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
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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On Wed, Sep 3, 2014 at 8:33 AM, PC
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?
"Why" is "because that's what the crystallographer submitted to the PDB". It's actually better to have both arrays: the intensities are (usually) the original data as measured on the detector, while the amplitudes have been processed such that negative intensities are either removed (in older versions of Phenix) or adjusted based on the French-Wilson protocol (in newer versions, and also in CCP4 utilities), and therefore do not exactly capture the original data. But the amplitudes are what the model was actually refined against, so to have a complete record of the experiment, it's helpful to have them too. (You're correct, however, that to just re-run phenix.refine we only need one of these. Note that since the original structure was refined with an older version, they may have used fewer reflections because the negative intensities were discarded.) -Nat
participants (3)
-
Nathaniel Echols -
Pavel Afonine -
PC