Re: [ccp4bb] Rfree from another mtz file
Hi, Thanks everyone for the answers! I was able to identify my R free sets and they are the same =D Best regards Mariana De: CCP4 bulletin board em nome de Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Enviado: terça-feira, 17 de setembro de 2019 11:29 Para: CCP4BB@JISCMAIL.AC.UK Assunto: Re: [ccp4bb] Rfree from another mtz file If you use either GUI2 or GUI you simply name the old file you want to take the FreeR flags from.. The pipeline then initiates the steps catalogued by Robbie.. Eleanor As Tim, and others say, you can assign new FreeR flags, but dont get upset when starting refinement with the prevuis model you see the Free R steadily increasing with refinement for several cycles! Eleanor On Tue, 17 Sep 2019 at 06:15, Robbie Joosten mailto:robbie_joos...@hotmail.com>> wrote: I totally agree. And because the new dataset is of higher resolution, there will be new reflections in the test set anyway. Now if you want to use the same testset always for series of isomorphous datasets (even though you do not need to), you can do this: - Use unique to make a full set of reflections given your space group and cell dimensions - Assign a testset to that file using the program freerflag Foreach dataset: - Copy over the testset from you master file End Note that the testsets in the datasets will be super/subsets of each other but assuming the data are complete they will be the same if you use the same resolution cut-offs. Cheers, Robbie On 17 Sep 2019 02:17, Tim Gruene mailto:tim.gru...@univie.ac.at>> wrote: Dear Mariana, you can simply create a new set for Rfree, independently of the previous one. It will be as good as the copied one, and there is no reason why you would need to maintain the same flags. As Ian Tickle explained only briefly ago, your new data set will have new, independent errors. Best regards, Tim On Tuesday, September 17, 2019 12:29:19 AM CEST Mariana Ajalla wrote: > Dear all, > > We tried to use the Rfree set from a lower resolution data with a higher > resolution from the same Crystal. To do so We used aimless at ccp4i with > the option use free flag from another mtz file and extend the data. > > I think it worked, but now we don't know how to be sure we have the same > Rfree set. Does anyone have a way to prove it? > Thank you in advance, > Best, > Mariana > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] [EXTERNAL] [ccp4bb] Rfree from another mtz file
On 09/16/2019 06:29 PM, Mariana Ajalla wrote: Dear all, We tried to use the Rfree set from a lower resolution data with a higher resolution from the same Crystal. To do so We used aimless at ccp4i with the option use free flag from another mtz file and extend the data. I think it worked, but now we don't know how to be sure we have the same Rfree set. Does anyone have a way to prove it? Thank you in advance, Best, Mariana To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwIFAg=ogn2iPkgF7TkVSicOVBfKg=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA=kL1VStzNS1Omx1vfcOm7a09DSPOnVQ2zVULHRmpq3hk=0ECMEpulh9gbnGLzli9TlEM9bb6ZwdFGdX0v6GK9YVg= Mariana, If you solve a new dataset with a structure previously refined in an isomorphous crystal, and use the same free set as was used for that refinement, you will generally notice that the initial Rfree is higher than initial Rwork, as it was with the old dataset. If you start with a new free set, Rfree and Rwork will initially be the same, and diverge with refinement. This implies that there is some correlation between Fo-Fc calculated with the new data and Fo-Fc from the old dataset. This would lead some to say your Rfree is "corrupted" if you choose a new set, and it will only be valid after many cycles of refinement to "shake out" the bias. Note that Ian Tickle qualified his results by saying it is necessary to refine to convergence for his conclusions to hold. How can the old and new Fo-Fc be correlated, if the errors in the new data are independent from the errors in the old dataset? Well, the errors in measurement contribute only a small fraction to the Fo-Fc differences, as evidenced by the fact that Rpim is much smaller than either Rfree or Rwork. Thinking in terms of "fitting the noise", if we define the noise to be the differences between Fo and Fc, there are two sources for that noise. One is error in measurement, and as noted these should be completely independent. The other "noise" is the difference between our best-refined structure and the actual structure- modeling solvent, fitting disorder with isotropic or even anisotropic B factors when in fact it is more complicated, single or few alternate conformations when in fact there is a range of positions, etc. If the new data actually represents the same structure, or even a new structure of the same protein in an isomorphous crystal, these errors are likely to be the same in the n ew dataset, and could account for the fact that the fit is better for the working reflections which the structure has been refined to minimize against the old dataset, when refined against the new dataset. Again thinking of "fitting the noise", we clearly do not want to fit the noise that comes from errors in measurement. But these are uncorrelated between the datasets, so choosing the same free set has no effect on this. As for fitting the "noise" that is the difference between our model and the real structure, this is a gray area. I tend to think fitting this noise (making our structure more like the true structure) would be a good thing, and if it can be biased by using all the reflections it would be a good thing. But the fact is it is going to make the R-free lower, at least initially, and give you an unfair advantage over the purist who insists on using the same free set for isomorphous structures. Until there is a general consensus on this it might be a good idea to keep the old free set, if only because your reviewer might be one of those purists! To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Rfree from another mtz file
