multi-xtal averaging vs twinning
Hi, I'm trying to to figure out how to transfer phases from a twinned SeMet dataset to the native one for refinement. 1) SeMet dataset (2.9A) is solved (despite twinning), structure built, refines 29/35 (ish) 2) SeMet crystals are hemihedrally twinned (confirmed by refining with twin law), native probably too. 3) Native dataset (2.7A) has 5A difference in the long cell edge (478 vs 483A). So I could (and will try to) simply copy the SeMet phases into the native dataset, even though CC Fnat and Fsme is rather low (80-20%). But would phenix.multi_crystal_average know what to do with this? It has no explicit options, so I expected not. Or how *would* one approach this? Cheers Frank
< snip >
Or how *would* one approach this?
Basic MR / refinement, guided by plain phenix.multi_crystal_average phases without anything special I guess ... (Like you indicate basically). Make sure that indexing between datasets is consistent (try something like phenix.xtriage native.sca reference.data.file=semet.sca). Lowish CC's can be explained by non-isomorphism issues as well as different twin fractions in different xtals. HTH P
Oh -- the argument being that it's not the phases that are twinned? Peter Zwart wrote:
< snip >
Or how *would* one approach this?
Basic MR / refinement, guided by plain phenix.multi_crystal_average phases without anything special I guess ... (Like you indicate basically).
Make sure that indexing between datasets is consistent (try something like phenix.xtriage native.sca reference.data.file=semet.sca). Lowish CC's can be explained by non-isomorphism issues as well as different twin fractions in different xtals.
HTH
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Hi Frank, To use phenix.multi_crystal_average you need one more step: take the model from your SeMet dataset and do MR on it in the native cell with native F. Now you have the correspondence between the two cells, and you can plug the 2 models and the one phase set and the native F's straight into phenix.multi_crystal_average to transfer the phase information to the native (and cross-crystal average). All the best, Tom T On Jun 23, 2009, at 1:44 AM, Frank von Delft wrote:
Hi, I'm trying to to figure out how to transfer phases from a twinned SeMet dataset to the native one for refinement.
1) SeMet dataset (2.9A) is solved (despite twinning), structure built, refines 29/35 (ish)
2) SeMet crystals are hemihedrally twinned (confirmed by refining with twin law), native probably too.
3) Native dataset (2.7A) has 5A difference in the long cell edge (478 vs 483A).
So I could (and will try to) simply copy the SeMet phases into the native dataset, even though CC Fnat and Fsme is rather low (80-20%). But would phenix.multi_crystal_average know what to do with this? It has no explicit options, so I expected not.
Or how *would* one approach this?
Cheers Frank
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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
Hi Tom, Yep, that I figured out, but do I need to detwin the native F's first? Cheers phx Tom Terwilliger wrote:
Hi Frank, To use phenix.multi_crystal_average you need one more step: take the model from your SeMet dataset and do MR on it in the native cell with native F. Now you have the correspondence between the two cells, and you can plug the 2 models and the one phase set and the native F's straight into phenix.multi_crystal_average to transfer the phase information to the native (and cross-crystal average). All the best, Tom T
On Jun 23, 2009, at 1:44 AM, Frank von Delft wrote:
Hi, I'm trying to to figure out how to transfer phases from a twinned SeMet dataset to the native one for refinement.
1) SeMet dataset (2.9A) is solved (despite twinning), structure built, refines 29/35 (ish)
2) SeMet crystals are hemihedrally twinned (confirmed by refining with twin law), native probably too.
3) Native dataset (2.7A) has 5A difference in the long cell edge (478 vs 483A).
So I could (and will try to) simply copy the SeMet phases into the native dataset, even though CC Fnat and Fsme is rather low (80-20%). But would phenix.multi_crystal_average know what to do with this? It has no explicit options, so I expected not.
Or how *would* one approach this?
Cheers Frank
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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] mailto:[email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org http://www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
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Hi Frank, I have not done this with twinned data....but I would say yes, detwin everything for this step if you can (but of course refine against the twinned data with a twin target). It is probably good to detwin because the density modification procedure does not know about twinning... All the best, Tom T On Jun 26, 2009, at 1:18 AM, Frank von Delft wrote:
Hi Tom,
Yep, that I figured out, but do I need to detwin the native F's first?
Cheers phx
Tom Terwilliger wrote:
Hi Frank, To use phenix.multi_crystal_average you need one more step: take the model from your SeMet dataset and do MR on it in the native cell with native F. Now you have the correspondence between the two cells, and you can plug the 2 models and the one phase set and the native F's straight into phenix.multi_crystal_average to transfer the phase information to the native (and cross-crystal average). All the best, Tom T
On Jun 23, 2009, at 1:44 AM, Frank von Delft wrote:
Hi, I'm trying to to figure out how to transfer phases from a twinned SeMet dataset to the native one for refinement.
1) SeMet dataset (2.9A) is solved (despite twinning), structure built, refines 29/35 (ish)
2) SeMet crystals are hemihedrally twinned (confirmed by refining with twin law), native probably too.
3) Native dataset (2.7A) has 5A difference in the long cell edge (478 vs 483A).
So I could (and will try to) simply copy the SeMet phases into the native dataset, even though CC Fnat and Fsme is rather low (80-20%). But would phenix.multi_crystal_average know what to do with this? It has no explicit options, so I expected not.
Or how *would* one approach this?
