Re: [ccp4bb] should the final model be refined against full datset
Hi, yes, shifts depend on resolution indeed. See pages 75-77 here: http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf Pavel On Fri, Oct 14, 2011 at 7:34 PM, Ed Pozharski wrote: > On Fri, 2011-10-14 at 23:41 +0100, Phil Evans wrote: > > I just tried refining a "finished" structure turning off the FreeR > > set, in Refmac, and I have to say I can barely see any difference > > between the two sets of coordinates. > > The amplitude of the shift, I presume, depends on the resolution and > data quality. With a very good 1.2A dataset refined with anisotropic > B-factors to R~14% what I see is ~0.005A rms shift. Which is not much, > however the reported ML DPI is ~0.02A, so perhaps the effect is not that > small compared to the precision of the model. > > On the other hand, the more "normal" example at 1.7A (and very good data > refining down to R~15%) shows ~0.03A general variation with a variable > test set. Again, not much, but the ML DPI in this case is ~0.06A - > comparable to the variation induced by the choice of the test set. > > Cheers, > > Ed. > > -- > Hurry up, before we all come back to our senses! > Julian, King of Lemurs >
[ccp4bb] How to calculate energy?
Dear all, I obtained 20 peptide models (with lowest energy) calculated by CNS program. Now I want to make a table for structure statistics, but I don't know how to calculate Ebond Eangle Eimproper Evdw ENOE Ecdih Etotal , r.m.s. deviation from experimental constraints, and r.m.s. deviations from idealized geometry. Where can I get these information? Just from the peptide pdb file output by CNS, or using another software? And what is idealized geometry? Thanks! Huayue Li, Ph. D College of Pharmacy Pusan National University Geumjeong-gu, Jangjeon-dong Busan 609-735, Korea Tel: +82-51-510-2185
Re: [ccp4bb] should the final model be refined against full datset
On Fri, 2011-10-14 at 23:41 +0100, Phil Evans wrote: > I just tried refining a "finished" structure turning off the FreeR > set, in Refmac, and I have to say I can barely see any difference > between the two sets of coordinates. The amplitude of the shift, I presume, depends on the resolution and data quality. With a very good 1.2A dataset refined with anisotropic B-factors to R~14% what I see is ~0.005A rms shift. Which is not much, however the reported ML DPI is ~0.02A, so perhaps the effect is not that small compared to the precision of the model. On the other hand, the more "normal" example at 1.7A (and very good data refining down to R~15%) shows ~0.03A general variation with a variable test set. Again, not much, but the ML DPI in this case is ~0.06A - comparable to the variation induced by the choice of the test set. Cheers, Ed. -- Hurry up, before we all come back to our senses! Julian, King of Lemurs
Re: [ccp4bb] should the final model be refined against full datset
Each R-free flag corresponds a particular HKL index. Redundancy refers to the number of times a reflection corresponding to a given HKL index is observed. The final structure factor of a given HKL can be thought of as an average of these redundant observations. Related to your question, someone once mentioned that for each particular space group, there should be a preferred R-free assignment. As far as I know, nothing tangible ever came of that idea. James On Oct 14, 2011, at 5:34 PM, D Bonsor wrote: > I may be missing something or someone could point out that I am wrong and why > as I am curious, but with a highly redundant dataset the difference between > refining the final model against the full dataset would be small based upon > the random selection of reflections for Rfree?
Re: [ccp4bb] should the final model be refined against full datset
Now it would be interesting to refine this structure to convergence, with the original free set. If I understood correctly Ian Tickle has done essentially this, and the Free R returns essentially to its original value: the minimum arrived at is independent of starting point, perhaps within limitation that one might get caught in a different false minimum (which is unlikely given the miniscule changes you see). If that is the case we should stop worrying about "corrupting" the free set by refining against it or even using it to make maps in which models will be adjusted. This is a perennial discussion but I never saw the report that in fact original free-R is _not_ recoverable by refining to convergence. Phil Evans wrote: I just tried refining a "finished" structure turning off the FreeR set, in Refmac, and I have to say I can barely see any difference between the two sets of coordinates. From this n=1 trial, I can't see that it improves the model significantly, nor that it ruins the model irretrievably for future purposes. I suspect we worry too much about these things Phil Evans Now it would be interesting to refine this structure to convergence, with the original free set. If I understood correctly Ian Tickle has done essentially this, and the Free R returns essentially to its original value: the minimum arrived at is independent of starting point, perhaps within limitation that one might get caught in a different false minimum (which is unlikely given the miniscule changes you see). If that is the case we should stop worrying about "corrupting" the free set by refining against it or even using it to make maps in which models will be adjusted. This is a perennial discussion but I never saw the report that in fact original free-R is _not_ recoverable by refining to convergence. Indeed, perhaps we worry too much about such things. On 14 Oct 2011, at 21:35, Nat Echols wrote: On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang wrote: Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all data. "Useless" was too strong a word (it's Friday, sorry). I guess simulated annealing can address the model-bias issue, but I'm not totally convinced that this solves the problem. And not every crystallographer will run SA every time he/she solves an isomorphous structure, so there's a real danger of misleading future users of the PDB file. The reported R-free, of course, is still meaningless in the context of the deposited model. Would your argument also apply to all the structures that were refined before R-free existed? Technically, yes - but how many proteins are there whose only representatives in the PDB were refined this way? I suspect very few; in most cases, a more recent model should be available. -Nat
Re: [ccp4bb] should the final model be refined against full datset
Dear Gerard, I'm very happy for the discussion to be on the CCP4 list (or on the IUCR forums, or both). I was only trying to not create too much traffic. All the best, Tom T >> Dear Tom, >> >> I am not sure that I feel happy with your invitation that views on >> such >> crucial matters as these deposition issues be communicated to you >> off-list. >> It would seem much healthier if these views were aired out within the BB. >> Again!, some will say ... but the difference is that there is now a forum >> for them, set up by the IUCr, that may eventually turn opinions into some >> form of action. >> >> I am sure that many subscribers to this BB, and not just you as a >> member of some committees, would be interested to hear the full variety of >> views on the desirable and the feasible in these areas, and to express >> their >> own for everyone to read and discuss. >> >> Perhaps John Helliwell can elaborate on this and on the newly created >> forum. >> >> >> With best wishes, >> >> Gerard. >> >> -- >> On Fri, Oct 14, 2011 at 04:56:20PM -0600, Thomas C. Terwilliger wrote: >>> For those who have strong opinions on what data should be deposited... >>> >>> The IUCR is just starting a serious discussion of this subject. Two >>> committees, the "Data Deposition Working Group", led by John Helliwell, >>> and the Commission on Biological Macromolecules (chaired by Xiao-Dong >>> Su) >>> are working on this. >>> >>> Two key issues are (1) feasibility and importance of deposition of raw >>> images and (2) deposition of sufficient information to fully reproduce >>> the >>> crystallographic analysis. >>> >>> I am on both committees and would be happy to hear your ideas >>> (off-list). >>> I am sure the other members of the committees would welcome your >>> thoughts >>> as well. >>> >>> -Tom T >>> >>> Tom Terwilliger >>> terwilli...@lanl.gov >>> >>> >>> >> This is a follow up (or a digression) to James comparing test set to >>> >> missing reflections. I also heard this issue mentioned before but >>> was >>> >> always too lazy to actually pursue it. >>> >> >>> >> So. >>> >> >>> >> The role of the test set is to prevent overfitting. Let's say I have >>> >> the final model and I monitored the Rfree every step of the way and >>> can >>> >> conclude that there is no overfitting. Should I do the final >>> refinement >>> >> against complete dataset? >>> >> >>> >> IMCO, I absolutely should. The test set reflections contain >>> >> information, and the "final" model is actually biased towards the >>> >> working set. Refining using all the data can only improve the >>> accuracy >>> >> of the model, if only slightly. >>> >> >>> >> The second question is practical. Let's say I want to deposit the >>> >> results of the refinement against the full dataset as my final model. >>> >> Should I not report the Rfree and instead insert a remark explaining >>> the >>> >> situation? If I report the Rfree prior to the test set removal, it >>> is >>> >> certain that every validation tool will report a mismatch. It does >>> not >>> >> seem that the PDB has a mechanism to deal with this. >>> >> >>> >> Cheers, >>> >> >>> >> Ed. >>> >> >>> >> >>> >> >>> >> -- >>> >> Oh, suddenly throwing a giraffe into a volcano to make water is >>> crazy? >>> >> Julian, King of >>> Lemurs >>> >> >> >> -- >> >> === >> * * >> * Gerard Bricogne g...@globalphasing.com * >> * * >> * Global Phasing Ltd. * >> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * >> * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * >> * * >> === >>
Re: [ccp4bb] should the final model be refined against full datset
I may be missing something or someone could point out that I am wrong and why as I am curious, but with a highly redundant dataset the difference between refining the final model against the full dataset would be small based upon the random selection of reflections for Rfree?
