problem with a twinned data set
Hi All This a question of general Crystallography and use of Phenix to deal with twinned data. I am having difficulties with a data set. We have data (2.6 ang resolution) that can be scaled and reduced in P222 with a Rmerge of 7%, the systematic absences show a screw axis ( it is P22(1)2). However MR in Phaser failed in this orthorhombic settings when searching for 2 molecules of the complex in the AU. If we reduce and scale the data in P2(1) and look at the diffraction pattern in HKLVIEW there is a /mmm symmetry. In the monoclinic P2(1) setting we can find 4 molecules of the complex (by MR in Phaser) and can refine it with Phenix to a Rfac/Rfree of 28%/34%. 2 molecules have good electron density whereas the two other ones have one of their domain very poorly defined in density. This is looking very suspicious to me and I am wondering if this refined structure is partially wrong? Meanwhile I used phenix.triage on the data processed in P222 and I am confused with the output. ##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------## Using data between 10.00 to 3.36 Angstrom. Determining possible twin laws. The following twin laws have been found: ------------------------------------------------------------------------ ------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ------------------------------------------------------------------------ ------- | PM | 4-fold | 2.851 | 0.000 | 0.013 | - l,k,h | ------------------------------------------------------------------------ ------- M: Merohedral twin law PM: Pseudomerohedral twin law 0 merohedral twin operators found 1 pseudo-merohedral twin operators found In total, 1 twin operator were found --------------------------------------------- Analysing possible twin law : -l,k,h --------------------------------------------- Results of the H-test on acentric data: (Only 50.0% of the strongest twin pairs were used) mean |H| : 0.368 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.194 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.132 Estimation of twin fraction via cum. dist. of H: 0.115 Britton analyses Extrapolation performed on 0.14 < alpha < 0.495 Estimated twin fraction: 0.127 Correlation: 0.9955 By comparison if I run the detect_twin routine of CNS it tells me that they are no merohedral twin laws for the point group 222 (using the statistical method of Yeates) ? This is confusing me quite a bit. Assuming that the twinning law suggested by Phenix is correct how should I proceed? I have noticed the section concerning refinement using twinned data in Phenix phenix.refine data.hkl model.pdb twin_law="-k,-h,-l" detwin.map_types.aniso_correct=true but It seems I only have a MR solution in P2(1) but not in P222(1) so how can I refine in P222(1) I will greatly appreciate your input, many thanks. Pascal F. Egea, PhD University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory [email protected]
Hi Pascal,
A couple of points.
1. If you cannot find an MR solution in P222 but you can in P2 pg's,
try pg P2. Twin law you have to use is missing two fold along a,b or
c.
2. Equivalent to the four-fold pseudo merohedral twinlaw you mention,
is the two fold 'k,h,-l'. Use that one instead when trying to refine
in pg p222. This is a bug/feature in phenix.xtriage. It is a pseudo
merohedral twin law and you will not find it in merohedral lookup
tables (which is why we don't use lookup tables).
3. When 'true' poing group is P2, there are 3 possible P2's you have
to try. When indexing in LABELIT, MOSFLM or D*TREK, you will have
three unique monoclinic choices (rather then a single one). You should
try all.
4. For the P222 case, make sure you don't bite yourself in the neck by
assuming specific absences / spacegroups. Try all! When 'absent data'
is twinned with 'non absent data', one can be easily fooled.
HTH
Peter
2008/3/1, Pascal EGEA
Hi All
This a question of general Crystallography and use of Phenix to deal with twinned data.
I am having difficulties with a data set. We have data (2.6 ang resolution) that can be scaled and reduced in P222 with a Rmerge of 7%, the systematic absences show a screw axis ( it is P22(1)2). However MR in Phaser failed in this orthorhombic settings when searching for 2 molecules of the complex in the AU. If we reduce and scale the data in P2(1) and look at the diffraction pattern in HKLVIEW there is a /mmm symmetry. In the monoclinic P2(1) setting we can find 4 molecules of the complex (by MR in Phaser) and can refine it with Phenix to a Rfac/Rfree of 28%/34%. 2 molecules have good electron density whereas the two other ones have one of their domain very poorly defined in density. This is looking very suspicious to me and I am wondering if this refined structure is partially wrong?
Meanwhile I used phenix.triage on the data processed in P222 and I am confused with the output.
##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------##
Using data between 10.00 to 3.36 Angstrom.
Determining possible twin laws.
