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 <CCP4BB@JISCMAIL.AC.UK> on behalf of Phil Jeffrey <pjeff...@princeton.edu> Sent: Thursday, August 29, 2019 5:24:48 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> 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 > > 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%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 > ######################################################################## 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 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