Re: [ccp4bb] should the final model be refined against full datset
Dear Tom, I am not sure that I feel happy with your invitation that views on such crucial matters as these deposition issues be communicated to you off-list. It would seem much healthier if these views were aired out within the BB. Again!, some will say ... but the difference is that there is now a forum for them, set up by the IUCr, that may eventually turn opinions into some form of action. I am sure that many subscribers to this BB, and not just you as a member of some committees, would be interested to hear the full variety of views on the desirable and the feasible in these areas, and to express their own for everyone to read and discuss. Perhaps John Helliwell can elaborate on this and on the newly created forum. With best wishes, Gerard. -- On Fri, Oct 14, 2011 at 04:56:20PM -0600, Thomas C. Terwilliger wrote: > For those who have strong opinions on what data should be deposited... > > The IUCR is just starting a serious discussion of this subject. Two > committees, the "Data Deposition Working Group", led by John Helliwell, > and the Commission on Biological Macromolecules (chaired by Xiao-Dong Su) > are working on this. > > Two key issues are (1) feasibility and importance of deposition of raw > images and (2) deposition of sufficient information to fully reproduce the > crystallographic analysis. > > I am on both committees and would be happy to hear your ideas (off-list). > I am sure the other members of the committees would welcome your thoughts > as well. > > -Tom T > > Tom Terwilliger > terwilli...@lanl.gov > > > >> This is a follow up (or a digression) to James comparing test set to > >> missing reflections. I also heard this issue mentioned before but was > >> always too lazy to actually pursue it. > >> > >> So. > >> > >> The role of the test set is to prevent overfitting. Let's say I have > >> the final model and I monitored the Rfree every step of the way and can > >> conclude that there is no overfitting. Should I do the final refinement > >> against complete dataset? > >> > >> IMCO, I absolutely should. The test set reflections contain > >> information, and the "final" model is actually biased towards the > >> working set. Refining using all the data can only improve the accuracy > >> of the model, if only slightly. > >> > >> The second question is practical. Let's say I want to deposit the > >> results of the refinement against the full dataset as my final model. > >> Should I not report the Rfree and instead insert a remark explaining the > >> situation? If I report the Rfree prior to the test set removal, it is > >> certain that every validation tool will report a mismatch. It does not > >> seem that the PDB has a mechanism to deal with this. > >> > >> Cheers, > >> > >> Ed. > >> > >> > >> > >> -- > >> Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > >> Julian, King of Lemurs > >> -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] should the final model be refined against full datset
For those who have strong opinions on what data should be deposited... The IUCR is just starting a serious discussion of this subject. Two committees, the "Data Deposition Working Group", led by John Helliwell, and the Commission on Biological Macromolecules (chaired by Xiao-Dong Su) are working on this. Two key issues are (1) feasibility and importance of deposition of raw images and (2) deposition of sufficient information to fully reproduce the crystallographic analysis. I am on both committees and would be happy to hear your ideas (off-list). I am sure the other members of the committees would welcome your thoughts as well. -Tom T Tom Terwilliger terwilli...@lanl.gov >> This is a follow up (or a digression) to James comparing test set to >> missing reflections. I also heard this issue mentioned before but was >> always too lazy to actually pursue it. >> >> So. >> >> The role of the test set is to prevent overfitting. Let's say I have >> the final model and I monitored the Rfree every step of the way and can >> conclude that there is no overfitting. Should I do the final refinement >> against complete dataset? >> >> IMCO, I absolutely should. The test set reflections contain >> information, and the "final" model is actually biased towards the >> working set. Refining using all the data can only improve the accuracy >> of the model, if only slightly. >> >> The second question is practical. Let's say I want to deposit the >> results of the refinement against the full dataset as my final model. >> Should I not report the Rfree and instead insert a remark explaining the >> situation? If I report the Rfree prior to the test set removal, it is >> certain that every validation tool will report a mismatch. It does not >> seem that the PDB has a mechanism to deal with this. >> >> Cheers, >> >> Ed. >> >> >> >> -- >> Oh, suddenly throwing a giraffe into a volcano to make water is crazy? >> Julian, King of Lemurs >>
Re: [ccp4bb] should the final model be refined against full datset
I just tried refining a "finished" structure turning off the FreeR set, in Refmac, and I have to say I can barely see any difference between the two sets of coordinates. From this n=1 trial, I can't see that it improves the model significantly, nor that it ruins the model irretrievably for future purposes. I suspect we worry too much about these things Phil Evans On 14 Oct 2011, at 21:35, Nat Echols wrote: > On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang wrote: > Sorry, I don't quite understand your reasoning for how the structure is > rendered useless if one refined it with all data. > > "Useless" was too strong a word (it's Friday, sorry). I guess simulated > annealing can address the model-bias issue, but I'm not totally convinced > that this solves the problem. And not every crystallographer will run SA > every time he/she solves an isomorphous structure, so there's a real danger > of misleading future users of the PDB file. The reported R-free, of course, > is still meaningless in the context of the deposited model. > > Would your argument also apply to all the structures that were refined before > R-free existed? > > Technically, yes - but how many proteins are there whose only representatives > in the PDB were refined this way? I suspect very few; in most cases, a more > recent model should be available. > > -Nat
Re: [ccp4bb] should the final model be refined against full datset
On Friday, October 14, 2011 02:45:08 pm Ed Pozharski wrote: > On Fri, 2011-10-14 at 13:07 -0700, Nat Echols wrote: > > > > The benefit of including those extra 5% of data is always minimal > > And so is probably the benefit of excluding when all the steps that > require cross-validation have already been performed. My thinking is > that excluding data from analysis should always be justified (and in the > initial stages of refinement, it might be as it prevents overfitting), > not the other way around. A model with error bars is more useful than a marginally more accurate model without error bars, not least because you are probably taking it on faith that the second model is "more accurate". Crystallographers were kind of late in realizing that a cross validation test could be useful in assessing refinement. What's more, we never really learned the whole lesson. Rather than using the full test, we use only one blade of the jackknife. http://en.wikipedia.org/wiki/Cross-validation_(statistics)#K-fold_cross-validation The full test would involve running multiple parallel refinements, each one omiting a different disjoint set of reflections. The ccp4 suite is set up to do this, since Rfree flags by default run from 0-19 and refmac lets you specify which 5% subset is to be omitted from the current run. Of course, evaluating the end point becomes more complex than looking at a single number "Rfree". Surely someone must have done this! But I can't recall ever reading an analysis of such a refinement protocol. Does anyone know of relevant reports in the literature? Is there a program or script that will collect K-fold parallel output models and their residuals to generate a net indicator of model quality? Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] should the final model be refined against full datset
Thanks for the clear explanation. I understood that. But I was trying to understand how this would negatively affects the initial model to render it useless or less useful. In the scenario that you presented, I would expect a better result (better model) if the initial model was refined with all data, thus more useful. Sure, again in your scenario, the "new" structure has seen R-free reflections in the equivalent indexes of its replacement model, but their intensities should be different anyway, so I am not sure how this is bad. Even if the bias is huge, let's say this bias results in 1% reduction in initial R-free (exaggerating here), how would this makes one's model bad or how would this be bad for one's science? In the end, our objective is to build the best model possible and I think that more data would likely result in better model, not the other way around. If we can agree that refining a model with all data would result in a better model, then wouldn't not doing so constitute a compromise of model quality for a more "pure" statistic? I had not refined a model with all data before (just to keep inline), but I wondered if I was doing the best thing. Cheers, Quyen On Oct 14, 2011, at 5:27 PM, Phil Jeffrey wrote: Let's say you have two isomorphous crystals of two different protein- ligand complexes. Same protein different ligand, same xtal form. Conventionally you'd keep the same free set reflections (hkl values) between the two datasets to reduce biasing. However if the first model had been refined against all reflections there is no longer a free set for that model, thus all hkl's have seen the atoms during refinement, and so your R-free in the second complex is initially biased to the model from the first complex. [*] The tendency is to do less refinement in these sort of isomorphous cases than in molecular replacement solutions, because the structural changes are usually far less (it is isomorphous after all) so there's a risk that the R-free will not be allowed to fully float free of that initial bias. That makes your R-free look better than it actually is. This is rather strongly analogous to using different free sets in the two datasets. However I'm not sure that this is as big of a deal as it is being made to sound. It can be dealt with straightforwardly. However refining against all the data weakens the use of R-free as a validation tool for that particular model so the people that like to judge structures based on a single number (i.e. R-free) are going to be quite put out. It's also the case that the best model probably *is* the one based on a careful last round of refinement against all data, as long as nothing much changes. That would need to be quantified in some way(s). Phil Jeffrey Princeton [* Your R-free is also initially model-biased in cases where the data are significant non-isomorphous or you're using two different xtal forms, to varying extents] I still don't understand how a structure model refined with all data would negatively affect the determination and/or refinement of an isomorphous structure using a different data set (even without doing SA first). Quyen On Oct 14, 2011, at 4:35 PM, Nat Echols wrote: On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang mailto:qqho...@gmail.com>> wrote: Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all data. "Useless" was too strong a word (it's Friday, sorry). I guess simulated annealing can address the model-bias issue, but I'm not totally convinced that this solves the problem. And not every crystallographer will run SA every time he/she solves an isomorphous structure, so there's a real danger of misleading future users of the PDB file. The reported R-free, of course, is still meaningless in the context of the deposited model. Would your argument also apply to all the structures that were refined before R-free existed? Technically, yes - but how many proteins are there whose only representatives in the PDB were refined this way? I suspect very few; in most cases, a more recent model should be available. -Nat
