Dear Matthias, the idea of paired refinement is to quantify the amount of information in your structure. For that purpose it is most likely counterproductive to disturb your parameter at all! In the worst case you end up comparing different structures.
Use the very same structure, do not reset B-values, do not stir or shake, just refine until the target value stabilises. With refmac5 and shelxl this happens usually quite quickly, a few hundred cycles should be sufficient. Best regards, Tim On Sunday, August 20, 2017 5:06:42 PM CEST Matthias Barone wrote: > Thanks James for your reply. I my naive way, I thought that when doing > paired refinement, it would be sufficient to run several cycles of > refinement with simulated annealing followed by a thorough real space > rebuilding. What is your thought about using the "jiggling" of additional > cartesian annealing steps (phenix) to check the influence of, say, an > additional 0.1A outermost shell? I used paired refinement over a couple of > cycles and thoroughly deleted what was not visible anymore. Less for the > removal of bias, but more to increase degrees of freedom... But now that I > read your answer, I have the impression that this was not enough to remove > bias of the sidechains? > > matthias > > >>> James Holton <jmhol...@slac.stanford.edu> 08/19/17 7:23 PM >>> > > 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: > > *.EmailQuote { > margin-left: 1.0pt; > padding-left: 4.0pt; > border-left: rgb(128,0,0) 2.0px solid; > } > p.x_MsoNormal, li.x_MsoNormal, div.x_MsoNormal { > margin: 0.0cm; > font-size: 11.0pt; > font-family: Calibri , sans-serif; > } > a:x_link, span.x_MsoHyperlink { > color: blue; > text-decoration: underline; > } > a:x_visited, span.x_MsoHyperlinkFollowed { > color: rgb(149,79,114); > text-decoration: underline; > } > *.x_MsoChpDefault { > } > div.x_WordSection1 { > } > 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 > Sent: 17 August 2017 17:29 > To: CCP4BB@JISCMAIL.AC.UK > 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 > > <graeme.win...@diamond.ac.uk> 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 -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A
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