Hi Jacob, I would agree with Nat. I think with the 3A data and the local environment, putting a Cl there is only justified by the need of supressing a peak in the difference map. Yes the peak can really be a Cl or a water or a mixture of the two (I would like to do an experiment with my Cl containing data, which has Cl sites identified by iodide data, see what would happen when resolution is reduced and SNR is weakened). But we have to be aware that with 3A data there can be significant phase errors that lead to generation of features that are either not there or not so significant as it appears. In the past I have even seen a structure that puts a putative sugar (completely unknown type of glycosylation) in a blob in >3A structure because the authors thought the blob looked like the particular sugar residue. The practice of putting a ion or a small ligand simply for supressing difference peaks, to my view is not good practice for two reasons: 1) compared to protein residues, ions, and small ligands in low res cases, lack the geometric constraints and can be easily abused for the purpose of flattening the difference maps (admittedly a lot of water molecules is doing that, but we are told to be very careful with that already); 2) practically it makes searching/analysis of the structures in PDB a lot more difficult that it should be. It would be much easier for users to search an incomplete but reliable database than one that contains a mixture of real and wrong data, especially considering that not all users are experts on interpreting electron density maps or protein structures. Zhijie
From: Keller, Jacob Sent: Wednesday, January 21, 2015 1:17 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] chloride or water I reiterate that assigning a chloride is not “wild speculation” or “just making something up” in light of what we know about the situation. I see your point about not knowing that it’s a chloride, but I think you would agree that it is certainly more likely a chloride than map-noise, and perhaps more likely than water as well. Would you agree that chloride is the best guess, at least? What are the options for that blob, and what is the probability of each? I think you want to make sure people don’t get misled by it, which is a good point and a noble aspiration. I would argue that “not choosing” is here, as everywhere else, indeed choosing. And if you choose nothing here, you are almost certainly wrong, given the data. Some might be surprised or misled that a cavity like that would be totally empty, and the map density is unequivocal evidence that something is indeed there. So what now? Maybe a solution would be dummy atoms, maybe call them agnostons (agn) or something? Perhaps this is a basic disagreement about what a protein structure model represents, with one opinion being “that which we can rely upon confidently” and the other being “that which is most likely considering the data.” Each has advantages depending on one’s goals. Since the PDB is certainly tainted by structures modeled in accordance with the “most likely” outlook, one now has to be cautious about all structures. I prefer the latter since I would try to be responsible/skeptical enough to go back to the original crystal data before making important conclusions based on it. Maybe there should be a disclaimer printed in each PDB file… JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nat Echols Sent: Wednesday, January 21, 2015 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] chloride or water On Wed, Jan 21, 2015 at 9:05 AM, Keller, Jacob <kell...@janelia.hhmi.org> wrote: Not sure why there is this level of suspicion about the poor halide when waters generally get assigned so haphazardly. I would say that there are probably more “wrong” waters in the PDB than wrong chlorides, but there’s not much fuss about that. Great, so leave it empty instead of just making something up. Perhaps future generations will figure out a more rigorous and quantitative method for handling such features than guessing based on screenshots posted to a mailing list. At this resolution water placement is difficult to justify anyway - and since neither the scattering properties nor the coordination distances are especially accurate, trying to assign chemical identity in the absence of any supporting information (for example anomalous data) is especially futile. (Although at least in this case the resolution is an obvious red flag - to a crystallographer, anyway - indicating that any lighter ions shouldn't be taken very seriously. Other biologists, of course, may be more trusting.) -Nat
