Surely using an absolute sigma cut-off is not a very sensible thing to
do - given that sigma is a function of so many different things that
have nothing to do with noise?
(Has anybody explored using local non-protein rmsd as sigma?)
phx.
On 07/06/2011 22:58, Seth Harris wrote:
Thanks Paul,
You think of everything, if only I always knew how to find it...
I added this line to my key bindings:
(add-key-binding "Goodbye weak waters" "z" (lambda ()
(delete-checked-waters-baddies 0 300 0.8 2.0 3.8 0 0 1)))
which followed from your post with arguments of imol, b factor limit,
sigma level limit, min dist, max dist, part_occ_contact_flag,
zero_occ_flag, logical_and_or_flag
So as advertised this seems to remove mostly the weak waters below 0.8
sigma of the (current?) map. And I was generous on the B factors and
the distances since often I find that a weak water near a good one can
taint the good one by its proximity, so best to remove the weak before
checking the remaining for distance.
Which brings to mind is there a "check-checked-waters-baddies" that I
could key bind?
Thanks a bunch,
Seth
On Fri, Jun 3, 2011 at 4:37 PM, Paul Emsley
<[email protected] <mailto:[email protected]>> wrote:
On 03/06/11 23:11, Seth Harris wrote:
Hi all,
I often use the Check/Delete waters dialog to delete only
those waters below 0.8 level in the map. I do this often
enough that it is high time to find/create a script version,
preferably even something I could launch from the command
line, or barring that maybe could generate a single-click
button on the main menu/control panel.
Would that be as simple as falling off a log for some out
there to give me pointers or a template to work from?
Basically it is scripting whatever that "Validate >
Check/Delete waters" dialog is doing.
Thanks so much,
Seth
Maybe this will be of some use?
http://lmb.bioch.ox.ac.uk/coot/doc/coot/delete_002dchecked_002dwaters_002dbaddies.html#delete_002dchecked_002dwaters_002dbaddies
If you need some help working that up into a menu item we can do
that tomorrow.
Paul.
