Hi Reza,

If you have the new scope in the .eff file, it will be used at all times. The behavior that you observed confirms it. You have the new scope, but was putting weight_scale=300 into the old one, which was ignored. I believe you should be able to remove the old scope from the .eff file to avoid any confusion.

For the emsley target function, rama_weight and scale_allowed
These are moved to ramachandran_plot_restraints.emsley subscope and named "weight" and "scale_allowed".

the oldfield target function, a grid of refinements was performed over plot_cutoff values from 0.01 to 1.0 and weight_scale
These are moved to ramachandran_plot_restraints.oldfield subscope and the names are the same.

Best regards,
Oleg Sobolev.

On Wed, Sep 9, 2020 at 8:37 AM Reza Khayat <rkhayat@ccny.cuny.edu> wrote:

Hi Oleg,


I figured it out, but please correct me if I'm wrong. Setting 


    peptide_link {
      ramachandran_restraints = False

and 
    ramachandran_plot_restraints {
      enabled = True


imposes the new enhanced protocol. Setting both to true does not impose the new protocol.


Best wishes,
Reza


Reza Khayat, PhD
Associate Professor 
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
From: phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Reza Khayat <rkhayat@ccny.cuny.edu>
Sent: Wednesday, September 9, 2020 9:21 AM
To: Oleg Sobolev
Cc: PHENIX user mailing list
Subject: Re: [phenixbb] [EXTERNAL] Re: Improving Ramachandran plot
 

Hi Oleg,


Thanks for the response. 

1. Yes, I am using the command line version

2. The run.eff file that I had included in my e-mail includes the lines you sent. I would appreciate the help in converting the old-style into the new style. ​


Best wishes,
Reza


Reza Khayat, PhD
Associate Professor 
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
From: Oleg Sobolev <osobolev@lbl.gov>
Sent: Tuesday, September 8, 2020 7:43 PM
To: Reza Khayat
Cc: PHENIX user mailing list
Subject: [EXTERNAL] Re: [phenixbb] Improving Ramachandran plot
 
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 <rkhayat@ccny.cuny.edu> wrote:

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) because focusing on the fraction of residues with favored CCmask and Ramachandran statistics alone often resulted in unrealistic models with serious problems (Figure 12, Table 2)."


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
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