If you use either GUI2 or GUI you simply name the old file you want to take the FreeR flags from.. The pipeline then initiates the steps catalogued by Robbie.. Eleanor As Tim, and others say, you can assign new FreeR flags, but dont get upset when starting refinement with the prevuis model you see the Free R steadily increasing with refinement for several cycles! Eleanor On Tue, 17 Sep 2019 at 06:15, Robbie Joosten wrote: > I totally agree. And because the new dataset is of higher resolution, > there will be new reflections in the test set anyway. > > Now if you want to use the same testset always for series of isomorphous > datasets (even though you do not need to), you can do this: > - Use unique to make a full set of reflections given your space group and > cell dimensions > - Assign a testset to that file using the program freerflag > Foreach dataset: > - Copy over the testset from you master file > End > > Note that the testsets in the datasets will be super/subsets of each other > but assuming the data are complete they will be the same if you use the > same resolution cut-offs. > > Cheers, > Robbie > > On 17 Sep 2019 02:17, Tim Gruene wrote: > > Dear Mariana, > > you can simply create a new set for Rfree, independently of the previous > one. > It will be as good as the copied one, and there is no reason why you would > need to maintain the same flags. As Ian Tickle explained only briefly ago, > your new data set will have new, independent errors. > > Best regards, > Tim > > On Tuesday, September 17, 2019 12:29:19 AM CEST Mariana Ajalla wrote: > > Dear all, > > > > We tried to use the Rfree set from a lower resolution data with a higher > > resolution from the same Crystal. To do so We used aimless at ccp4i with > > the option use free flag from another mtz file and extend the data. > > > > I think it worked, but now we don't know how to be sure we have the same > > Rfree set. Does anyone have a way to prove it? > > Thank you in advance, > > Best, > > Mariana > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > -- > -- > Tim Gruene > Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Rfree from another mtz file
I totally agree. And because the new dataset is of higher resolution, there will be new reflections in the test set anyway. Now if you want to use the same testset always for series of isomorphous datasets (even though you do not need to), you can do this: - Use unique to make a full set of reflections given your space group and cell dimensions - Assign a testset to that file using the program freerflag Foreach dataset: - Copy over the testset from you master file End Note that the testsets in the datasets will be super/subsets of each other but assuming the data are complete they will be the same if you use the same resolution cut-offs. Cheers, Robbie On 17 Sep 2019 02:17, Tim Gruene wrote: Dear Mariana, you can simply create a new set for Rfree, independently of the previous one. It will be as good as the copied one, and there is no reason why you would need to maintain the same flags. As Ian Tickle explained only briefly ago, your new data set will have new, independent errors. Best regards, Tim On Tuesday, September 17, 2019 12:29:19 AM CEST Mariana Ajalla wrote: > Dear all, > > We tried to use the Rfree set from a lower resolution data with a higher > resolution from the same Crystal. To do so We used aimless at ccp4i with > the option use free flag from another mtz file and extend the data. > > I think it worked, but now we don't know how to be sure we have the same > Rfree set. Does anyone have a way to prove it? > Thank you in advance, > Best, > Mariana > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Rfree from another mtz file
Dear Mariana, you can simply create a new set for Rfree, independently of the previous one. It will be as good as the copied one, and there is no reason why you would need to maintain the same flags. As Ian Tickle explained only briefly ago, your new data set will have new, independent errors. Best regards, Tim On Tuesday, September 17, 2019 12:29:19 AM CEST Mariana Ajalla wrote: > Dear all, > > We tried to use the Rfree set from a lower resolution data with a higher > resolution from the same Crystal. To do so We used aimless at ccp4i with > the option use free flag from another mtz file and extend the data. > > I think it worked, but now we don't know how to be sure we have the same > Rfree set. Does anyone have a way to prove it? > Thank you in advance, > Best, > Mariana > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] Rfree from another mtz file
You should be able to get an idea of whether it has worked or not with viewHKL in the old GUI e.g. find a few reflections with R-free flag zero in your old dataset and note the indices. Then you can search the new dataset for these reflections and see if they are still flagged zero. You may need to export the MTZ's from the new GUI first. On Monday, 16 September 2019, 23:39:28 BST, Mariana Ajalla wrote: Dear all, We tried to use the Rfree set from a lower resolution data with a higher resolution from the same Crystal. To do so We used aimless at ccp4i with the option use free flag from another mtz file and extend the data. I think it worked, but now we don't know how to be sure we have the same Rfree set. Does anyone have a way to prove it? Thank you in advance, Best, Mariana To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Rfree from another mtz file
Dear all, We tried to use the Rfree set from a lower resolution data with a higher resolution from the same Crystal. To do so We used aimless at ccp4i with the option use free flag from another mtz file and extend the data. I think it worked, but now we don't know how to be sure we have the same Rfree set. Does anyone have a way to prove it? Thank you in advance, Best, Mariana To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
