Re: [ccp4bb] Way to resolve Ramachandra outliers in a structure

[Medhanjali DasGupta]

Very helpful, thank you so much!

Medhanjali

On Fri, Mar 3, 2023, 10:48 AM Nicholas Clark  wrote:

> Hi Medhanjali,
>
> In Coot, there are two additional options for "automated" correction of
> Ramachandran outliers. You can find them under "Calculate".
>
> For the entire structure in the "Calculate->all molecule" tab, select
> Refine/Improve Ramachandran Plot. For a specific region, you can use the
> "Calculate->fit loop->fit loop by rama search". These will attempt to fit
> to the Ramachandran plot but may still revert during subsequent refinement.
> Hope this helps.
>
> Best,
>
> Nick Clark
>
> On Fri, Mar 3, 2023 at 11:24 AM Medhanjali DasGupta <
> medhanjalidasgu...@gmail.com> wrote:
>
>> Hello all!
>>
>> Is there an easy way to fix the backbone angles in a protein structure to
>> fix the Ramachandran outliers in said structure?
>>
>> Coot has the "Edit backbone torsions" option but wondering if there's any
>> other tools available in coot or elsewhere?
>>
>> Thanks
>> Medhanjali Dasgupta
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
>>
>
>
> --
> Nicholas D. Clark (He/Him)
> PhD Candidate
> Malkowski Lab
> University at Buffalo
> Department of Structural Biology
> Jacob's School of Medicine & Biomedical Sciences
> 955 Main Street, RM 5130
> Buffalo, NY 14203
>
> Cell: 716-830-1908
>



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Re: [ccp4bb] Way to resolve Ramachandra outliers in a structure

[Nicholas Clark]

Hi Medhanjali,

In Coot, there are two additional options for "automated" correction of
Ramachandran outliers. You can find them under "Calculate".

For the entire structure in the "Calculate->all molecule" tab, select
Refine/Improve Ramachandran Plot. For a specific region, you can use the
"Calculate->fit loop->fit loop by rama search". These will attempt to fit
to the Ramachandran plot but may still revert during subsequent refinement.
Hope this helps.

Best,

Nick Clark

On Fri, Mar 3, 2023 at 11:24 AM Medhanjali DasGupta <
medhanjalidasgu...@gmail.com> wrote:

> Hello all!
>
> Is there an easy way to fix the backbone angles in a protein structure to
> fix the Ramachandran outliers in said structure?
>
> Coot has the "Edit backbone torsions" option but wondering if there's any
> other tools available in coot or elsewhere?
>
> Thanks
> Medhanjali Dasgupta
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
>


-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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[ccp4bb] Way to resolve Ramachandra outliers in a structure

[Medhanjali DasGupta]

Hello all!

Is there an easy way to fix the backbone angles in a protein structure to
fix the Ramachandran outliers in said structure?

Coot has the "Edit backbone torsions" option but wondering if there's any
other tools available in coot or elsewhere?

Thanks
Medhanjali Dasgupta



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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

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