Re: [ccp4bb] should the final model be refined against full datset
We have obligations that extend beyond simply presenting a "best" model. In an ideal world, the PDB would accept two coordinate sets and two sets of statistics, one for the last step where the cross-validation set was valid, and a final model refined against all the data. Until there is a clear way to do that, and an unambiguous presentation of them to the public, IMO, the gains won by refinement against all the data are outweighed by the Confusion that it can cause when presenting model and associated statistics to the public. On Oct 14, 2011, at 3:32 PM, Jan Dohnalek wrote: > Regarding refinement against all reflections: the main goal of our work is to > provide the best possible representation of the experimental data in the form > of the structure model. Once the structure building and refinement process is > finished keeping the Rfree set separate does not make sense any more. Its > role finishes once the last set of changes have been done to the model and > verified ... > > J. Dohnalek
Re: [ccp4bb] should the final model be refined against full datset
On Fri, 2011-10-14 at 13:07 -0700, Nat Echols wrote: > You should enter the statistics for the model and data that you > actually deposit, not statistics for some other model that you might > have had at one point but which the PDB will never see. If you read my post carefully, you'll see that I never suggested reporting statistics for one model and depositing the other > Not only does refining against R-free make it impossible to verify and > validate your structure, it also means that any time you or anyone > else wants to solve an isomorphous structure by MR using your > structure as a search model, or continue the refinement with > higher-resolution data, you will be starting with a model that has > been refined against all reflections. So any future refinements done > with that model against isomorphous data are pre-biased, making your > model potentially useless. Frankly, I think you are exaggerating the magnitude of model bias in the situation that I described. You assume that the refinement will become severely unstable after tossing in the test reflections. Depending on the resolution etc, the rms shift of the model may vary but if it even is, say half an angstrom the model hardly becomes useless (and that is hugely overestimated). And at least in theory including *all the data* should make the model more, not less accurate. > The benefit of including those extra 5% of data is always minimal And so is probably the benefit of excluding when all the steps that require cross-validation have already been performed. My thinking is that excluding data from analysis should always be justified (and in the initial stages of refinement, it might be as it prevents overfitting), not the other way around. Cheers, Ed. -- "Hurry up before we all come back to our senses!" Julian, King of Lemurs
Re: [ccp4bb] should the final model be refined against full datset
Recently we (I mean WE - community) frequently refine structures around 1 Angstrom resolution. This is not what for the Rfree was invented. It was invented to go away with 3.0-2.8 Angstrom data in times when people did not possess facilities good enough to look on the electron density maps…. We finish (WE - I again mean - community) the refinement of our structures too early. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 14, 2011, at 22:35 , Nat Echols wrote: > On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang wrote: > Sorry, I don't quite understand your reasoning for how the structure is > rendered useless if one refined it with all data. > > "Useless" was too strong a word (it's Friday, sorry). I guess simulated > annealing can address the model-bias issue, but I'm not totally convinced > that this solves the problem. And not every crystallographer will run SA > every time he/she solves an isomorphous structure, so there's a real danger > of misleading future users of the PDB file. The reported R-free, of course, > is still meaningless in the context of the deposited model. > > Would your argument also apply to all the structures that were refined before > R-free existed? > > Technically, yes - but how many proteins are there whose only representatives > in the PDB were refined this way? I suspect very few; in most cases, a more > recent model should be available. > > -Nat
Re: [ccp4bb] should the final model be refined against full datset
Let's say you have two isomorphous crystals of two different protein-ligand complexes. Same protein different ligand, same xtal form. Conventionally you'd keep the same free set reflections (hkl values) between the two datasets to reduce biasing. However if the first model had been refined against all reflections there is no longer a free set for that model, thus all hkl's have seen the atoms during refinement, and so your R-free in the second complex is initially biased to the model from the first complex. [*] The tendency is to do less refinement in these sort of isomorphous cases than in molecular replacement solutions, because the structural changes are usually far less (it is isomorphous after all) so there's a risk that the R-free will not be allowed to fully float free of that initial bias. That makes your R-free look better than it actually is. This is rather strongly analogous to using different free sets in the two datasets. However I'm not sure that this is as big of a deal as it is being made to sound. It can be dealt with straightforwardly. However refining against all the data weakens the use of R-free as a validation tool for that particular model so the people that like to judge structures based on a single number (i.e. R-free) are going to be quite put out. It's also the case that the best model probably *is* the one based on a careful last round of refinement against all data, as long as nothing much changes. That would need to be quantified in some way(s). Phil Jeffrey Princeton [* Your R-free is also initially model-biased in cases where the data are significant non-isomorphous or you're using two different xtal forms, to varying extents] I still don't understand how a structure model refined with all data would negatively affect the determination and/or refinement of an isomorphous structure using a different data set (even without doing SA first). Quyen On Oct 14, 2011, at 4:35 PM, Nat Echols wrote: On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang mailto:qqho...@gmail.com>> wrote: Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all data. "Useless" was too strong a word (it's Friday, sorry). I guess simulated annealing can address the model-bias issue, but I'm not totally convinced that this solves the problem. And not every crystallographer will run SA every time he/she solves an isomorphous structure, so there's a real danger of misleading future users of the PDB file. The reported R-free, of course, is still meaningless in the context of the deposited model. Would your argument also apply to all the structures that were refined before R-free existed? Technically, yes - but how many proteins are there whose only representatives in the PDB were refined this way? I suspect very few; in most cases, a more recent model should be available. -Nat
Re: [ccp4bb] should the final model be refined against full datset
I still don't understand how a structure model refined with all data would negatively affect the determination and/or refinement of an isomorphous structure using a different data set (even without doing SA first). Quyen On Oct 14, 2011, at 4:35 PM, Nat Echols wrote: On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang wrote: Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all data. "Useless" was too strong a word (it's Friday, sorry). I guess simulated annealing can address the model-bias issue, but I'm not totally convinced that this solves the problem. And not every crystallographer will run SA every time he/she solves an isomorphous structure, so there's a real danger of misleading future users of the PDB file. The reported R-free, of course, is still meaningless in the context of the deposited model. Would your argument also apply to all the structures that were refined before R-free existed? Technically, yes - but how many proteins are there whose only representatives in the PDB were refined this way? I suspect very few; in most cases, a more recent model should be available. -Nat
Re: [ccp4bb] should the final model be refined against full datset
On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang wrote: > Sorry, I don't quite understand your reasoning for how the structure is > rendered useless if one refined it with all data. > "Useless" was too strong a word (it's Friday, sorry). I guess simulated annealing can address the model-bias issue, but I'm not totally convinced that this solves the problem. And not every crystallographer will run SA every time he/she solves an isomorphous structure, so there's a real danger of misleading future users of the PDB file. The reported R-free, of course, is still meaningless in the context of the deposited model. Would your argument also apply to all the structures that were refined > before R-free existed? Technically, yes - but how many proteins are there whose only representatives in the PDB were refined this way? I suspect very few; in most cases, a more recent model should be available. -Nat
