Is it harmful to to use Imean SigImean in Phenix Refine by default?
Dear All, I noticed Phenix refine default settings are using data labels "Imean" and "SigImean" instead of F and SigF. I searched this on the internet and found a post that titled "Phenix.refine Defaults Considered Harmful" ( web link http://xray0.princeton.edu/~phil/Facility/phenix_fubar.html ). One point in this post shows that "the first thing the program does is ignore that structure factor data and use the IMEAN data instead." This may force rejecting weak data according to the post. The latest Phenix version may be updated from the version the post author used, I wonder if this risk is still in the newest version of Phenix ?
On 12/02/2017 09:05 PM, Xiao Lei wrote:
Dear All,
I noticed Phenix refine default settings are using data labels "Imean" and "SigImean" instead of F and SigF. I searched this on the internet and found a post that titled "Phenix.refine Defaults Considered Harmful" ( web link http://xray0.princeton.edu/~phil/Facility/phenix_fubar.html ). One point in this post shows that "the first thing the program does is ignore that structure factor data and use the IMEAN data instead." This may force rejecting weak data according to the post.
The latest Phenix version may be updated from the version the post author used, I wonder if this risk is still in the newest version of Phenix ?
You can see the defaults with the command: erie 233% phenix.refine --show-defaults . . . . xray_data { file_name = None labels = None high_resolution = None low_resolution = None outliers_rejection = True french_wilson_scale = True french_wilson { max_bins = 60 min_bin_size = 40 } So it seems the default now is to use F&W procedure to preserve the weak data. Some reflections are rejected as outliers, but that is a different criterion. I have seen it argued that there are significant advantages to refining against I instead of F (after all I is you observed value) and I think one of the advantages was that you can refine with negative I's whereas to convert to F's you have to either discard negatives or do F&W. Ed
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
Hi,
I noticed Phenix refine default settings are using data labels "Imean" and "SigImean" instead of F and SigF.
ok, what you say: a) makes sense to me and b) matched my expectations.. So that's a good start, all right!
I searched this on the internet and found a post that titled "Phenix.refine Defaults Considered Harmful"
Ha-ha! I thought folk learned from recent hugely embarrassing ContaMiner rant on ccp4bb recently. It sounds like not all may be then. Regardless: Take home message is: please contact developers to resolve the issue first before posting controversial issues. Most of the time developers will be happy to collaborate and do their best to solve the issue.
( web link http://xray0.princeton.edu/~phil/Facility/phenix_fubar.html http://xray0.princeton.edu/%7Ephil/Facility/phenix_fubar.html ). One point in this post shows that "the first thing the program does is ignore that structure factor data and use the IMEAN data instead."
Sure! Iobs are more important than Fobs. Isn't it obvious? If it is not obvious then I'm really keen to hear why. I'm sure that's going to be a learning experience (for me at least!)! All the best, Pavel
participants (3)
-
Edward A. Berry -
Pavel Afonine -
Xiao Lei