On 29/12/13 14:51, Oliver Clarke wrote:
> Thanks Paul - Initially I tried rigid body + 10 cycles of
> morph_fit_chain at a radius of 11 Å - that seemed to work better than
> rigid body alone, although some of the larger domain shifts are still
> not corrected.
>
> Perhaps I need a larger radius for that - I’ll try doing 10 cycles at
> a radius of 20 Å, followed by 5 each at 10 Å and 5 Å.
Yes... that will help somewhat, I imagine. But I suspect an unsharpened
map is what you (also) want.
>
> Regarding blurred maps, is there any way to adjust the sharpening
> factor on the fly in a script, in such a manner that it can be
> returned to normal afterwards?
Yes.
sharpen(imol, 200) # blurs
and
sharpen(imol, 0) # restores
You can see from that, that the argument is by how much the original
data should be sharpened.
>
> Also, Coot seems to write out a copy of the pdb to the coot-backup
> directory after every cycle of morph_chain - is there any way to turn
> off this behavior?
Yes.
turn_off_backups(imol)
I routinely do this for looped functions. You might like to try the
with_no_backups() macro/function.
> Normally it would be fine, but with a few hundred operations that adds
> up to several GB of backup files, which probably slows down the whole
> process somewhat.
Probably.
As an aside, you might want to adjust these settings in your ~/.coot.py
file:
clear_out_backup_run_n_days = 7 # run every 7 days
clear_out_backup_old_days = 7 # Files older than 7 days are
considered for deletion
Paul.
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