[phenixbb] [EXTERNAL] Re: Improving Ramachandran plot

Oleg Sobolev osobolev at lbl.gov
Wed Sep 9 09:49:20 PDT 2020


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 at 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 at phenix-online.org <
> phenixbb-bounces at phenix-online.org> on behalf of Reza Khayat <
> rkhayat at 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 at 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
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1016_j.str.2020.08.005&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&s=ptg6ZgZREaTRrW9ujd0LnZ-8kkjQnOgvn0w4NVpj8jI&e=>
>
> Let me know if you have any questions.
>
> Best regards,
> Oleg Sobolev.
>
> On Sun, Sep 6, 2020 at 9:12 PM Reza Khayat <rkhayat at 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
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_38888&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&s=AL0jOsHeTv1ypmAgBkrS4fg6oj-WdYhsXDJ4qWcKh50&e=>
>>
>>
>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_38888-23bib37&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&s=A-IYsxXhwe3dvl7oZ8JRr0rxyZ4W29522VR7YCPRmKg&e=>)
>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_38888-23fig12&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&s=e7ESAeeMjGInzQkzBfSgzzZPRTccskQn25ODvsw4nlQ&e=>
>> , Table 2
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_38888-23table2&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&s=lgVCnWzCNio89ZUuhejZ7-iD0MwdtumGbIm5-yMuYLw&e=>
>> )."
>>
>>
>> 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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