I am aware of to opposing schools of thought about modelling residues
without density:
- You can argue that since you know those residues are present in the
sequence, you can model them, even though there is no or hardly any
density. If you do so, you must set the occupancy of those
I think if you cant see it dont build it, but deposit the data..
There are many (most?) structures with missing loops
Eleanor
Pavel Afonine wrote:
This might help:
Acta Cryst. (1997). D53, 540-543 Local Improvement of
Electron-Density Maps
Pavel.
PS It will be implemented in PHENIX
On Tue, 2008-12-09 at 09:31 +0100, Tim Gruene wrote:
...you must set the occupancy of those residues to
zero...
I think this approach (which Tim is not supporting) makes no sense.
When I place an ATOM record into a pdb-file, what I am really saying is
based on the data, this atom's
I am trying to build a model of a 6 Da protein from the diffraction data
collected at 2.0 A resolution. There is a 10-residue stretch that has such bad
electron density that even at 0.4 sigma level one can hardly see any well
defined density for residues with long side chains.
My question
This might help:
Acta Cryst. (1997). D53, 540-543
Local Improvement of Electron-Density Maps
Pavel.
PS It will be implemented in PHENIX sometime in future, but for the
moment you will need to so some scripting.
On 12/8/2008 11:08 AM, Andy Millston wrote:
I am trying to build a model of
