Hi Reza,
I assume that you run Phenix via command line. We have a new enhanced
"ramachandran_plot_restraints" scope to define these (similar) parameters.
The previous one is there (for a short while) for backward compatibility
(so users can restore old GUI jobs). The new scope looks like:
ramachandran_plot_restraints {
enabled = True
favored = *oldfield emsley emsley8k
allowed = *oldfield emsley emsley8k
outlier = *oldfield emsley emsley8k
selection = None
inject_emsley8k_into_oldfield_favored = True
oldfield {
weight = 0.
weight_scale = 0.01
distance_weight_min = 2.0
distance_weight_max = 10.0
plot_cutoff = 0.027
}
emsley {
weight = 1.0
scale_allowed = 1.0
}
emsley8k {
weight_favored = 5.0
weight_allowed = 10.0
weight_outlier = 10.0
}
}
So please use this one. Notable change is that now you can restrain
favored/allowed/outliers separately (or not restrain one or another).
Please let me know if you need to know exactly how to convert old-style
parameters into new ones.
In case you are going to perform a similar study as you are mentioning, I
would like to suggest adding the Rama-Z metric to the set of validation
metrics. It was included particularly to judge the distribution of residues
on Ramachandran plot: https://doi.org/10.1016/j.str.2020.08.005
Let me know if you have any questions.
Best regards,
Oleg Sobolev.
On Sun, Sep 6, 2020 at 9:12 PM Reza Khayat
Hi,
I'm trying to follow the protocol described in White et al., Structural principles of SNARE complex recognition by the AAA+ protein NSF e-life 2018
https://elifesciences.org/articles/38888
Here is the pertinent paragraph:
"To improve the Ramachandran statistics and geometry of the models, a two-parameter grid search of real space refinements was performed in which 3–5 macrocycles of global minimization and local grid search were performed in the presence of secondary structure restraints. First, a grid refinement search was performed for both target functions with around 1000 refinements each. For the *emsley* target function, *rama_weight* and *scale_allowed* were varied from 0.01 to 300; for the *oldfield* target function, a grid of refinements was performed over *plot_cutoff* values from 0.01 to 1.0 and *weight_scale* values from 0.1 to 300. Results were judged empirically and based primarily on a balance between *CCmask* and a minimal fraction of residues flagged by the program CaBLAM (Richardson et al., 2018 https://elifesciences.org/articles/38888#bib37) because focusing on the fraction of residues with favored *CCmask* and Ramachandran statistics alone often resulted in unrealistic models with serious problems (Figure 12 https://elifesciences.org/articles/38888#fig12, Table 2 https://elifesciences.org/articles/38888#table2)."
There are no differences in the refined structures regardless of what parameters I change. Attached is the input file I use for phenix.real_space_refine (1.18.2). Altering the oldfield weight_scale (0.1 to 300) and plot_cutoff (0.1 to 0.5) makes no difference. Any help is highly appreciated.
Best wishes, Reza
Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]