Re: [ccp4bb] should the final model be refined against full datset
Regarding refinement against all reflections: the main goal of our work is to provide the best possible representation of the experimental data in the form of the structure model. Once the structure building and refinement process is finished keeping the Rfree set separate does not make sense any more. Its role finishes once the last set of changes have been done to the model and verified ... J. Dohnalek On Fri, Oct 14, 2011 at 10:23 PM, Craig A. Bingman < cbing...@biochem.wisc.edu> wrote: > Recent experience indicates that the PDB is checking these statistics very > closely for new depositions. The checks made by the PDB are intended to > prevent accidents and oversights made by honest people from creeping into > the database. "Getting away" with something seems to imply some intention > to deceive, and that is much more difficult to detect. > > On Oct 14, 2011, at 3:09 PM, Robbie Joosten wrote: > > The deposited R-free sets in the PDB are quite frequently 'unfree' or the > wrong set was deposited (checking this is one of the recommendations in the > VTF report in Structure). So at the moment you would probably get away with > depositing an unfree R-free set ;) > > > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] should the final model be refined against full datset
Recent experience indicates that the PDB is checking these statistics very closely for new depositions. The checks made by the PDB are intended to prevent accidents and oversights made by honest people from creeping into the database. "Getting away" with something seems to imply some intention to deceive, and that is much more difficult to detect. On Oct 14, 2011, at 3:09 PM, Robbie Joosten wrote: > The deposited R-free sets in the PDB are quite frequently 'unfree' or the > wrong set was deposited (checking this is one of the recommendations in the > VTF report in Structure). So at the moment you would probably get away with > depositing an unfree R-free set ;) >
Re: [ccp4bb] should the final model be refined against full datset
Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all data. Would your argument also apply to all the structures that were refined before R-free existed? Quyen You should enter the statistics for the model and data that you actually deposit, not statistics for some other model that you might have had at one point but which the PDB will never see. Not only does refining against R-free make it impossible to verify and validate your structure, it also means that any time you or anyone else wants to solve an isomorphous structure by MR using your structure as a search model, or continue the refinement with higher- resolution data, you will be starting with a model that has been refined against all reflections. So any future refinements done with that model against isomorphous data are pre-biased, making your model potentially useless. I'm amazed that anyone is still depositing structures refined against all data, but the PDB does still get a few. The benefit of including those extra 5% of data is always minimal in every paper I've seen that reports such a procedure, and far outweighed by having a reliable and relatively unbiased validation statistic that is preserved in the final deposition. (The situation may be different for very low resolution data, but those structures are a tiny fraction of the PDB.) -Nat
Re: [ccp4bb] should the final model be refined against full datset
Hi Ed, > This is a follow up (or a digression) to James comparing test set to > missing reflections. I also heard this issue mentioned before but was > always too lazy to actually pursue it. > > So. > > The role of the test set is to prevent overfitting. Let's say I have > the final model and I monitored the Rfree every step of the way and can > conclude that there is no overfitting. Should I do the final refinement > against complete dataset? > > IMCO, I absolutely should. The test set reflections contain > information, and the "final" model is actually biased towards the > working set. Refining using all the data can only improve the accuracy > of the model, if only slightly. Hmm, if your R-free set is small the added value will also be small. If it is relatively big, then your previously established optimal weights may no longer be optimal. A more elegant thing to would be refine the model with, say, 20 different 5% R-free sets, deposit the ensemble and report the average R(-free) plus a standard deviation. AFAIK, this is what the R-free set numbers that CCP4's FREERFLAG generates are for. Of course, in that case you should do enough refinement (and perhaps rebuilding) to make sure each R-free set is free. > The second question is practical. Let's say I want to deposit the > results of the refinement against the full dataset as my final model. > Should I not report the Rfree and instead insert a remark explaining the > situation? If I report the Rfree prior to the test set removal, it is > certain that every validation tool will report a mismatch. It does not > seem that the PDB has a mechanism to deal with this. The deposited R-free sets in the PDB are quite frequently 'unfree' or the wrong set was deposited (checking this is one of the recommendations in the VTF report in Structure). So at the moment you would probably get away with depositing an unfree R-free set ;) Cheers, Robbie > > Cheers, > > Ed. > > > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs
Re: [ccp4bb] should the final model be refined against full datset
On Fri, Oct 14, 2011 at 12:52 PM, Ed Pozharski wrote: > The second question is practical. Let's say I want to deposit the > results of the refinement against the full dataset as my final model. > Should I not report the Rfree and instead insert a remark explaining the > situation? If I report the Rfree prior to the test set removal, it is > certain that every validation tool will report a mismatch. It does not > seem that the PDB has a mechanism to deal with this. > You should enter the statistics for the model and data that you actually deposit, not statistics for some other model that you might have had at one point but which the PDB will never see. Not only does refining against R-free make it impossible to verify and validate your structure, it also means that any time you or anyone else wants to solve an isomorphous structure by MR using your structure as a search model, or continue the refinement with higher-resolution data, you will be starting with a model that has been refined against all reflections. So any future refinements done with that model against isomorphous data are pre-biased, making your model potentially useless. I'm amazed that anyone is still depositing structures refined against all data, but the PDB does still get a few. The benefit of including those extra 5% of data is always minimal in every paper I've seen that reports such a procedure, and far outweighed by having a reliable and relatively unbiased validation statistic that is preserved in the final deposition. (The situation may be different for very low resolution data, but those structures are a tiny fraction of the PDB.) -Nat
[ccp4bb] should the final model be refined against full datset
This is a follow up (or a digression) to James comparing test set to missing reflections. I also heard this issue mentioned before but was always too lazy to actually pursue it. So. The role of the test set is to prevent overfitting. Let's say I have the final model and I monitored the Rfree every step of the way and can conclude that there is no overfitting. Should I do the final refinement against complete dataset? IMCO, I absolutely should. The test set reflections contain information, and the "final" model is actually biased towards the working set. Refining using all the data can only improve the accuracy of the model, if only slightly. The second question is practical. Let's say I want to deposit the results of the refinement against the full dataset as my final model. Should I not report the Rfree and instead insert a remark explaining the situation? If I report the Rfree prior to the test set removal, it is certain that every validation tool will report a mismatch. It does not seem that the PDB has a mechanism to deal with this. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Ice rings...
Automated outlier rejection in scaling will handle a lot of things, including ice. Works better with high multiplicity. Unless, of course, your ice rings are "even", then any integration error due to ice will be the same for all the symmetry mates and the scaling program will be none the wiser. That said, the integration programs these days tend to have pretty sensible defaults for rejecting spots that have "weird" backgrounds. Plenty of structures get solved from data that has horrible-looking ice rings using just the defaults. In fact, I am personally unconvinced that ice rings are a significant problem in and of themselves. More often, they are simply an indication that something else is wrong, like the crystal warmed up at some point. Nevertheless, if you suspect your ice rings are causing a problem, you can try to do something about them. The "deice" program already mentioned sounds cool, but if you just want to try something quick, excluding the resolution ranges of your ice rings can be done in sftools like this: select resol > 3.89 select resol < 3.93 absent col F SIGF DANO SIGDANO if col F > 0 and repeat this for each resolution range you want to exclude. Best to get these ranges from your integration program's graphics display. In mosflm, you can put "EXCLUDE ICE" on either the "AUTOINDEX" or "RESOLUTION" keywords and have any spots on the canonical hexagonal ice spacings removed automatically. The problem with excluding resolution ranges, of course, is that your particular "ice rings" may not be where they are supposed to be. Either due to something physical, like the cooling rate, or something artificial, like an error in the camera parameters. It is also possible that what you think are "ice rings" are actually "salt rings". Some salts will precipitate out upon cryo-cooling. Large ice/salt crystals can also produce a lot of non-Bragg scatter, which means that you can get sharp features far away from the resolution range you expect. On the other hand, if you have cubic ice