The following twin laws have been found:
------------------------------------------------------------------------------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ------------------------------------------------------------------------------- | PM | 4-fold | 2.851 | 0.000 | 0.013 | -l,k,h | ------------------------------------------------------------------------------- M: Merohedral twin law PM: Pseudomerohedral twin law
0 merohedral twin operators found 1 pseudo-merohedral twin operators found In total, 1 twin operator were found
--------------------------------------------- Analysing possible twin law : -l,k,h ---------------------------------------------
Results of the H-test on acentric data:
(Only 50.0% of the strongest twin pairs were used)
mean |H| : 0.368 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.194 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.132 Estimation of twin fraction via cum. dist. of H: 0.115
Britton analyses
Extrapolation performed on 0.14 < alpha < 0.495 Estimated twin fraction: 0.127 Correlation: 0.9955
By comparison if I run the detect_twin routine of CNS it tells me that they are no merohedral twin laws for the point group 222 (using the statistical method of Yeates) ? This is confusing me quite a bit.
Assuming that the twinning law suggested by Phenix is correct how should I proceed? I have noticed the section concerning refinement using twinned data in Phenix phenix.refine data.hkl model.pdb twin_law="-k,-h,-l" detwin.map_types.aniso_correct=true
but It seems I only have a MR solution in P2(1) but not in P222(1) so how can I refine in P222(1)
I will greatly appreciate your input, many thanks.
Pascal F. Egea, PhD University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Pascal, the reason CNS tells you that there are no twin laws is that it only considers true merohedral twinning and not pseudo-merohedral - the latter is what xtriage is reporting. Cheers, Paul On Mar 1, 2008, at 4:04 PM, Pascal EGEA wrote:
Hi All
This a question of general Crystallography and use of Phenix to deal with twinned data.
I am having difficulties with a data set. We have data (2.6 ang resolution) that can be scaled and reduced in P222 with a Rmerge of 7%, the systematic absences show a screw axis ( it is P22(1)2). However MR in Phaser failed in this orthorhombic settings when searching for 2 molecules of the complex in the AU. If we reduce and scale the data in P2(1) and look at the diffraction pattern in HKLVIEW there is a /mmm symmetry. In the monoclinic P2(1) setting we can find 4 molecules of the complex (by MR in Phaser) and can refine it with Phenix to a Rfac/Rfree of 28%/ 34%. 2 molecules have good electron density whereas the two other ones have one of their domain very poorly defined in density. This is looking very suspicious to me and I am wondering if this refined structure is partially wrong?
Meanwhile I used phenix.triage on the data processed in P222 and I am confused with the output.
##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------##
Using data between 10.00 to 3.36 Angstrom.
Determining possible twin laws.
The following twin laws have been found:
---------------------------------------------------------------------- --------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ---------------------------------------------------------------------- --------- | PM | 4-fold | 2.851 | 0.000 | 0.013 | -l,k,h | ---------------------------------------------------------------------- --------- M: Merohedral twin law PM: Pseudomerohedral twin law
0 merohedral twin operators found 1 pseudo-merohedral twin operators found In total, 1 twin operator were found
--------------------------------------------- Analysing possible twin law : -l,k,h ---------------------------------------------
Results of the H-test on acentric data:
(Only 50.0% of the strongest twin pairs were used)
mean |H| : 0.368 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.194 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.132 Estimation of twin fraction via cum. dist. of H: 0.115
Britton analyses
Extrapolation performed on 0.14 < alpha < 0.495 Estimated twin fraction: 0.127 Correlation: 0.9955
By comparison if I run the detect_twin routine of CNS it tells me that they are no merohedral twin laws for the point group 222 (using the statistical method of Yeates) ? This is confusing me quite a bit.
Assuming that the twinning law suggested by Phenix is correct how should I proceed? I have noticed the section concerning refinement using twinned data in Phenix phenix.refine data.hkl model.pdb twin_law="-k,-h,-l" detwin.map_types.aniso_correct=true
but It seems I only have a MR solution in P2(1) but not in P222(1) so how can I refine in P222(1)
I will greatly appreciate your input, many thanks.
Pascal F. Egea, PhD University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
In addition to what has been suggested, another option is to merge the data in P1 and look for 8 copies. Now that you have a reasonable refined model from the monoclinic solution, this should find a solution. Then you can look for the symmetry in the molecular replacement solution to decide what symmetry is crystallographic. An easy shortcut is to run a self-rotation function on the Fcalcs from the model. (At the moment, I think you'll have to go outside Phenix to do that -- we're intending to put a self-rotation function into Phaser but it's still on the to-do list!) Regards Randy Read On Mar 2 2008, Pascal EGEA wrote:
Hi All
This a question of general Crystallography and use of Phenix to deal with twinned data.
