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 location supposed to support? A specific strong claim or hypothesis demands the corresponding degree of solid evidence and high plausibility of the model. If the pose of your ligand is a crucial part of your claim or hypothesis (and a small molecule at a specific location in a specific conformation is generally a pretty strong claim), both the electron density and environment, as well as the plausibility given prior knowledge need to be convincing. Also recall that the RSCC is a crude measure generally applied to the entirety of your ligand. So you may have a somewhat lower RSCC in certain situations like a piece of a ligand being floppy, or, with very weak density, suffer from solvent intrusion in omit maps (although in this context I caution against a variety of tricks and methods if you you do not exactly know what you are doing). Even in such cases, the rest needs to make sense. Really bad ligands that score high in the 'bad' lists generally exhibit multiple features like poor density fit, no convincing binding site contacts, collisions, and poor stereochemistry. Your 0.8 RSCC is not super good, but not bad either. You need to make the case to the reviewers based on your specific claim/case. It is important not mistake this disclaimer for a postmodern argument justifying ‘Anything goes’. Again, if one’s claim is to support a certain mechanistic detail or ligand pose, one better cough up some convincing, properly generated and adequately contoured (difference omit) electron density and a model that is not delusional in view of basic stereochemistry. A problem I see is as a consequence of the 'positive results only' philosophy, in order to make the high impact list, it is almost imperative to make powerful statements and associated exaggerated claims. The moment you voice the slightest doubt (i.e. meaning you are in fact honest about what you can say with a given certainty and what is doubtful), some reviewer (usually the 3rd one) will make a clueless comment about R-merge and it is Acta F. :-) Best, BR ----------------------------------------------------------------- Bernhard Rupp b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ ----------------------------------------------------------------- The hard part about playing chicken is to know when to flinch ----------------------------------------------------------------- On Thu, Feb 23, 2017 at 5:56 AM, Mohamed Noor <mohamed.n...@staffmail.ul.ie> 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 >
