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: [email protected]
Sent: Sat, 30 Aug 2014 09:45:58 -0700
To: [email protected], [email protected]
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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