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Yes, B factors are indeed a super-absorbent sponge for model bias. Best to re-set those before re-refinement. But you should also do something with the coordinates, and probably the occupancies too. My jiffy to add to Graeme's list of options is this script: http://bl831.als.lbl.gov/~jamesh/scripts/jigglepdb.awk It has a variety of options, including separate rms shifts for coordinates, B factors and occupancies (shift=, Bshift=, and Oshift=), and a special option called "shift=byB" that moves coordinates in accordance to the atom's B factor. The distribution of the shifts can be Gaussian (default), Lorentzian or uniform sphere. The latter is useful if you want to avoid very large shifts (see below). By default, one conformer (i.e. A, B, C) is randomly given an occupancy of "1" for all residues and all the other conformers are given zero. This is an attempt to simulate the cell-to-cell variation of the structure, which can only have one conformer at a time. If you specify "keepocc=1" this behavior gets turned off. Any non-zero "Oshift" will add random noise to all occupancies. I'm sure all this functionality would be easy to re-create using CCTBX as well. I've actually played around with "jiggling" pdb files a fair bit. Turns out that in order to remove "bias" completely you need to kick the atoms by an rms distance comparable to the relevant resolution. That is, 1.5 A for 1.5 A spots, but also 6 A if you want to un-bias 6 A spots. This tends to be outside the radius of convergence of most refinement programs. In fact, kicking atoms by as little as 0.5 A can often result in some side chains falling into alternate rotamers and the like. Waters can also fall out of place and drift into nearby pockets of liberated density. You can do a "cleanup" after re-refinement to correct for such gross errors. Looking for the largest differences between starting and re-refined models generally lights these up. But before you "fix" these things you have to start asking questions about what "bias" really is. It seems a popular "bias-reduction" approach is to re-run Phaser or other molecular replacement job, but all that really does is put your model onto an alternative origin or asu choice. These choices are arbitrary, of course, and crystallographically equivalent. Once you have corrected for the origin shift using something like "reforigin" you can see that all your Phaser run has produced is a slight rigid-body shift relative to where you started. Hardly a bias-removal technique. So, what is "bias"? We tend to think of "bias" the same way we think of "twinning": as a synonym for "evil". Something to be kept out of our models and data at all costs. But if you think about it a bit you may realize that even having the backbone structure itself intact is a form of "bias". As in you are "biasing" your model to resemble the overall fold you originally assigned to the structure. You may or may not be all that worried about this. And if you are certain that the main chain trace is correct, then enforcing it in further analysis is not "bias", it is "prior knowledge". I suppose knowing the difference between these two things is what science is all about. So, I'd say that "resetting" a structure depends on what aspect of the structure you're trying to test. If you made a mistake in the backbone trace, or even a rotamer assignment, then doing a 0.5A jiggle isn't going to reset that mistake. But if your trying to test the influence of data between 1.5 A and 1.4 A, then I'd say do a jiggle of at least half that distance. -James Holton MAD Scientist On 8/17/2017 8:40 AM, Robbie Joosten wrote: > > In most cases resetting the B-factors would be enough to perturb the > model. > > Cheers, > > Robbie > > Sent from my Windows 10 phone > > *From: *Andrew Leslie <mailto:[log in to unmask]> > *Sent: *17 August 2017 17:29 > *To: *[log in to unmask] <mailto:[log in to unmask]> > *Subject: *Re: [ccp4bb] "reset" a structure before re-refinement > > Hi Graeme, > > You can do this with PDBSET, keyword NOISE > Cheers, > > > Andrew > > > On 17 Aug 2017, at 16:17, Graeme Winter > <[log in to unmask]> wrote: > > > > Dear All, > > > > Is there a protocol out there to gently perturb atomic positions so > that re-running refinement can essentially put them back without bias > from the original refinement? In particular, if trying to perform the > Karplus and Diederichs paired refinement protocol, I do not want to > run the lower resolution refinements with the "memory" of the weak > high resolution data present... and only have the refined structure to > work from... > > > > Am using refmac5, but any pdb randomizer would hit the spot > > > > Many thanks Graeme > > > > -- > > This e-mail and any attachments may contain confidential, copyright > and or privileged material, and are for the use of the intended > addressee only. 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