I'd second the request for water picking using both maps. ARP/wARP does this, but with either program you are going to have to refine B factors after picking. Its much more convient working in COOT because of the excellent water validation tools, the automatic symmetry generation for hand picked waters, and the blob warning.
-----Original Message-----
From: Thomas Stout [mailto:[log in to unmask]]
Sent: Thu 11/22/2007 12:41 PM
To: [log in to unmask]
Subject: Re: Enhancement requests
With regard to placing waters, these are very nice requests & I'd like to throw in one more "wrinkle" -- something I've often wished auto-water-pickers would implement was selecting only peaks that appear in two density maps, say both the Fo-Fc map and the mFo-nFc (2,1 or 3,2; your pick) map. This would cut down on many of the spurious peaks that only appear in the difference map......
Cheers,
Tom
________________________________
From: Mailing list for users of COOT Crystallographic Software on behalf of Roni Gordon
Sent: Thu 11/22/2007 5:19 AM
To: [log in to unmask]
Subject: Re: [COOT] Enhancement requests
I'll throw in my request too, then -- perhaps after adding a water
molecule, coot would be so kind as to display the "nearest neighbour"
environment distances to the newly added O atom? Yet another "save a
click" request.
And speaking of delete waters... are there any plans to implement a
criterion regarding # of H-bonds?
Is there any way to turn off distances to C-atoms (e.g. hydrophobic
neighbours) and just leave the polar contacts? I know that coot colours
them different already... just a thought.
Roni
On Wed, 2007-11-21 at 01:26 +0000, Mark Mayer wrote:
> God I love this program ... In addition to building refinement I now use it for adding and checking
> solvent (rather than ARP/wARP) ... which brings me to my request. Pure lazy bones on my part.
>
> After having run the check waters script, built a list of suspects, and turned on delete waters to
> pounce on bad guys, it would be so nice if space bar could be made to jump to next atom in check
> list, rather than next atom in water chain. Saves having to click back on list, and sometimes I miss
> where I am, because active water button (actually all active buttons) are hard to distinguish from the
> off state - maybe more shading/red or something here.
>
> Thanks, MLM.
This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.
Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.
|