Cheers Frank
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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] mailto:[email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org <http://www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
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_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
On a side note, for those who have successfully applied multi-xtal averaging, Under what criteria would one embark on using multi-xtal averaging? -Same unit cell / s.g. (isomorphism) -Data was collected from xtals from different conditions? -MR model shows different/unrecognizable features in 2Fo-Fc maps for each xtal individually? -What if some residues are dynamic (different orientations in each xtal) or disordered? Would these show up garbage or not at all in the averaged map? Any *good* (i.e. well detailed) papers discussing the details of multi- xtal averaging would be great. Tom: Are only model phases used? In other words, are/can experimental phases used? Would having experimental phases from any of the xtals help in cases where the current model is incomplete (say 60%/70% built or Rfree in the 30's) ? On Jun 26, 2009, at 7:39 AM, Tom Terwilliger wrote:
Hi Frank, I have not done this with twinned data....but I would say yes, detwin everything for this step if you can (but of course refine against the twinned data with a twin target). It is probably good to detwin because the density modification procedure does not know about twinning... All the best, Tom T
On Jun 26, 2009, at 1:18 AM, Frank von Delft wrote:
Hi Tom,
Yep, that I figured out, but do I need to detwin the native F's first?
Cheers phx
Tom Terwilliger wrote:
Hi Frank, To use phenix.multi_crystal_average you need one more step: take the model from your SeMet dataset and do MR on it in the native cell with native F. Now you have the correspondence between the two cells, and you can plug the 2 models and the one phase set and the native F's straight into phenix.multi_crystal_average to transfer the phase information to the native (and cross-crystal average). All the best, Tom T
On Jun 23, 2009, at 1:44 AM, Frank von Delft wrote:
Hi, I'm trying to to figure out how to transfer phases from a twinned SeMet dataset to the native one for refinement.
1) SeMet dataset (2.9A) is solved (despite twinning), structure built, refines 29/35 (ish)
2) SeMet crystals are hemihedrally twinned (confirmed by refining with twin law), native probably too.
3) Native dataset (2.7A) has 5A difference in the long cell edge (478 vs 483A).
So I could (and will try to) simply copy the SeMet phases into the native dataset, even though CC Fnat and Fsme is rather low (80-20%). But would phenix.multi_crystal_average know what to do with this? It has no explicit options, so I expected not.
Or how *would* one approach this?
Cheers Frank
_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] mailto:[email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org <http://www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
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_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http:// solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ cbss
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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Hi Francis, I think multi-crystal averaging is going to be useful only if the crystals are completely different or the amplitudes are nearly uncorrelated. In cases where there are only small changes the averaging procedure has almost nothing different in the two structures to work with and it won't do much. Another way to say this is that multi-crystal averaging works because two or more very different ways of sampling the Fourier transform of the molecule are occurring, and each must be consistent with the corresponding measured data. If the molecules are nearly the same and the measured data are nearly the same in all cases, then there are few constraints on the phases. Yes, experimental phases can be included in multi-crystal averaging, just as for NCS averaging. And yes, experimental phases are most helpful. If some regions are different in the different crystals, then the masking procedure needs to be adjusted to exclude the variable regions from the averaging process. Perhaps someone else can suggest a good paper to read on this. Kevin Cowtan's paper on dmmulti is listed on his program documentation as: K. Cowtan (1998) Joint CCP4 and ESF-ECBM Newsletter on Protein Crystallography, 31, p34-38. All the best, Tom T On Jun 26, 2009, at 8:37 AM, Francis E Reyes wrote:
On a side note, for those who have successfully applied multi-xtal averaging,
Under what criteria would one embark on using multi-xtal averaging?
-Same unit cell / s.g. (isomorphism) -Data was collected from xtals from different conditions? -MR model shows different/unrecognizable features in 2Fo-Fc maps for each xtal individually? -What if some residues are dynamic (different orientations in each xtal) or disordered? Would these show up garbage or not at all in the averaged map?
Any *good* (i.e. well detailed) papers discussing the details of multi-xtal averaging would be great.
Tom: Are only model phases used? In other words, are/can experimental phases used? Would having experimental phases from any of the xtals help in cases where the current model is incomplete (say 60%/70% built or Rfree in the 30's) ?
On Jun 26, 2009, at 7:39 AM, Tom Terwilliger wrote:
Hi Frank, I have not done this with twinned data....but I would say yes, detwin everything for this step if you can (but of course refine against the twinned data with a twin target). It is probably good to detwin because the density modification procedure does not know about twinning... All the best, Tom T
On Jun 26, 2009, at 1:18 AM, Frank von Delft wrote:
Hi Tom,
Yep, that I figured out, but do I need to detwin the native F's first?
Cheers phx
Tom Terwilliger wrote:
Hi Frank, To use phenix.multi_crystal_average you need one more step: take the model from your SeMet dataset and do MR on it in the native cell with native F. Now you have the correspondence between the two cells, and you can plug the 2 models and the one phase set and the native F's straight into phenix.multi_crystal_average to transfer the phase information to the native (and cross-crystal average). All the best, Tom T
On Jun 23, 2009, at 1:44 AM, Frank von Delft wrote:
Hi, I'm trying to to figure out how to transfer phases from a twinned SeMet dataset to the native one for refinement.
1) SeMet dataset (2.9A) is solved (despite twinning), structure built, refines 29/35 (ish)
2) SeMet crystals are hemihedrally twinned (confirmed by refining with twin law), native probably too.
3) Native dataset (2.7A) has 5A difference in the long cell edge (478 vs 483A).
So I could (and will try to) simply copy the SeMet phases into the native dataset, even though CC Fnat and Fsme is rather low (80-20%). But would phenix.multi_crystal_average know what to do with this? It has no explicit options, so I expected not.
Or how *would* one approach this?
Cheers Frank
_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] mailto:[email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org <http://www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
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_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
participants (4)
-
Francis E Reyes -
Frank von Delft -
Peter Zwart -
Tom Terwilliger