instead of hexagonal ice (very common in MX samples), then there are no rings at 3.91A, 3.45A, 2.68A and throwing out these resolution ranges would be a waste. Another way to exclude ice is to crank up background-based rejection criteria. In denzo/HKL2K, you do this with the "reject fraction" keyword, and in mosflm, REJECT MINBG does pretty much the same thing. There are lots of rejection options in integration programs, and which one works in your particular case depends on what your ice rings look like. Noone has written a machine-vision type program that can recognize and handle all the cases. You will need to play with these options until the spots you "don't like" turn red in the display. Of course, the best way to deal with ice rings would be to inspect each and every one of the spots you have near ice rings and decide on its intensity manually. Then edit the hkl file. Which brings me to perhaps a more important point: What, exactly, is the "problem" you are having that makes you think the ice rings are to blame? Can't get an MR solution? Can't get MAD/SAD phases? Ice has a bad rep in MX, and an undeserved one IMHO. In fact, by controlling either cryoprotectant concentration or cooling rate carefully, you can achieve a mixture of amorphous and cubic ice, and this mixture has a specific volume (density) intermediate between the two. Many crystals diffract much better when you are able to match the specific volume of the stuff in the solvent channels to the specific volume protein lattice is "trying" to achieve on its own. A great deal of effort has gone into characterizing this phenomenon (authors: Juers, Weik, Warkentin, Thorne and many others), but I often meet frustrated cryo-screeners who seem to have never heard of any of it! In general, the automated "outlier rejection" protocols employed by modern software have taken care of most of the problems ice rings introduce. For example, difference Pattersons are VERY sensitive to outliers, and all it takes is one bad spot to give you huge ripples that swamp all you peaks, but every heavy-atom finding program I am aware of calculates Pattersons only after fist doing an "outlier rejection" step. You might also think that ice rings would mess up your preciously subtle anomalous differences, but again, outlier rejection to the rescue. Now, that said, depending on automated outlier rejection to save you is of course a questionable policy, but it is an equally bad idea to pretend that it doesn't exist either. It is funny how in MX we are all ready to grab our torch and pitchfork if we hear of someone manually editing their hkl files to get rid of reflections they "don't like", but as long as "the software" does it, it is okay. Plausible deniability runs deep. -James Holton MAD Scientist On 10/11/2011 8:16 AM, Francis E Reyes wrote: All, So I have two intense ic
Re: [ccp4bb] Ice rings... [maps and missing reflections]
On 10/11/2011 12:33 PM, Garib N Murshudov wrote: We need better way of estimating "unobserved" reflections. Indeed we do! Because this appears to be the sum total of how the correctness of the structure is judged. It is easy to forget I think that from the "point of view" of the refinement program, all reflections flagged as belonging to the "free" set are, in effect, "missing". So Rfree is really just a score for how well DFc agrees with Fobs? -James Holton MAD Scientist
Re: [ccp4bb] data processing problem with ice rings
These rings are nanocrystalline cubic ice (ice Ic, as opposed to the "usual" ice Ih). It is an interesting substance in that noone has ever prepared a large single crystal of it. In fact, for very small crystals it can be hard to distinguish it from amorphous ice (or "glassy water"). The three main rings that you see from ice Ic coincide almost exactly with the centroids of the three main diffuse rings of glassy water, and as the ice Ic crystals get smaller, the rings get fatter (Scherrer broadening). You can even measure the size of the crystallites by measuring the width of the rings. At the limit of 1-2 unit cells wide, the diffraction pattern of ice Ic powder looks almost exactly like that of glassy water, so I suppose one could say that there is a continuum of phases between the two. And yes, there are crystals that "like" a certain mixture of cubic ice and amorphous water in their solvent channels. Other's don't like it at all. But I agree with JS below that the problem here is not the ice rings. Probably overlaps? Best to look only at spots inside the 3.8A circle until you figure out what is going on. -James Holton MAD Scientist On 10/13/2011 11:20 PM, James Stroud wrote: First of all, are you sure those are ice rings? They do not look typical. I think you might have salt crystals from dehydration *before* freezing. Otherwise, I think your freezing went well. Maybe try a humidity controlled environment when you freeze. Second, I'm not so sure the bad stats come from the contaminating rings. The lattice seems to have some sort of problem, like a split lattice. You might be able to tackle this problem by increasing your spot size or skewing it's shape to compensate for the split. You need to investigate several images throughout the run to see whether and how to manipulate your spot size. Sometimes, the split lengthens the spots in the direction of the phi axis and you get lucky. But I think the phi axis might be horizontal in this picture, which makes things a little trickier. From one image, it is difficult to tell the pathology of this crystal. In principle, if you can accurately measure the most high-resolution spots visible (which appear to be about 1.9 Å, guessing from your log file) then you will have a pretty good data set, even with the contaminating rings. Personally, I'd use Denzo for this data, but I don't know what is vogue with the community right now. I still use O, so my tastes might be somewhat antiquated. James On Oct 13, 2011, at 11:12 PM, ChenTiantian wrote: Hi there, I am processing a dataset which has bad ice rings (as you can see in the attach png file). I tried both XDS and imosflm, and got similar results, it seems that adding " EXCLUDE_RESOLUTION_RANGE" cannot get rid of the effects of the ice rings. the following is part of the CORRECT.LP which is the second attached file, you can find more details there. SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE>= -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 4.24 371525537 5545 99.9% 46.9% 52.7% 371502.4850.8%19.4% -28% 0.5135136 3.01 553449002 9840 91.5% 62.7% 65.1% 551161.7668.3%48.1% -28% 0.5207760 2.46 84636 12699 12703 100.0% 67.4% 84.7% 846341.5573.0%54.2% -19% 0.513 12104 2.13 97910 14743 14987 98.4% 254.5%199.3% 979080.16 276.2% 4899.9% -23% 0.473 14037 1.90 110260 16846 16940 99.4% 299.2%303.3% 1102450.06 325.0% -99.9% -17% 0.422 15995 1.74 118354 18629 18744 99.4%1062.0% 1043.6% 118317 -0.20 1156.4% -99.9% -13% 0.380 17414 1.61 122958 20193 20331 99.3% 967.5% 1571.1% 1228680.10 1059.7% 987.3%-2% 0.402 18348 1.51 125075 21554 21794 98.9% 838.9% 1355.1% 1249330.08 922.6% 1116.9%-1% 0.402 18977 1.42 72057 17042 23233 73.4% 640.8%775.3% 703910.08 732.5% 826.7%-8% 0.425 10003 total 823746 136245144117 94.5% 166.4%166.7% 8215620.40 181.1% 296.7% -15% 0.435 119774 Note that I/SIGMA of each resolution shell is<2.5, so how should I do to process the dataset properly? Any suggestion about this super ice rings? Thanks! Tiantian -- Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Shanghai, 201203
[ccp4bb] Quips about "stunning" software and the first structure it helped solve
Hi all, The Protein Data Bank in Europe (PDBe; pdbe.org) regularly produces Quips, short stories about QUite Interesting Pdb Structures (pdbe.org/quips). Quips address biologically interesting aspects of one or more PDB entries, coupled with interactive graphics views and often a mini-tutorial or suggestions for further exploration using PDBe services and resources. Today another Quips episode was released. It looks back at the first crystal structure that was solved with the program Phaser and also tries to explain in (almost) layman's terms how Molecular Replacement works. The accompanying mini-tutorial shows you how to do multiple structure superimposition using PDBeFold (SSM). The Quips story can be found here: http://pdbe.org/quips?story=Phaser There is also an RSS feed that informs you whenever there is a new Quips article available. For links to this and several other feeds, see http://pdbe.org/rss --- If you have an interesting structure whose story you would like to tell (with our help) in the form of a Quips episode, please contact us at p...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] First contours of a vision for the future of validation at the PDB
(Posted on behalf of wwPDB) The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is pleased to direct PDB depositors and users to the recommendations of the wwPDB X-ray Validation Task Force (VTF) that were published in the journal Structure this week (2011, vol. 19: 1395-1412; http://www.cell.com/structure/abstract/S0969-2126(11)00285-1). The wwPDB X-ray VTF was convened in 2008 to collect expert recommendations and develop consensus on validation methods that should be applied to crystal structures (models and data) in the PDB and to identify software applications to perform these validation tasks. These recommendations are the basis of a new validation suite that will be part of the new Common Tool for Deposition and Annotation (D&A) that is currently being developed by the wwPDB partners. The D&A tool and the X-ray validation pipeline will go into production by the end of 2012 at all wwPDB deposition sites (RCSB PDB, PDBe, PDBj and BMRB). From that moment in time on, depositors of X-ray crystal structures at the PDB will be provided with a detailed validation report. Such reports can be submitted to journals to accompany manuscripts describing new structures, and several publishers are working towards making such reports mandatory. Once the D&A tool is in production, the wwPDB partners also plan to provide the validation pipeline as a server, allowing crystallographers to assess their models before deposition and publication. Additional VTFs have been convened for NMR (by wwPDB) and 3DEM (by EMDataBank). The wwPDB greatly appreciates the efforts of the authors of the X-ray VTF report: Randy J. Read, Paul D. Adams, W. Bryan Arendall III, Axel T. Brunger, Paul Emsley, Robbie P. Joosten, Gerard J. Kleywegt, Eugene B. Krissinel, Thomas Ltteke, Zbyszek Otwinowski, Anastassis Perrakis, Jane S. Richardson, William H. Sheffler, Janet L. Smith, Ian J. Tickle, Gert Vriend and Peter H. Zwart. -- --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb]
Respected Sir, I am sorry I wrote it wrongly, its resolution- independent X-ray weight rather. I use ccp4i so the input for the weight is what i mentioned previously- "Refinement parameters- weighing term (when auto weighing is turned off)" in refmac. Thanking you With Regads M. Kavyashree -Ian Tickle wrote: - To: ka...@rishi.serc.iisc.ernet.in From: Ian Tickle Date: 10/14/2011 04:34PM Cc: CCP4 bulletin board Subject: Re: > Yes, the weight mentioned in the paper was > weight matrix, but the one i used was the > option under "Refinement parameters- weighing > term (when auto weighing is turned off)". > But If I really wasnt to change the weight matrix > where should I change (in the code?)? No, the weights referred to in the paper are definitely the ones given as "WEIGHT AUTO x". I can say that with confidence because I never use "WEIGHT MATRIX x" for reasons I explained. I think what I said is that it's _related_ to the matrix weight, which it obviously is by some constant but unknown factor. You don't have to change any code (that has been done for you!), but if you're using CCP4I (sorry I don't so I can't give you precise instructions), you probably have to edit the script before submission (there should be a button in the "Run" menu for that). Cheers -- Ian > No, I dint mean a big difference, not in the > coordinates, but the values of R-factors and > other terms. I thought it was quite different. > So you mean that it is not of much concern? I would say that it's not a big difference, just tightening up of the geometry, as I said. Cheers -- Ian -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb]
> Yes, the weight mentioned in the paper was > weight matrix, but the one i used was the > option under "Refinement parameters- weighing > term (when auto weighing is turned off)". > But If I really wasnt to change the weight matrix > where should I change (in the code?)? No, the weights referred to in the paper are definitely the ones given as "WEIGHT AUTO x". I can say that with confidence because I never use "WEIGHT MATRIX x" for reasons I explained. I think what I said is that it's _related_ to the matrix weight, which it obviously is by some constant but unknown factor. You don't have to change any code (that has been done for you!), but if you're using CCP4I (sorry I don't so I can't give you precise instructions), you probably have to edit the script before submission (there should be a button in the "Run" menu for that). Cheers -- Ian > No, I dint mean a big difference, not in the > coordinates, but the values of R-factors and > other terms. I thought it was quite different. > So you mean that it is not of much concern? I would say that it's not a big difference, just tightening up of the geometry, as I said. Cheers -- Ian
[ccp4bb]
Respected Sir, Yes, the weight mentioned in the paper was weight matrix, but the one i used was the option under "Refinement parameters- weighing term (when auto weighing is turned off)". But If I really wasnt to change the weight matrix where should I change (in the code?)? No, I dint mean a big difference, not in the coordinates, but the values of R-factors and other terms. I thought it was quite different. So you mean that it is not of much concern? Thanking you With Regards M. Kavyashree -Ian Tickle wrote: - To: ka...@rishi.serc.iisc.ernet.in From: Ian Tickle Date: 10/14/2011 04:00PM Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Optimisation of weights Hi your X-ray weight of .08 seems very small, the optimal value is normally in the range 1 to 4 (I usually set it initially at the median, i.e. 2.5). But which weight keyword did you use "WEIGHT MATRIX .08" or "WEIGHT AUTO .08" (the latter is I think undocumented, so I'm guessing the first)? Anyway I would strongly advise the latter: the difference is that the MATRIX weight is on a completely arbitrary scale, whereas the AUTO weight is at least relative to the theoretical value of 1 (even though the optimal value may not be 1 in practice, at least your initial guess will be in the same ball park). Note that what Refmac calls "automatic weighting" is not the same as what X-PLOR, CNS & phenix call "automatic weighting" (at least that's my understanding). "WEIGHT AUTO" in Refmac is the same as "WEIGHT AUTO 10", whereas auto-weighting in X-PLOR corresponds to "WEIGHT AUTO 1" in Refmac. Not surprisingly these give quite different results! The optimal B factor weight is also around 1, see the paper for typical values. I'm still not clear precisely what you meant by ""there was quite a difference". I don't see that big a difference between the 2 runs, just a slight tightening up of the geometry. Are you saying you see big differences in the refined co-ordinates? That would be a cause for concern. Cheers -- Ian -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] "Insufficient virtual memory"
> Try the GNU (compiler) and see what it says. ;) Hi Francois - I won't bore you with the long list of compiler errors that gfortran gives with my code (ifort compiles the identical code without error and up until now it has worked just fine on both 32 & 64 bit machines as long as don't try to allocate > 2Gb). I think we'll have to splash out on an Intel license for a 64-bit machine (thanks for the low-down on the bugs, Harry). Anyway thanks to all for the suggestions. Cheers -- Ian
Re: [ccp4bb] Optimisation of weights
Hi your X-ray weight of .08 seems very small, the optimal value is normally in the range 1 to 4 (I usually set it initially at the median, i.e. 2.5). But which weight keyword did you use "WEIGHT MATRIX .08" or "WEIGHT AUTO .08" (the latter is I think undocumented, so I'm guessing the first)? Anyway I would strongly advise the latter: the difference is that the MATRIX weight is on a completely arbitrary scale, whereas the AUTO weight is at least relative to the theoretical value of 1 (even though the optimal value may not be 1 in practice, at least your initial guess will be in the same ball park). Note that what Refmac calls "automatic weighting" is not the same as what X-PLOR, CNS & phenix call "automatic weighting" (at least that's my understanding). "WEIGHT AUTO" in Refmac is the same as "WEIGHT AUTO 10", whereas auto-weighting in X-PLOR corresponds to "WEIGHT AUTO 1" in Refmac. Not surprisingly these give quite different results! The optimal B factor weight is also around 1, see the paper for typical values. I'm still not clear precisely what you meant by ""there was quite a difference". I don't see that big a difference between the 2 runs, just a slight tightening up of the geometry. Are you saying you see big differences in the refined co-ordinates? That would be a cause for concern. Cheers -- Ian On Fri, Oct 14, 2011 at 11:19 AM, wrote: > Respected Sir, > > For one of the structures that I did optimisation > had values - (resolution of the data - 2.35Ang) > > Before optimization- (Bfactor weight=1.0, X-ray Weight - auto) > R factor 0.2362 > R free 0.2924 > -LLfree 7521.8 > rmsBOND 0.0160 > zBOND 0.660 > > After optimisation- (B-factor weight=0.2, X-ray Weight - 0.08) > R factor 0.2327 > R free 0.2882 > -LLfree 7495.7 > rmsBOND 0.0111 > zBOND 0.460 > > Also can you tell me what is the limit for B-factor weight hat can be varied. > > Thanking you > With Regards > M. Kavyashree > > > Sorry I just re-read your last email and realised and didn't read it > properly the first time. But what I said still stands: you can of > course try to optimise the weights at an early stage (before adding > waters say), there's no harm doing that, but there's also not much > point since you'll have to do it all again with the complete model, > since adding a lot of waters will undoubtedly change the optimal > weights. So I just leave the weight optimisation until the model is > complete. As long as the initial weights are "in the same ball park", > so that your RMSZ(bonds) is around 0.5 for typical resolutions (a bit > lower for low resolution, a bit higher for very high resolution) it > won't affect interpretation of maps etc. > > Cheers > > -- Ian > > On Fri, Oct 14, 2011 at 9:37 AM, Ian Tickle wrote: >> It must be the same complete model that you refined previously, I >> doubt that it will give the correct answer if you leave out the waters >> for example. >> >> You say "there was quite a difference". Could you be more specific: >> what were the values of the weights, R factors and RMSZ(bonds/angles) >> before and after weight optimisation? >> >> Cheers >> >> -- Ian >> > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > >
Re: [ccp4bb] Optimisation of weights
Respected Sir, For one of the structures that I did optimisation had values - (resolution of the data - 2.35Ang) Before optimization- (Bfactor weight=1.0, X-ray Weight - auto) R factor 0.2362 R free0.2924 -LLfree 7521.8 rmsBOND 0.0160 zBOND 0.660 After optimisation- (B-factor weight=0.2, X-ray Weight - 0.08) R factor 0.2327 R free0.2882 -LLfree 7495.7 rmsBOND 0.0111 zBOND 0.460 Also can you tell me what is the limit for B-factor weight hat can be varied. Thanking you With Regards M. Kavyashree Sorry I just re-read your last email and realised and didn't read it properly the first time. But what I said still stands: you can of course try to optimise the weights at an early stage (before adding waters say), there's no harm doing that, but there's also not much point since you'll have to do it all again with the complete model, since adding a lot of waters will undoubtedly change the optimal weights. So I just leave the weight optimisation until the model is complete. As long as the initial weights are "in the same ball park", so that your RMSZ(bonds) is around 0.5 for typical resolutions (a bit lower for low resolution, a bit higher for very high resolution) it won't affect interpretation of maps etc. Cheers -- Ian On Fri, Oct 14, 2011 at 9:37 AM, Ian Tickle wrote: > It must be the same complete model that you refined previously, I > doubt that it will give the correct answer if you leave out the waters > for example. > > You say "there was quite a difference". Could you be more specific: > what were the values of the weights, R factors and RMSZ(bonds/angles) > before and after weight optimisation? > > Cheers > > -- Ian > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] "Insufficient virtual memory"
