Dear all
First of all, thanks for the replies here and off-list. I reprocessed the data
to 2 A, and modeled two copies of the ligand in each of the two protein NCS
molecules, without using NCS restraints for refinement. I also calculated an SA
omit map and a polder map. In the end, the ligand m
PanDDA tries to arrive at an objective score metric for presence:
http://biorxiv.org/content/early/2016/09/05/073411
But in the end, you still have to apply all the scientific rigour that
Bernard mentions.
On 23/02/2017 13:56, Mohamed Noor wrote:
Dear all
I think I have a ligand (substrate
At the risk of being redundant, I can only restate what I and many others
have posted before:
No simple answer or single universal statistic for your justified question
or concern exists. The crucial question to ask first is what hypothesis or
claims is your (ligand) model at that specific locatio
Well - I certainly would do more refinement - if something is bound there
will be other changes in solvent etc.
then search the difference map for peaks/ find ligand etc, and see what it
shows..
If your original model and this one are isomorphous you can also check the
Fobs-lig -Fobs-nolig Phi-no
Dear all
I think I have a ligand (substrate) placed in the active site of my model
correctly. The CC is 0.785, B factor of 60 A^2 which is roughly similar to the
neighboring residues and there was no ligand in my search model*. The data
extends to 2.2 A, although I think I can get something hig
