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.