On 10/14/2011 06:31 PM, Ian Tickle wrote: Hello all, some Fortran developer out there must know the answer to this one. I'm getting a "forrtl: severe (41): insufficient virtual memory" error when allocating dynamic memory from a F95 program compiled with Intel Fortran v11.1.059. The program was compiled on an old ia-32 Linux box with 1Gb RAM + 2Gb swap (I only have one Intel license to compile on this machine), but I'm running it on a brand new x86-64 box with 12Gb RAM + 8Gb swap. This should be ample: the program's maximum total memory requirement (code + static data + dynamic data) should be no more than 3Gb. My question is: what do I have to do to make it work? According to the ifort man page I need to specify "-mcmodel=medium -shared-intel". It says: "If your program has COMMON blocks and local data with a total size smaller than 2GB -mcmodel=small is sufficient. COMMONs larger than 2GB require mcmodel=medium or -mcmodel=large. Allocation of memory larger than 2GB can be done with any setting of -mcmodel." I'm a bit confused about the difference here between COMMONS> 2Gb (which I don't have) and "allocation of memory"> 2Gb (which I assume I do). When I try setting -mcmodel=medium (and -shared-intel) I get "ifort: command line warning #10148: option '-mcmodel' not supported". Is this telling me that I have to compile on the 64-bit machine? Whatever happened to cross-compilation? All suggestions greatly appreciated! Try the GNU (compiler) and see what it says. ;)
[ccp4bb] "Insufficient virtual memory"
Hello all, some Fortran developer out there must know the answer to this one. I'm getting a "forrtl: severe (41): insufficient virtual memory" error when allocating dynamic memory from a F95 program compiled with Intel Fortran v11.1.059. The program was compiled on an old ia-32 Linux box with 1Gb RAM + 2Gb swap (I only have one Intel license to compile on this machine), but I'm running it on a brand new x86-64 box with 12Gb RAM + 8Gb swap. This should be ample: the program's maximum total memory requirement (code + static data + dynamic data) should be no more than 3Gb. My question is: what do I have to do to make it work? According to the ifort man page I need to specify "-mcmodel=medium -shared-intel". It says: "If your program has COMMON blocks and local data with a total size smaller than 2GB -mcmodel=small is sufficient. COMMONs larger than 2GB require mcmodel=medium or -mcmodel=large. Allocation of memory larger than 2GB can be done with any setting of -mcmodel." I'm a bit confused about the difference here between COMMONS > 2Gb (which I don't have) and "allocation of memory" > 2Gb (which I assume I do). When I try setting -mcmodel=medium (and -shared-intel) I get "ifort: command line warning #10148: option '-mcmodel' not supported". Is this telling me that I have to compile on the 64-bit machine? Whatever happened to cross-compilation? All suggestions greatly appreciated! -- Ian
[ccp4bb]
Sorry I just re-read your last email and realised and didn't read it properly the first time. But what I said still stands: you can of course try to optimise the weights at an early stage (before adding waters say), there's no harm doing that, but there's also not much point since you'll have to do it all again with the complete model, since adding a lot of waters will undoubtedly change the optimal weights. So I just leave the weight optimisation until the model is complete. As long as the initial weights are "in the same ball park", so that your RMSZ(bonds) is around 0.5 for typical resolutions (a bit lower for low resolution, a bit higher for very high resolution) it won't affect interpretation of maps etc. Cheers -- Ian On Fri, Oct 14, 2011 at 9:37 AM, Ian Tickle wrote: > It must be the same complete model that you refined previously, I > doubt that it will give the correct answer if you leave out the waters > for example. > > You say "there was quite a difference". Could you be more specific: > what were the values of the weights, R factors and RMSZ(bonds/angles) > before and after weight optimisation? > > Cheers > > -- Ian > > On Fri, Oct 14, 2011 at 8:42 AM, wrote: >> Respected Sir, >> >> Thank you for your clarification. I had adopted this >> method recently. My doubt was if we have to optimize >> these two parameters during refinement, should we have >> the whole model along with water and ligands or only >> protein with few water positioning is enough. The reason >> why I am asking because there was quite a difference >> when I refined the same structure without the optimization >> and with optimization of these two parameters. >> >> Thanking you >> With regards >> M. Kavyashree >> >> -CCP4 bulletin board wrote: - >> >> To: CCP4BB@JISCMAIL.AC.UK >> From: Ian Tickle >> Sent by: CCP4 bulletin board >> Date: 10/14/2011 12:34PM >> Subject: Re: [ccp4bb] Optimisation of weights >> >> Hi Kavya >> >> The resolutions of the structures mentioned in the paper were only >> examples, the Rfree/-LLfree minimisation method (which are actually >> due to Axel Brunger & Gerard Bricogne respectively) does not depend on >> resolution. >> >> If the structures are already solved & refined, you don't need to do >> any model building, it should be within the radius of convergence with >> the new weights - it's only a small adjustment after all. >> >> Cheers >> >> -- Ian >> >> On Fri, Oct 14, 2011 at 6:12 AM, wrote: >> > Dear users, >> > >> > Can the optimization of the X-ray weighing factor >> > and B-factor (overall wt) as mentioned in the paper >> > Acta Cryst. (2007). D63, 1274–1281 by Dr.Ian Tickel, >> > be used for the refinement of the data sets beyond >> > the resolution range mentioned in the paper: 1.33 - >> > 2.55 Ang? >> > >> > Also the structures that were used to optimize these >> > parameters were already solved and refined, so when >> > we are solving a new structure to what extent does the >> > model has to be built before starting the optimization? >> > >> > Thanking you >> > With Regards >> > M. Kavyashree >> > >> > >> > -- >> > This message has been scanned for viruses and >> > dangerous content by MailScanner, and is >> > believed to be clean. >> > >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >
[ccp4bb]
It must be the same complete model that you refined previously, I doubt that it will give the correct answer if you leave out the waters for example. You say "there was quite a difference". Could you be more specific: what were the values of the weights, R factors and RMSZ(bonds/angles) before and after weight optimisation? Cheers -- Ian On Fri, Oct 14, 2011 at 8:42 AM, wrote: > Respected Sir, > > Thank you for your clarification. I had adopted this > method recently. My doubt was if we have to optimize > these two parameters during refinement, should we have > the whole model along with water and ligands or only > protein with few water positioning is enough. The reason > why I am asking because there was quite a difference > when I refined the same structure without the optimization > and with optimization of these two parameters. > > Thanking you > With regards > M. Kavyashree > > -CCP4 bulletin board wrote: - > > To: CCP4BB@JISCMAIL.AC.UK > From: Ian Tickle > Sent by: CCP4 bulletin board > Date: 10/14/2011 12:34PM > Subject: Re: [ccp4bb] Optimisation of weights > > Hi Kavya > > The resolutions of the structures mentioned in the paper were only > examples, the Rfree/-LLfree minimisation method (which are actually > due to Axel Brunger & Gerard Bricogne respectively) does not depend on > resolution. > > If the structures are already solved & refined, you don't need to do > any model building, it should be within the radius of convergence with > the new weights - it's only a small adjustment after all. > > Cheers > > -- Ian > > On Fri, Oct 14, 2011 at 6:12 AM, wrote: > > Dear users, > > > > Can the optimization of the X-ray weighing factor > > and B-factor (overall wt) as mentioned in the paper > > Acta Cryst. (2007). D63, 1274–1281 by Dr.Ian Tickel, > > be used for the refinement of the data sets beyond > > the resolution range mentioned in the paper: 1.33 - > > 2.55 Ang? > > > > Also the structures that were used to optimize these > > parameters were already solved and refined, so when > > we are solving a new structure to what extent does the > > model has to be built before starting the optimization? > > > > Thanking you > > With Regards > > M. Kavyashree > > > > > > -- > > This message has been scanned for viruses and > > dangerous content by MailScanner, and is > > believed to be clean. > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. >
Re: [ccp4bb] Akta Prime
Dear Michael, alternative people to service FPLC systems in the UK are called LC Services http://www.lcservs.com/ and came highly recommended to us. cheers charlie From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Michael Colaneri Sent: 12 October 2011 19:29 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Akta Prime Dear all, We have an AktaPrime and GE Lifesciences stop servicing these instruments because they are getting old. Does anyone know of a third party company that gives contracts to maintain these instruments? Thank you. Mike Colaneri
[ccp4bb] PhD position in Structural Immunology/Bacteriology at the Karolinska Institute in Stockholm, Sweden
Karolinska Institutet has a vacancy for A doctoral student with doctoral grant in Structural Immunology/Bacteriology Department Department of Medicine, Huddinge Description of research group and project Center for Infectious Medicine (CIM), Department of Medicine, Huddinge is looking for a PhD student who will work with Associate Professor Adnane Achour and his colleagues in order to determine the three-dimensional structures of virulence-associated proteins derived from various pathogens. The Achour research group is a part of the Center for Infectious Medicine (CIM), Department of Medicine Huddinge, and is localized within the Department of Microbiology, Tumor and Cell biology (MTC) at Solna campus. The research projects of the Achour group are bridging immunology and structural biology. The PhD student candidate will actively participate in projects aiming to unravel the molecular basis of action of specific pathogen-associated proteins. Besides X-ray crystallography, techniques and approaches included within the proposed projects include molecular biology, biochemistry and biophysical approaches such as surface plasmon resonance. The overall aim of the projects is to assess the molecular basis for recognition of ligands by specific pathogen-associated proteins and their mode of action. Duties and responsibilities The proposed projects represent a unique opportunity for a PhD student to acquire deep insights into immunology/microbiology, biochemistry and structural biology using a variety of techniques already well established within the Achour laboratory. The duties and responsibilities of the PhD candidate are to lead the proposed project(s) under the close supervision of his/her supervisors, and in close collaboration with his/her colleagues within the research group. By the end of the PhD study period, the candidate should