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) 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 higher with manual
processing**. How can I be really sure that it is the ligand that I think it
is? And assuming you are a reviewer, what would you expect to see in a
manuscript?
* The unliganded model was obtained by molecular replacement using a search
model that did not have the ligand. I then used this model to simply do one
cycle of rigid-body refinement and another one cycle of coordinate/ADP
refinement.
** The data was auto-processed during data collection using xia2/XDS. I have a
dozen of datasets so I am just taking the autoprocessed ones and see if my
ligand is there.
Thanks.
Mohamed
