Hi Francis,
Once I had asked Pavel Afonine the same questions and these were his
suggestions but most of these can be implemented in phenix...
I guess there is no general/unified procedure to do this, and in most of
cases the tools and outcomes vary case by case.
Some general points:
- Removing p
-----Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Francis E Reyes
> Sent: Tuesday, August 23, 2011 8:37 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Modeling ligands in binding pockets when the density
> is weak.
>
> Seems
On Tue, 2011-08-23 at 15:01 -0400, Ed Pozharski wrote:
> On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote:
> > Seems to be a quiet day on the BB
>
> So you need an earthquake :)
>
> This is similar, imho, to the issue of disordered side chains:
>
> https://docs.google.com/spreadsheet/gfo
buffer may interfere
with proper ligand binding etc.
Best,
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Francis E Reyes
Sent: Tuesday, August 23, 2011 8:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Modeling ligands in binding pockets when the
David Schuller wrote:
On 08/23/11 15:01, Ed Pozharski wrote:
On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote:
Seems to be a quiet day on the BB
So you need an earthquake :)
Had one already, thanks.
Apparently sent from the vicinity of U. Maryland and JHSPH, thanks.
On 08/23/11 15:01, Ed Pozharski wrote:
On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote:
Seems to be a quiet day on the BB
So you need an earthquake :)
Had one already, thanks.
--
===
All Things Serve the Beam
=
(3a) You could give GraphENT a shot first and see if you can do magic on
visualizing the remaining bits of density.
You could also have multiple conformations, try refining with a low occupancy
first and see what you get back.
(3b) use AFitt
Jürgen
P.S. I would set the occupancy to zero for th
On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote:
> Seems to be a quiet day on the BB
So you need an earthquake :)
This is similar, imho, to the issue of disordered side chains:
https://docs.google.com/spreadsheet/gform?key=0Ahe0ET6Vsx-kdHVNa3VodUtfbVQtZ2pnUFcxQkx6RHc&hl=en_US&gridId=0#c
Seems to be a quiet day on the BB, so I propose this question:
Suppose you have a ligand in the binding pocket and some mediocre data (3 A or
so), the 'core' of the ligand is well defined in 2Fo-Fc map using the model
phases of your protein, however there are 'chains/tails' of the ligand whic
