight those reflections that needs to? And if you have one single reflection at 1A resolution, while the data extends complete up to 2A resolution, you would use it up to 2A anyway? Anyway, I hope Randy might comment on this...

Regardless, as I wrote yesterday I will add this functionality as soon as I get a chance.

Pavel.

On 10/6/10 6:48 AM, crystallogrphy wrote:

...
Hi, Pavel: I actually also need this function: sigma vs resolution, because I want to determine what is the real resolution of my crystal data. Randy Read and Axel Brunger had a paper talking about it.

On Wed, Oct 6, 2010 at 12:47 AM, Pavel Afonine wrote: Hi Bryan,

how might one start to go about getting phenix to automatically write out the value of sigma_A vs. resolution?

e.g. when making maps, to get that nice table in Randy Read's SIGMAA program output of ln(sigma_A) vs. resolution.

easy -:) Simply nobody asked for this so far so it's not there. I will add it within next few weeks and let you know once it is available. It's not computed at the moment (we use different parametrization) but I can reformulate it to get what you want.

May I ask you why you need it?

Thanks! Pavel.

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

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

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

------ 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

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Randy Read

11:41 a.m.

Oh yes, I forgot to make one point. If you use data to too-high resolution (where you've collected indices not data, as Keith Wilson would put it), at the least you're wasting significant computer time. By going from 3.5 to 2.8A resolution in the 1bos case, we doubled the amount of data, which is only worth doing if there's real information there. I'm not sure I trust even ML refinement to cope with a significant chunk of data representing pure noise -- the measurement errors would have to be estimated very well, and we would have to trust the refinement procedure to make good use of those measurement errors. If all this doesn't work perfectly, adding data to too-high resolution will introduce errors in your model (being fit to noise) and into your maps. Not to mention the inconvenience that your R-factors will go up! Regards, Randy On 6 Oct 2010, at 15:10, Pavel Afonine wrote:

Hi,

isn't it better to use all data in refinement and expect that the ML target will down-weight those reflections that needs to? And if you have one single reflection at 1A resolution, while the data extends complete up to 2A resolution, you would use it up to 2A anyway? Anyway, I hope Randy might comment on this...

Regardless, as I wrote yesterday I will add this functionality as soon as I get a chance.

Pavel.

On 10/6/10 6:48 AM, crystallogrphy wrote:

...
Hi, Pavel: I actually also need this function: sigma vs resolution, because I want to determine what is the real resolution of my crystal data. Randy Read and Axel Brunger had a paper talking about it.

On Wed, Oct 6, 2010 at 12:47 AM, Pavel Afonine wrote: Hi Bryan,

how might one start to go about getting phenix to automatically write out the value of sigma_A vs. resolution?

e.g. when making maps, to get that nice table in Randy Read's SIGMAA program output of ln(sigma_A) vs. resolution.

easy -:) Simply nobody asked for this so far so it's not there. I will add it within next few weeks and let you know once it is available. It's not computed at the moment (we use different parametrization) but I can reformulate it to get what you want.

May I ask you why you need it?

Thanks! Pavel.

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

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

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

------ 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

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Pavel Afonine

21 Oct 21 Oct

2:04 p.m.

New subject: Sigma-A vs Resolution plot

Hi Bryan, the plot "Sigma-A vs Resolution" will be available in the next PHENIX nightly build: http://www.phenix-online.org/download/nightly_builds.cgi (anything built after October 22). Usage example: phenix.model_vs_data model.pdb data.hkl or mmtbx.model_vs_data model.pdb data.hkl if you are not interested in geometry statistics. Currently this is not available for datasets from twinned crystals. Nat, could you please add this plot somewhere in PHENIX GUI "Comprehensive Validation"? (An example of how this plot looks like you can find here: http://journals.iucr.org/d/issues/2006/08/00/dz5074/index.html) Pavel. On 10/5/10 4:36 PM, Lepore, Bryan wrote:

how might one start to go about getting phenix to automatically write out the value of sigma_A vs. resolution?

e.g. when making maps, to get that nice table in Randy Read's SIGMAA program output of ln(sigma_A) vs. resolution.

-bryan

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crystallogrphy
Lepore, Bryan
Pavel Afonine
Randy Read