have acquired a deep knowledge in molecular biology and biochemistry as well as a broad knowledge in immunology and structural biology. The PhD candidate should demonstrate excellent ability to design, perform, interpret, critically assess and contextualize generated data from experimental work. Furthermore, he/she should demonstrate aptitude to discuss and spread research results to both the national and international scientific community as well as to the non-scientific community. Eligibility/Qualifications The eligible candidate must hold a Master´s degree in immunology, biophysics, mathematics, biomedicine, bacteriology, cell biology or equivalent. Previous experience in molecular biology and/or biochemistry is desirable but not absolutely required. We are seeking a highly motivated, creative person with good technical skills. The successful applicant should be fluent in English, with excellent communication capacity combined with the ability to interact effectively and work productively in a team. Emphasis will be placed on personal suitability as well as genuine enthusiasm for the topic. To be eligible, an applicant must 1. hold a Master’s (second-cycle) degree 2. have completed course requirements of at least 240 HECs, of which at least 60 at second-cycle level, or 3. have otherwise acquired essentially equivalent competence in Sweden or abroad. Those who meet the requirements for general eligibility before July 1st, 2007, i.e. had completed a programme of higher education for at least 180 HEC or the equivalent, will continue to do so until the end of July, 2015. Selection of qualified applicants is made on the grounds of their ability to benefit from doctoral (third-cycle) education. Karolinska Institutet applies the following assessment criteria: - Documented subject knowledge of significance to the research project - Analytical skills confirmed by a scientific dissertation or the equivalent - Other documented knowledge/experience of potential significance to doctoral (third-cycle) education in the subject An overall assessment of the applicants’ qualifications will be made. The vacancy will be filled on condition that the successful applicant is admitted to doctoral (third-cycle) education. For further information on doctoral (third-cycle) education at Karolinska Institutet, see www.ki.se/doctoral. Contact person: Ass. Prof. Adnane Achour, phone: 08-5248 6216, 076-8090567, adnane.ach...@ki.se Union representatives: SACO: Ingrid Dahlman, ingrid.dahlman@ki., OFR: Eva Sjölin, eva.sjo...@ki.se Form of employment: Doctoral student Notes A doctoral student with doctoral grant yrs 1, and 2. Temporary doctoral student yrs 3, and 4. Please send your application, marked with reference number 6187/2011, to reach us by no later than November 6 2011 to KI jobb or, to Anna Maria Bernstein, M 54; Karolinska Institutet, 141 86 Stockholm, anna.maria.bernst...@ki.se. The following documents should be enclosed with your application in English or Swedish: - Personal letter of introduction and CV - Copy of
Re: [ccp4bb] data processing problem with ice rings
Hello , Can any one send me pdf of this paper as its a old paper and not accessible here . M.F. Perutz, Preparation of haemoglobin crystals. *J. Cryst. Growth* , * 2 * (1968), pp. 54–56. On Fri, Oct 14, 2011 at 10:42 AM, ChenTiantian wrote: > Hi there, > I am processing a dataset which has bad ice rings (as you can see in the > attach png file). > I tried both XDS and imosflm, and got similar results, it seems that adding > " EXCLUDE_RESOLUTION_RANGE" cannot get rid of the effects of the ice rings. > the following is part of the CORRECT.LP which is the second attached file, > you can find more details there. > > SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF > RESOLUTION > RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR > COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano >LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed > expected Corr > > 4.24 371525537 5545 99.9% 46.9% 52.7% > 371502.4850.8%19.4% -28% 0.5135136 > 3.01 553449002 9840 91.5% 62.7% 65.1% > 551161.7668.3%48.1% -28% 0.5207760 > 2.46 84636 12699 12703 100.0% 67.4% 84.7% > 846341.5573.0%54.2% -19% 0.513 12104 > 2.13 97910 14743 14987 98.4% 254.5%199.3% > 979080.16 276.2% 4899.9% -23% 0.473 14037 > 1.90 110260 16846 16940 99.4% 299.2%303.3% > 1102450.06 325.0% -99.9% -17% 0.422 15995 > 1.74 118354 18629 18744 99.4%1062.0% 1043.6% > 118317 -0.20 1156.4% -99.9% -13% 0.380 17414 > 1.61 122958 20193 20331 99.3% 967.5% 1571.1% > 1228680.10 1059.7% 987.3%-2% 0.402 18348 > 1.51 125075 21554 21794 98.9% 838.9% 1355.1% > 1249330.08 922.6% 1116.9%-1% 0.402 18977 > 1.42 72057 17042 23233 73.4% 640.8% > 775.3%703910.08 732.5% 826.7%-8% 0.425 10003 > total 823746 136245144117 94.5% 166.4%166.7% > 8215620.40 181.1% 296.7% -15% 0.435 119774 > > Note that I/SIGMA of each resolution shell is <2.5, so how should I do to > process the dataset properly? Any suggestion about this super ice rings? > Thanks! > > Tiantian > > -- > Shanghai Institute of Materia Medica, Chinese Academy of Sciences > Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, > Shanghai, 201203 > -- Vandana kukshal
[ccp4bb]
Respected Sir, Thank you for your clarification. I had adopted this method recently. My doubt was if we have to optimize these two parameters during refinement, should we have the whole model along with water and ligands or only protein with few water positioning is enough. The reason why I am asking because there was quite a difference when I refined the same structure without the optimization and with optimization of these two parameters. Thanking you With regards M. Kavyashree -CCP4 bulletin board wrote: - To: CCP4BB@JISCMAIL.AC.UK From: Ian Tickle Sent by: CCP4 bulletin board Date: 10/14/2011 12:34PM Subject: Re: [ccp4bb] Optimisation of weights Hi Kavya The resolutions of the structures mentioned in the paper were only examples, the Rfree/-LLfree minimisation method (which are actually due to Axel Brunger & Gerard Bricogne respectively) does not depend on resolution. If the structures are already solved & refined, you don't need to do any model building, it should be within the radius of convergence with the new weights - it's only a small adjustment after all. Cheers -- Ian On Fri, Oct 14, 2011 at 6:12 AM, wrote: > Dear users, > > Can the optimization of the X-ray weighing factor > and B-factor (overall wt) as mentioned in the paper > Acta Cryst. (2007). D63, 12741281 by Dr.Ian Tickel, > be used for the refinement of the data sets beyond > the resolution range mentioned in the paper: 1.33 - > 2.55 Ang? > > Also the structures that were used to optimize these > parameters were already solved and refined, so when > we are solving a new structure to what extent does the > model has to be built before starting the optimization? > > Thanking you > With Regards > M. Kavyashree > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] data processing problem with ice rings
Your main problem is not the ice rings but a wrong lattice/indexing solution. R factors are very high for even low res shells and I/sigma very low. To me this tells you are not finding your diffraction spots at all. First thing to try: Take more images for the indexing step and use only the strongest spots. And do not refine distance during indexing, as you probably have a pretty high mosaicity. Petri On Oct 14, 2011, at 7:12 AM, ChenTiantian wrote: > Hi there, > I am processing a dataset which has bad ice rings (as you can see in the > attach png file). > I tried both XDS and imosflm, and got similar results, it seems that adding " > EXCLUDE_RESOLUTION_RANGE" cannot get rid of the effects of the ice rings. > the following is part of the CORRECT.LP which is the second attached file, > you can find more details there. > > SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION > RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR > COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano >LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected > Corr > > 4.24 371525537 5545 99.9% 46.9% 52.7% > 371502.4850.8%19.4% -28% 0.5135136 > 3.01 553449002 9840 91.5% 62.7% 65.1% > 551161.7668.3%48.1% -28% 0.5207760 > 2.46 84636 12699 12703 100.0% 67.4% 84.7% > 846341.5573.0%54.2% -19% 0.513 12104 > 2.13 97910 14743 14987 98.4% 254.5%199.3% > 979080.16 276.2% 4899.9% -23% 0.473 14037 > 1.90 110260 16846 16940 99.4% 299.2%303.3% > 1102450.06 325.0% -99.9% -17% 0.422 15995 > 1.74 118354 18629 18744 99.4%1062.0% 1043.6% > 118317 -0.20 1156.4% -99.9% -13% 0.380 17414 > 1.61 122958 20193 20331 99.3% 967.5% 1571.1% > 1228680.10 1059.7% 987.3%-2% 0.402 18348 > 1.51 125075 21554 21794 98.9% 838.9% 1355.1% > 1249330.08 922.6% 1116.9%-1% 0.402 18977 > 1.42 72057 17042 23233 73.4% 640.8%775.3% > 703910.08 732.5% 826.7%-8% 0.425 10003 > total 823746 136245144117 94.5% 166.4%166.7% > 8215620.40 181.1% 296.7% -15% 0.435 119774 > > Note that I/SIGMA of each resolution shell is <2.5, so how should I do to > process the dataset properly? Any suggestion about this super ice rings? > Thanks! > > Tiantian > > -- > Shanghai Institute of Materia Medica, Chinese Academy of Sciences > Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, > Shanghai, 201203 > --- Petri Kursula, PhD Group Leader, Docent of Neurobiochemistry Department of Biochemistry, University of Oulu, Finland Department of Chemistry, University of Hamburg, Germany Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany) www.biochem.oulu.fi/kursula www.desy.de/~petri petri.kurs...@oulu.fi petri.kurs...@desy.de ---
Re: [ccp4bb] Optimisation of weights
Hi Kavya The resolutions of the structures mentioned in the paper were only examples, the Rfree/-LLfree minimisation method (which are actually due to Axel Brunger & Gerard Bricogne respectively) does not depend on resolution. If the structures are already solved & refined, you don't need to do any model building, it should be within the radius of convergence with the new weights - it's only a small adjustment after all. Cheers -- Ian On Fri, Oct 14, 2011 at 6:12 AM, wrote: > Dear users, > > Can the optimization of the X-ray weighing factor > and B-factor (overall wt) as mentioned in the paper > Acta Cryst. (2007). D63, 1274–1281 by Dr.Ian Tickel, > be used for the refinement of the data sets beyond > the resolution range mentioned in the paper: 1.33 - > 2.55 Ang? > > Also the structures that were used to optimize these > parameters were already solved and refined, so when > we are solving a new structure to what extent does the > model has to be built before starting the optimization? > > Thanking you > With Regards > M. Kavyashree > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. >
