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First advice - are you sure the images etc are OK? Green lights are not as useful as detailed analysis. I like the CCP4I2 report - it provides enough information to dig down for problems... Again - do try SIMBAD or similar is very sensible. But Beta sheet structures are a pain! As was noted your solutions are all (or almost all) simply solution 1 plus translations of that solution. There are several possibilities - your partial model of the beta sheet need to be extended by a second, third, fourth copy moved by a fixed translation. That is possible of course if the beta sheet is very much more extensive than the model and very flat, but that seems a bit unlikely. More likely - these overlaping solutions with high LLG are a misleading artefact . There isnt much symmetry in P1 to fix down such aberrations,, What happens if you try refining only the first solution? . On Thu, 29 Aug 2019 at 18:57, Roger Rowlett <[log in to unmask]> wrote: > EPMR is also a good alternative for finding multiple placements per ASU. > > If a reasonable packing MR solution can be found and there is significant > NCS, then DM followed by NCS enhanced automated model building from initial > MR phases can do wonders. Improvement goes as the square root of NCS > numbers, though, so 2 is not a great improvement, e.g. > > __________________ > Roger Rowlett > > On Thu, Aug 29, 2019, 1:42 PM Jonathan Cooper < > [log in to unmask]> wrote: > >> It would be useful to know the number of molecules per asymmetric unit >> and the sequence similarity of the search model and target. There is always >> Molrep to try which is good at NCS ;- >> >> Sent from Yahoo Mail on Android >> <https://go.onelink.me/107872968?pid=InProduct&c=Global_Internal_YGrowth_AndroidEmailSig__AndroidUsers&af_wl=ym&af_sub1=Internal&af_sub2=Global_YGrowth&af_sub3=EmailSignature> >> >> On Thu, 29 Aug 2019 at 18:30, David Briggs >> <[log in to unmask]> wrote: >> Following on from Ivan's suggestion, SIMBAD might he worth a shot. >> >> https://journals.iucr.org/d/issues/2018/07/00/rr5159/ >> >> The other thing you might try is handing the MR phases to the density >> modifying and autobuilding program of your choice, increasing the number of >> cycles by $arbitarylargenumber and then leaving it to run for a few >> hours/over night. >> >> This has worked for me in the past when resolution was decent, phaser had >> found an obviously correct MR solution, but the domain placed was only >> ~30-40% of the total scattering mass of the ASU, and more conventional >> refinement was not yielding decent maps outside the aforementioned domain. >> >> Good luck! >> >> Dave >> >> -- >> Dr David C. Briggs >> Senior Laboratory Research Scientist >> Signalling and Structural Biology Lab >> The Francis Crick Institute >> London, UK >> == >> about.me/david_briggs >> >> ------------------------------ >> *From:* CCP4 bulletin board <[log in to unmask]> on behalf of Phil >> Jeffrey <[log in to unmask]> >> *Sent:* Thursday, August 29, 2019 5:24:48 PM >> *To:* [log in to unmask] <[log in to unmask]> >> *Subject:* Re: [ccp4bb] Another difficult MR case >> >> Are you *sure* there's no translational NCS ? >> >> For example your first molecular replacement solution out of Phenix shows >> >> EULER 293.6 27.7 288.7 >> FRAC -0.02 0.02 0.02 >> (that's "first molecule at origin in P1") >> >> and >> >> EULER 294.0 27.9 288.8 >> FRAC -0.37 0.02 0.02 >> >> which is essentially the same orientation, and a translation down one >> crystallographic axis (a*) >> >> And this suggests to me that either Xtriage or Phaser is missing >> something here. Does Phaser find translational NCS in its initial data >> analysis ? Unmodeled translational NCS could cause significant problems >> with the molecular replacement search. >> >> Phil Jeffrey >> Princeton >> >> >> >> >> On 8/29/19 11:28 AM, Napoleão wrote: >> > Deal all, >> > Sorry for the long post. >> > I have a data set obtained from a crystal produced after incubating a >> > protease with a protein which is mostly composed by an antiparallel >> beta >> > sheet. I have tried numerous approaches to solve it, and failed. >> > Molecular replacement using Phaser, and the protease or the protein as >> a >> > template yields no solution. However, molecular replacement using only >> > part of the beta sheet yields LLG=320 TFZ==28.0 (see below). >> > >> > The apparently good data extends to 1.9 A, as processed by XDS, and the >> > space group is P1 (pointless agree). XDS info below: >> > >> > SPACE_GROUP_NUMBER= 1 >> > UNIT_CELL_CONSTANTS= 44.43 72.29 77.30 97.802 89.939 101.576 >> > >> > a b ISa >> > 9.647E-01 3.176E-03 18.07 >> > >> > RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR >> > R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano >> > LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed >> > expected Corr >> > 1.90 24890 19149 23814 80.4% 58.1% >> > 63.7% 11482 0.77 82.2% 63.8* 3 0.694 492 >> > total 163756 125884 146938 85.7% 10.6% >> > 10.8% 75744 3.78 15.0% 99.0* -3 0.761 5834 >> > >> > >> > Xtriage in Phenix 1.16-3549 gives me all green lights (print below), >> > suggesting the data presents no twinning, no translational NCS, no ice >> > rings and is not anisotropic. >> > >> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffullonline.org%2Fscience%2Fphenix_xtriage_green.png&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=RMV8abo87ybMyxaqD%2FHgOakRhGvzGgsQXzkuzC4c8HI%3D&reserved=0 >> <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffullonline.org%2Fscience%2Fphenix_xtriage_green.png&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=RMV8abo87ybMyxaqD%2FHgOakRhGvzGgsQXzkuzC4c8HI%3D&reserved=0> >> > >> > Molecular replacement in Phaser yields single solutions like: >> > >> > Solution annotation (history): >> > SOLU SET RFZ=3.0 TFZ=* PAK=0 LLG=29 RFZ=2.8 TFZ=8.8 PAK=1 LLG=310 >> > TFZ==27.6 >> > LLG=320 TFZ==28.0 >> > SOLU SPAC P 1 >> > SOLU 6DIM ENSE ensemble1 EULER 293.6 27.7 288.7 FRAC -0.02 >> > 0.02 0.02 BFAC >> > -6.03 >> > SOLU 6DIM ENSE ensemble1 EULER 294.0 27.9 288.8 FRAC -0.37 >> > 0.02 0.02 BFAC >> > -6.52 >> > SOLU ENSEMBLE ensemble1 VRMS DELTA -0.1983 RMSD 0.49 #VRMS 0.21 >> > >> > or partial solutions like: >> > >> > Partial Solution #1 annotation (history): >> > SOLU SET RFZ=3.7 TFZ=* PAK=0 LLG=32 RFZ=2.8 TFZ=13.0 PAK=0 LLG=317 >> > TFZ==30.2 >> > LLG=331 TFZ==30.5 RFZ=2.4 TFZ=7.2 PAK=0 LLG=464 TFZ==18.5 RFZ=2.7 >> > TFZ=5.7 PAK=1 >> > LLG=501 TFZ==6.8 LLG=509 TFZ==6.6 >> > SOLU SPAC P 1 >> > SOLU 6DIM ENSE ensemble1 EULER 85.4 153.0 138.5 FRAC -0.01 >> -0.00 >> > -0.00 BFAC >> > -12.30 >> > SOLU 6DIM ENSE ensemble1 EULER 86.2 153.2 139.5 FRAC -0.36 >> -0.01 >> > -0.01 BFAC >> > -9.16 >> > SOLU 6DIM ENSE ensemble1 EULER 83.8 152.3 135.9 FRAC -0.00 >> 0.00 >> > -0.25 BFAC >> > 1.52 >> > SOLU 6DIM ENSE ensemble1 EULER 191.2 109.1 39.3 FRAC -0.27 >> > -0.01 0.22 BFAC >> > 10.18 >> > SOLU ENSEMBLE ensemble1 VRMS DELTA -0.0447 RMSD 0.49 #VRMS 0.44 >> > >> > >> > However, after 1 refinement round in Phenix_Refine (Final: r_work = >> > 0.4881 r_free = 0.5009) I got densities that are part good and part >> bad, >> > and if I delete the bad parts and refine again, the good parts become >> > bad. Please check the prints: >> > >> > >> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffullonline.org%2Fscience%2Fgood_part_of_density.png&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=TZ69yTqXL1Kr%2FsAlUYJbxuCM1RQH0hDa9quwlz3Hueo%3D&reserved=0 >> <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffullonline.org%2Fscience%2Fgood_part_of_density.png&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=TZ69yTqXL1Kr%2FsAlUYJbxuCM1RQH0hDa9quwlz3Hueo%3D&reserved=0> >> > >> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffullonline.org%2Fscience%2Fbad_part_of_density.png&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=F%2B07eOV%2FziEwrhISIkbbRaWM8pdP3md94r%2FIgSZ9gWc%3D&reserved=0 >> <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffullonline.org%2Fscience%2Fbad_part_of_density.png&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=F%2B07eOV%2FziEwrhISIkbbRaWM8pdP3md94r%2FIgSZ9gWc%3D&reserved=0> >> > >> > What is the explanation for these molecular replacement results? >> > What else should I try? Arcimboldo takes 2 days+ to run and yields no >> > good solution. >> > >> > Thank you! >> > Regards, >> > Napo >> > >> > >> > ------------------------------------------------------------------------ >> > >> > To unsubscribe from the CCP4BB list, click the following link: >> > >> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=AvS1I%2FiA93Rsehqlo4EJegKMYonIG9QCs8iO3aAmfq0%3D&reserved=0 >> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=AvS1I%2FiA93Rsehqlo4EJegKMYonIG9QCs8iO3aAmfq0%3D&reserved=0> >> > >> >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> >> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=AvS1I%2FiA93Rsehqlo4EJegKMYonIG9QCs8iO3aAmfq0%3D&reserved=0 >> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=AvS1I%2FiA93Rsehqlo4EJegKMYonIG9QCs8iO3aAmfq0%3D&reserved=0> >> >> The Francis Crick Institute Limited is a registered charity in England >> and Wales no. 1140062 and a company registered in England and Wales no. >> 06885462, with its registered office at 1 Midland Road London NW1 1AT >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1