Re: [modeller_usage] Per-residue RMSD

[Oscar Conchillo-Solé <>]

Hi For that purpose I use a program call profit: http://www.bioinf.org.uk/software/profit/ There is a function called "RESIDUE" which will give what you want. You will have to read the manual in order to se choose the right options for you

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    Hi
    For that purpose I use a program call profit:
    
    http://www.bioinf.org.uk/software/profit/
    
    There is a function called "RESIDUE" which will give what you want.
    You will have to read the manual in order to se choose the right
    options for you (READALIGNMENT, LIMIT, ZONE, ATOMS, etc) but it will
    give you what you want.
    
    I hope this helps
    OCS
    
Oscar Conchillo Solé
Computational Biology Group
Data Center Manager, Sysadmin and Bioinformatics
Institut de Biotecnologia i Biomedicina (UAB)
mail: " moz-do-not-send="true">
telf:0034 93586 8939; 0034 93581 4431

On 15/4/22 19:48, Modeller Caretaker wrote:

> On
>       4/13/22 11:00 PM, Karolina Mitusińska (Markowska) wrote: 
> > I would like to compare my predicted model
> >         with a crystal structure. I know how to calculate RMSD between
> >         these two models, but I would also like to have more detailed
> >         information on the RMSD between corresponding atoms, for example
> >         C-alphas. 
> >       
>       
>       Perhaps I am misunderstanding what you want to do here, but the
>       RMSD between a single pair of atoms is just the Cartesian
>       distance. So you can call superpose() to first fit the two models:
>       
>       https://salilab.org/modeller/10.2/manual/node255.html
>       
>       
>       Then access the two Atom objects you're interested in and
>       calculate the distance in Python using their x,y,z coordinates: 
>       https://salilab.org/modeller/10.2/manual/node383.html
>       
>       
>       If you mean you want the RMSD over *all* C-alphas or some other
>       subset, first do superpose() to fit the models, then select that
>       subset of atoms and do superpose() again with fit=False. This
>       won't change the superposition but will report the RMSD of the
>       subset. 
>       
>           Ben Webb, Modeller Caretaker 
>