Hi Bernhard,
I could see the key binding in coot under the tab extension/settings/key
bindings as a user-defined key binding (button)
And when I pressed this button or typed shift+R, there was nothing happening
on the screen.
But you are right, it didn't work because I just tried the sphere refinement
after starting up coot, and no map was selected. I didn't realize that.
Normally, when you e.g. do real space refinement it always asks for a map
the first time, which it didn't for sphere refinement...
Thanks a lot for pointing that out to me!
And thanks to everybody else who helped: today I learned a lot more about
coot!
Have a nice evening,
Sara
Summary of how to do sphere refinement:
Prepare a .coot.py file carrying only the appropriate code snippet, stored
in your home folder (or add the code to your already existing ~/.coot.py)
Choose a map to refine against in coot.
:)
-----Ursprüngliche Nachricht-----
Von: Bernhard Lohkamp [mailto:[log in to unmask]]
Gesendet: Dienstag, 12. Januar 2010 17:08
An: Sara Zueger, Biochemisches Inst.
Cc: [log in to unmask]
Betreff: Re: [COOT] how to do sphere refinement
Hi Sara,
> Ok, now, thanks to Miguel I figured out what I did wrong:
>
> I had to make a .coot.py file with only my new code inside.
>
> Key binding was now present.
How do you know?
> However sphere refinement still did not work.
How do you know?
> There was another error (which seems to be somehow similar to the error
> at the very beginning when I used the script from the coot documentary):
>
> from the terminal:
> -----------------------------------------------
>
> (graphics-general-key-press-hook 82)
> Key 82 not found in bindings
This is a guile message, i.e. no key binding for 82 in guile (*).
> imol: 0 residues: [['L', 251, ''], ['L', 28, ''], ['L', 252, ''], ['S',
> 7, ''], ['L', 25, ''], ['S', 161, ''], ['L', 27, ''], ['S', 104, ''],
> ['S', 178, ''], ['L', 253, ''], ['S', 199, ''], ['L', 26, ''], ['S',
> 207, ''], ['L', 3, ''], ['L', 2, ''], ['S', 13, '']]
This is from python which you just successfully included (there is a
line in the script which prints this, i.e. shows you which residues will
be used in refinement).
If nothing happens then, i.e you dont get refinement (residues show up
in white and an accept/reject dialog appears), then you maybe havent set
a map to refine to.
>
> ------------------------------------------------
>
> L251 is my first NAG, and L25 the ASN to which it is linked and then
> some waters on chain S...
>
>
> Any suggestions ?
>
> Sorry for the trouble (I start to feel a little awkward...)
B
(*) note to self (and Paul): sort out the coexistence of guile and
python key bindings.
(x) note to self (and Paul): we should check for a refinement map before
using refine_residues.
--
***************************************************
Dr. Bernhard Lohkamp
Assistant Professor
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487673
fax: (+46) 08-327626
email: [log in to unmask]
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