[phenixbb] phenix.refine and R free values
Pavel Afonine
pafonine at lbl.gov
Wed Sep 3 08:41:29 PDT 2014
Hi,
F(+),SIGF(+),F(-),SIGF(-) are derived from I(+),SIGI(+),I(-),SIGI(-)
using various approximations that depend on underlying model. In this
sense I(+),SIGI(+),I(-),SIGI(-) is more original and richer data than
F(+),SIGF(+),F(-),SIGF(-).
If F(+),SIGF(+),F(-),SIGF(-) were used in refinement to obtain deposited
structure then this would be a good reason to have both, F and I.
Pavel
On 9/3/14 8:33 AM, PC wrote:
> Hi Pavel and Phenix users.
>
> Thank you for your reply.
>
> I see in 2y78.mtz (example I used below) has both in the MTZ:
>
> F(+),SIGF(+),F(-),SIGF(-)
> I(+),SIGI(+),I(-),SIGI(-)
>
> I am confused, why? One is sufficient isn't it?
>
> Thank you,
>
>
>
> -----Original Message-----
> *From:* pafonine at lbl.gov
> *Sent:* Sat, 30 Aug 2014 09:45:58 -0700
> *To:* patrick.cossins at inbox.com, phenixbb at phenix-online.org
> *Subject:* Re: [phenixbb] phenix.refine and R free values
>
> Hello,
>
>> Hi Phenix users,
>>
>> I was trying to experiment with phenix.refine using default
>> parameters (2Y78.pdb) and I got the following message.
>>
>> Multiple equally suitable arrays of observed X-ray data found.
>>
>> Possible choices:
>> 2Y78.mtz:IOBS,SIGIOBS
>> 2Y78.mtz:I(+),SIGI(+),I(-),SIGI(-)
>>
>> Please use refinement.input.xray_data.labels
>> to specify an unambiguous substring of the target label.
>>
>> Anyway, two questions related to this:
>>
>> 1) How does one pick of the two options above?
>
> If your question is about the syntax:
>
> phenix.refine model.pdb data.mtz xray_data.labels="IOBS,SIGIOBS"
> or
> phenix.refine model.pdb data.mtz xray_data.labels="I(+),SIGI(+"
> (sub-string should work).
>
> If your question is about choice anomalous vs non-anomalous data
> to be used: I would use anomalous because it is a richer source of
> information, you will get anomalous difference map, you can refine
> anomalous f'&f'', etc.
>
>> 2) If R work/R free went from 0.1044/0.1142 to 0.1096/0.1200 is
>> that bad or is it acceptable?
>
> R-factors look similar to me. Systematic slight increase may mean
> you need to adjust target weights or choose refinement strategy
> more tailored to the quality of input data and model.
>
> Pavel
>
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