Dear Piotrek You can find some info on the use of prior phase information in refinement with Refmac in
Acta Crystallogr D Biol Crystallogr.<https://www.ncbi.nlm.nih.gov/pubmed/?term=steiner+pannu#> 2011 Apr;67(Pt 4):355-67. doi: 10.1107/S0907444911001314. Epub 2011 Mar 18. REFMAC5 for the refinement of macromolecular crystal structures. Murshudov GN<https://www.ncbi.nlm.nih.gov/pubmed/?term=Murshudov%20GN%5BAuthor%5D&cauthor=true&cauthor_uid=21460454>1, Skubák P<https://www.ncbi.nlm.nih.gov/pubmed/?term=Skub%C3%A1k%20P%5BAuthor%5D&cauthor=true&cauthor_uid=21460454>, Lebedev AA<https://www.ncbi.nlm.nih.gov/pubmed/?term=Lebedev%20AA%5BAuthor%5D&cauthor=true&cauthor_uid=21460454>, Pannu NS<https://www.ncbi.nlm.nih.gov/pubmed/?term=Pannu%20NS%5BAuthor%5D&cauthor=true&cauthor_uid=21460454>, Steiner RA<https://www.ncbi.nlm.nih.gov/pubmed/?term=Steiner%20RA%5BAuthor%5D&cauthor=true&cauthor_uid=21460454>, Nicholls RA<https://www.ncbi.nlm.nih.gov/pubmed/?term=Nicholls%20RA%5BAuthor%5D&cauthor=true&cauthor_uid=21460454>, Winn MD<https://www.ncbi.nlm.nih.gov/pubmed/?term=Winn%20MD%5BAuthor%5D&cauthor=true&cauthor_uid=21460454>, Long F<https://www.ncbi.nlm.nih.gov/pubmed/?term=Long%20F%5BAuthor%5D&cauthor=true&cauthor_uid=21460454>, Vagin AA<https://www.ncbi.nlm.nih.gov/pubmed/?term=Vagin%20AA%5BAuthor%5D&cauthor=true&cauthor_uid=21460454>. and references therein. As stated in the paper (paragraph 2.2.2), the incorporation of prior phase information by the refinement function is especially useful in the early and middle stages of model building and at all stages of structure solution at lower resolutions, owing to the improvement in the observation-to-parameter ratio. Refinement in Refmac is very fast therefore the best thing (as you just did) is to try both options and see. With best wishes Roberto On 4 Jan 2019, at 09:55, Piotr Wilk <[email protected]<mailto:[email protected]>> wrote: Dear Eleanor, I have used the ACORN previously for structure solution but I will have to read more about its functionality in structure refinement. I have run two Refmac jobs using either native or anomalous data with otherwise default parameters resulting in R/Rfree of 0.2013/0.2458 and 0.1862/0.2274 respectively for crystal diffracting to ~1.85A. This seems to me, that using anomalous signal in refinement can be useful at least in some cases. Regards, Piotrek Hmm - you can certainly generate "MAD" phases using the anom signal from one data set, and then PARROT or some such density modification tool to extend those phases for the higher resolution reflections.. Or ACORN can work well if he data resolution is high enough to give good phases for all the data Then you can use those phases in the initial refinement procedure - the usual idea is to use them till the R factor drops below 30% or 35% then just refine against the Fobs, phasing just from the model . But I dont think it is ever worth working at a limited resolution.. Dear Eleanor, thank you for your comment. My crystals of interest diffract with dmin usually between 1.4 and 1.9 A (in high energy data set) and significant anomalous signal extends usually to approx. 4 A (in low energy data set). Certainly I do agree, that in "EITHER, OR" situation one can check both approaches, compare the results and take the more convincing one. I can easily do that in Refmac running one job against data with Friedel pairs merged and parallel one against data with Friedel pairs unmerged. I was considering rather an "AND" scenario in which in addition to high resolution data (FP) I'd include information from anomalous signal (F+ F-, DANO). I understand that this should increase number of observations from a given sample and therefore help to refine positions, occupancies and perhaps ADPs for at least a fraction of atoms in a model (Mn ions and S in my case). I imagine it as somehow analogical to adding geometrical restrains derived from very high resolution data to refinement protocols. I was wondering first of all if my reasoning is sensible and if there is an existing protocol to try this? With kind regards, Piotrek czw., 3 sty 2019 o 22:00 Eleanor Dodson <[email protected]<mailto:[email protected]>> napisał(a): Hmm - you can certainly generate "MAD" phases using the anom signal from one data set, and then PARROT or some such density modification tool to extend those phases for the higher resolution reflections.. Or ACORN can work well if he data resolution is high enough to give good phases for all the data Then you can use those phases in the initial refinement procedure - the usual idea is to use them till the R factor drops below 30% or 35% then just refine against the Fobs, phasing just from the model . But I dont think it is ever worth working at a limited resolution.. eleanor On Thu, 3 Jan 2019 at 20:40, Piotr Wilk <[email protected]<mailto:[email protected]>> wrote: Dear Eleanor, thank you for your comment. My crystals of interest diffract with dmin usually between 1.4 and 1.9 A (in high energy data set) and significant anomalous signal extends usually to approx. 