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Thanks Miguel, 

but is there another way to do this sphere refinement? I'm working on a
shared computer and have no administrator rights and also no experience with
python/file handling of coot.

Or else, if there is no other way, can somebody explain me exactly what I
have to do/type (like copying a coot.py file into a local folder and change
that, but how then to tell coot to use this file?)

Thanks a lot!

Sara

-----Ursprüngliche Nachricht-----
Von: Mailing list for users of COOT Crystallographic Software
[mailto:[log in to unmask]] Im Auftrag von Miguel Ortiz Lombardia
Gesendet: Freitag, 8. Januar 2010 18:17
An: [log in to unmask]
Betreff: Re: [COOT] how to do sphere refinement

Hi Sara,

I have the python version in my ~/.coot.py file:

<---cut--->
def key_binding_func_1():
    from types import ListType
    active_atom = active_residue()
    if (not active_atom):
        add_status_bar_text("No active residue")
    else:
        imol      = active_atom[0]
        chain_id  = active_atom[1]
        res_no    = active_atom[2]
        ins_code  = active_atom[3]
        atom_name = active_atom[4]
        alt_conf  = active_atom[5]
        centred_residue = active_atom[1:4]
        other_residues = residues_near_residue(imol, centred_residue, 5)
        all_residues = [centred_residue]
        if (type(other_residues) is ListType):
            all_residues += other_residues
        print "imol: %s residues: %s" %(imol, all_residues)
        refine_residues(imol, all_residues)
            
add_key_binding("Refine residues in a sphere", "R", lambda:
key_binding_func_1())
<---cut--->

In principle, if you place your scheme script in your ~/.coot file it will
work next time you open coot (without having to load the script).

Having said that, it would be great if sphere refinement would take into
account atoms on residues from symmetry-related molecules (perhaps it does
already so? I tried a few weeks/months ago...)

HTH,


Miguel

Le 8 janv. 2010 à 17:22, Sara Züger a écrit :

> Good evening everybody,
> 
> I wanted to try sphere refinement for the real space refinement of a
> glycosidic bond, however it did not work out... (Coot 0.6-pre-1/Durham
> (revision 2264)) 
> That's what I did:
> 
> I copied this script into a text file:
> 
> (add-key-binding "Refine residues in a sphere" "R"
>    (lambda ()
>      (let ((active-atom (active-residue)))
>        (if (list? active-atom)
>            (let* ((centred-residue (list-head (cdr active-atom) 3))
>                   (imol (car active-atom))
>                   (other-residues (residues-near-residue 
>                                    imol centred-residue 3.5))
>                   (all-residues (if (list? other-residues)
>                                     (cons centred-residue other-residues)
>                                     (list centred-residue))))
>              (refine-residues imol all-residues))))))
> 
> and then loaded into coot by using "run script". Then I centered on an
atom
> of my glycan and pressed shift-r, or opened the key bindings under
> extensions/settings and used the button for my new key binding.
> Nothing happened, but I got this error message in the terminal, where I
> started coot:
> 
> (graphics-general-key-press-hook 82)
> 82 not found in key_bindings
> (graphics-general-key-press-hook 114)
> 114 not found in ((82 "R" "Refine residues in a sphere" #<procedure #f
()>))
> 114 not found in key_bindings
> 
> What did I miss or do wrong?
> 
> Thanks for you help!
> 
> Sara
> 
> -- 
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> 

-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
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