[ccp4bb] REFMAC - TWIN OPTION
Can someone point me to bulletpoint documentation on using the twin refinement in CCP4? Here's what I did. 1. I'm in space group P3, and the see a very clean diffraction pattern that looks like one single lattice. Very clean spots, so merohedral twinning. 2. You can use various programs to estimate the twin fraction and select various twin laws. 3. You run DETWIN in the UTILITIES section of DATA REDUCTION and ANALYSIS. I have both intensities IMEAN and amplitudes FMEAN, and selected amplitudes. The FMEAN changes to something like FMEAN_detw. You have to select a twin fraction, but does it matter what the twin factor you assign is? (It seems to get refined, or just estimated, in refinement?) 4. There are potentially 3 twin laws, so do you run DETWIN three times? You can, in fact, get amplitudes that are FMEAN_detw_detw_detw. I've run it once and three times, and seems to give the same result in REFMAC refinement. 5. Select the Free R subset. Will uniqueify choose correctly? 6. In REFMAC, it looks for the F_detw amplitude, or you can select it. Then it seems to select and test three twin laws, even if you only ran DETWIN once, with one selected twin law. It tests if the twin laws give low R(merge). If not, it tosses them out. It seems like the R(merge) calculation depends on the starting model, and not just on the modified Fobs data. It also seems like it tries to calculate the twin fraction, and then refine the structure. Or, is it just giving an estimate, and I need to go back to original data and rerun DETWIN? 7. I tried to work with intensities instead of amplitudes, and it can blow up. I've also refined, got a good refinement (3 twin laws, each with twin fraction around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of the structure, and it blows up, suggesting no twinning, but Rs around 35%. Does REFMAC refine the twin fraction? Do I have to assign a twin fraction in DETWIN, or does it just set up the relationships between reflections and amplitudes? Should I try to work with intensities or amplitudes. The calculation is presumably done on intensities, but seems to be more unstable using that option. I haven't tried the PHENIX option. Just a quick step-by-step guide on what to do would be useful. Thanks, Bernie -- Bernard D. Santarsiero Research Professor Center for Structural Biology University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMJ
[ccp4bb] AW: [ccp4bb] REFMAC - TWIN OPTION
Dear Berni, DETWIN will detwin your Fobs, which can be done if the twin fraction is sufficiently far from 0.5. However, as you discovered, you need to know the twin fraction, which is by convention specified by the smaller fraction. Once your data is detwinned, it should just be that, a file with regular fobs and not twinned anymore, so in Refmac you should not use any TWIN keywords. However, this is not the best way to proceed. The best way is to provide Refmac with your twinned dataset and let Refmac figure it all out for you! As you mentioned, Refmac will test the different possible twinning operators and will refine the twinning fraction. In my hands it works very well and is extremely easy even for crystals with multiple twinning operators. Good luck! Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Santarsiero, Bernard D. Gesendet: Mittwoch, 17. September 2014 14:20 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] REFMAC - TWIN OPTION Can someone point me to bulletpoint documentation on using the twin refinement in CCP4? Here's what I did. 1. I'm in space group P3, and the see a very clean diffraction pattern that looks like one single lattice. Very clean spots, so merohedral twinning. 2. You can use various programs to estimate the twin fraction and select various twin laws. 3. You run DETWIN in the UTILITIES section of DATA REDUCTION and ANALYSIS. I have both intensities IMEAN and amplitudes FMEAN, and selected amplitudes. The FMEAN changes to something like FMEAN_detw. You have to select a twin fraction, but does it matter what the twin factor you assign is? (It seems to get refined, or just estimated, in refinement?) 4. There are potentially 3 twin laws, so do you run DETWIN three times? You can, in fact, get amplitudes that are FMEAN_detw_detw_detw. I've run it once and three times, and seems to give the same result in REFMAC refinement. 5. Select the Free R subset. Will uniqueify choose correctly? 6. In REFMAC, it looks for the F_detw amplitude, or you can select it. Then it seems to select and test three twin laws, even if you only ran DETWIN once, with one selected twin law. It tests if the twin laws give low R(merge). If not, it tosses them out. It seems like the R(merge) calculation depends on the starting model, and not just on the modified Fobs data. It also seems like it tries to calculate the twin fraction, and then refine the structure. Or, is it just giving an estimate, and I need to go back to original data and rerun DETWIN? 7. I tried to work with intensities instead of amplitudes, and it can blow up. I've also refined, got a good refinement (3 twin laws, each with twin fraction around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of the structure, and it blows up, suggesting no twinning, but Rs around 35%. Does REFMAC refine the twin fraction? Do I have to assign a twin fraction in DETWIN, or does it just set up the relationships between reflections and amplitudes? Should I try to work with intensities or amplitudes. The calculation is presumably done on intensities, but seems to be more unstable using that option. I haven't tried the PHENIX option. Just a quick step-by-step guide on what to do would be useful. Thanks, Bernie -- Bernard D. Santarsiero Research Professor Center for Structural Biology University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMJ
Re: [ccp4bb] REFMAC - TWIN OPTION
Hi Bernie, I agree with Herman. I think you will be all set if you simply change the no twin refinement option near the top of the Refmac interface to intensity based or amplitude based twin refinement. Refmac will determine the appropriate twin operators/fractions and refine. Best, Chris On Sep 17, 2014, at 14:19, Santarsiero, Bernard D. b...@uic.edu wrote: Can someone point me to bulletpoint documentation on using the twin refinement in CCP4? Here's what I did. 1. I'm in space group P3, and the see a very clean diffraction pattern that looks like one single lattice. Very clean spots, so merohedral twinning. 2. You can use various programs to estimate the twin fraction and select various twin laws. 3. You run DETWIN in the UTILITIES section of DATA REDUCTION and ANALYSIS. I have both intensities IMEAN and amplitudes FMEAN, and selected amplitudes. The FMEAN changes to something like FMEAN_detw. You have to select a twin fraction, but does it matter what the twin factor you assign is? (It seems to get refined, or just estimated, in refinement?) 4. There are potentially 3 twin laws, so do you run DETWIN three times? You can, in fact, get amplitudes that are FMEAN_detw_detw_detw. I've run it once and three times, and seems to give the same result in REFMAC refinement. 5. Select the Free R subset. Will uniqueify choose correctly? 6. In REFMAC, it looks for the F_detw amplitude, or you can select it. Then it seems to select and test three twin laws, even if you only ran DETWIN once, with one selected twin law. It tests if the twin laws give low R(merge). If not, it tosses them out. It seems like the R(merge) calculation depends on the starting model, and not just on the modified Fobs data. It also seems like it tries to calculate the twin fraction, and then refine the structure. Or, is it just giving an estimate, and I need to go back to original data and rerun DETWIN? 7. I tried to work with intensities instead of amplitudes, and it can blow up. I've also refined, got a good refinement (3 twin laws, each with twin fraction around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of the structure, and it blows up, suggesting no twinning, but Rs around 35%. Does REFMAC refine the twin fraction? Do I have to assign a twin fraction in DETWIN, or does it just set up the relationships between reflections and amplitudes? Should I try to work with intensities or amplitudes. The calculation is presumably done on intensities, but seems to be more unstable using that option. I haven't tried the PHENIX option. Just a quick step-by-step guide on what to do would be useful. Thanks, Bernie -- Bernard D. Santarsiero Research Professor Center for Structural Biology University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMJ
