[phenixbb] maps : sigma-a

Randy Read rjr27 at cam.ac.uk
Wed Oct 6 07:41:47 PDT 2010


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 <pafonine at lbl.gov> 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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------
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: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk

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