4 A (in low energy data set). Certainly I do agree, that in "EITHER, OR" situation one can check both approaches, compare the results and take the more convincing one. I can easily do that in Refmac running one job against data with Friedel pairs merged and parallel one against data with Friedel pairs unmerged. I was considering rather an "AND" scenario in which in addition to high resolution data (FP) I'd include information from anomalous signal (F+ F-, DANO). I understand that this should increase number of observations from a given sample and therefore help to refine positions, occupancies and perhaps ADPs for at least a fraction of atoms in a model (Mn ions and S in my case). I imagine it as somehow analogical to adding geometrical restrains derived from very high resolution data to refinement protocols. I was wondering first of all if my reasoning is sensible and if there is an existing protocol to try this? With kind regards, Piotrek czw., 3 sty 2019 o 17:02 Eleanor Dodson <[email protected]<mailto:[email protected]>> napisał(a): I think any decision depends on the resolution of your two data sets. If they are very different I would choose the higher resolution one. If that is the Anom data then I would use the anom signal at least in the first cycles to improve the phases.. Eleanor On Thu, 3 Jan 2019 at 14:59, Piotr Wilk <[email protected]<mailto:[email protected]>> wrote: Dear CCP4 experts, I'd like to ask your opinion about using anomalous signal in refinement of crystal structures in addition to using high resolution native data. I am working on a series of structures for which I have collected two data sets (from the same crystal): 1 - native with higher resolution 2 - anomalous at MN absorption edge peak. The structures were solved with MR and preliminary refinement using the native data only yields decent statistics, but I also use anomalous data to verify presence and position of manganese ions. For this I used ANODE which lists four strong peaks (~30 sigma) as expected for manganese ions and around 45 weaker peaks (~9-5 sigma) for sulfur atoms in Cys and Met. I am happy to use this information in model building but I was also wondering if (and how) beneficial would it be to use both high resolution structure factors and somehow lower resolution yet highly specific anomalous signal in the same round of refinement? In Refmac5 I can use either refinement with "no prior phase information" taking FP and SIGFP or "SAD data directly" with SIGFP F(+) SIGF(+) F(-) SIGF(-), but I didn't find any "MAD" option to use both. I have the following columns in my mtz files: for native data: H K L FP SIGFP FreeRflag for anomalous data : H K L FP SIGFP F(+) SIGF(+) F(-) SIGF(-) FreeRflag or : H K L FP SIGFP DANO SIGDANO ISYM FreeRflag I could use CAD to merge the interesting columns into a single mtz file containing: H K L FP SIGFP FreeRflag F(+) SIGF(+) F(-) SIGF(-) DANO SIGDANO I'd appreciate any comments or advise how to use both sources of information in the refinement. I wish you all a Happy New Year. Kind regards, Piotrek ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data=01%7C01%7Croberto.steiner%40KCL.AC.UK%7Cc45305549ccb4bb9124108d6722af1d5%7C8370cf1416f34c16b83c724071654356%7C0&sdata=5w8tWKZWS03jEt42moJLZRIB3W9dO7CpXXeZzWVTW8Y%3D&reserved=0> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data=01%7C01%7Croberto.steiner%40KCL.AC.UK%7Cc45305549ccb4bb9124108d6722af1d5%7C8370cf1416f34c16b83c724071654356%7C0&sdata=5w8tWKZWS03jEt42moJLZRIB3W9dO7CpXXeZzWVTW8Y%3D&reserved=0> Roberto A. Steiner Professor of Biomolecular Structure Randall Centre of Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London [email protected]<mailto:[email protected]> Phone 0044 20 78488216 Fax 0044 20 78486435 Room 3.10A New Hunt's House Guy's Campus SE1 1UL London ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