I am having difficulties with a data set. We have data (2.6 ang resolution) that can be scaled and reduced in P222 with a Rmerge of 7%, the systematic absences show a screw axis ( it is P22(1)2). However MR in Phaser failed in this orthorhombic settings when searching for 2 molecules of the complex in the AU. If we reduce and scale the data in P2(1) and look at the diffraction pattern in HKLVIEW there is a /mmm symmetry. In the monoclinic P2(1) setting we can find 4 molecules of the complex (by MR in Phaser) and can refine it with Phenix to a Rfac/Rfree of 28%/34%. 2 molecules have good electron density whereas the two other ones have one of their domain very poorly defined in density. This is looking very suspicious to me and I am wondering if this refined structure is partially wrong?
Meanwhile I used phenix.triage on the data processed in P222 and I am confused with the output.
##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------##
Using data between 10.00 to 3.36 Angstrom.
Determining possible twin laws.
The following twin laws have been found:
------------------------------------------------------------------------ ------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ------------------------------------------------------------------------ ------- | PM | 4-fold | 2.851 | 0.000 | 0.013 | - l,k,h | ------------------------------------------------------------------------ ------- M: Merohedral twin law PM: Pseudomerohedral twin law
0 merohedral twin operators found 1 pseudo-merohedral twin operators found In total, 1 twin operator were found
--------------------------------------------- Analysing possible twin law : -l,k,h ---------------------------------------------
Results of the H-test on acentric data:
(Only 50.0% of the strongest twin pairs were used)
mean |H| : 0.368 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.194 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.132 Estimation of twin fraction via cum. dist. of H: 0.115
Britton analyses
Extrapolation performed on 0.14 < alpha < 0.495 Estimated twin fraction: 0.127 Correlation: 0.9955
By comparison if I run the detect_twin routine of CNS it tells me that they are no merohedral twin laws for the point group 222 (using the statistical method of Yeates) ? This is confusing me quite a bit.
Assuming that the twinning law suggested by Phenix is correct how should I proceed? I have noticed the section concerning refinement using twinned data in Phenix phenix.refine data.hkl model.pdb twin_law="-k,-h,-l" detwin.map_types.aniso_correct=true
but It seems I only have a MR solution in P2(1) but not in P222(1) so how can I refine in P222(1)
I will greatly appreciate your input, many thanks.
Pascal F. Egea, PhD University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory [email protected]
2008/3/2, Randy J. Read
In addition to what has been suggested, another option is to merge the data in P1 and look for 8 copies. Now that you have a reasonable refined model from the monoclinic solution, this should find a solution. Then you can look for the symmetry in the molecular replacement solution to decide what symmetry is crystallographic. An easy shortcut is to run a self-rotation function on the Fcalcs from the model. (At the moment, I think you'll have to go outside Phenix to do that -- we're intending to put a self-rotation function into Phaser but it's still on the to-do list!)
Actually, you can run xtriage on your calculated data and get merging stats for crystallographic sym. ops. : much easier to interpret ascompared to a self rotation (and done for you!). Alternatively, you can get aproximate operators using phenix.simple_ncs_from_pdb. This might bit prove a bit of a hassle though. hth P
Regards
Randy Read
On Mar 2 2008, Pascal EGEA wrote:
Hi All
This a question of general Crystallography and use of Phenix to deal with twinned data.
I am having difficulties with a data set. We have data (2.6 ang resolution) that can be scaled and reduced in P222 with a Rmerge of 7%, the systematic absences show a screw axis ( it is P22(1)2). However MR in Phaser failed in this orthorhombic settings when searching for 2 molecules of the complex in the AU. If we reduce and scale the data in P2(1) and look at the diffraction pattern in HKLVIEW there is a /mmm symmetry. In the monoclinic P2(1) setting we can find 4 molecules of the complex (by MR in Phaser) and can refine it with Phenix to a Rfac/Rfree of 28%/34%. 2 molecules have good electron density whereas the two other ones have one of their domain very poorly defined in density. This is looking very suspicious to me and I am wondering if this refined structure is partially wrong?
Meanwhile I used phenix.triage on the data processed in P222 and I am confused with the output.
##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------##
Using data between 10.00 to 3.36 Angstrom.
Determining possible twin laws.
The following twin laws have been found:
------------------------------------------------------------------------ ------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ------------------------------------------------------------------------ ------- | PM | 4-fold | 2.851 | 0.000 | 0.013 | - l,k,h | ------------------------------------------------------------------------ ------- M: Merohedral twin law PM: Pseudomerohedral twin law
0 merohedral twin operators found 1 pseudo-merohedral twin operators found In total, 1 twin operator were found
--------------------------------------------- Analysing possible twin law : -l,k,h ---------------------------------------------
Results of the H-test on acentric data:
(Only 50.0% of the strongest twin pairs were used)
mean |H| : 0.368 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.194 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.132 Estimation of twin fraction via cum. dist. of H: 0.115
Britton analyses
Extrapolation performed on 0.14 < alpha < 0.495 Estimated twin fraction: 0.127 Correlation: 0.9955
By comparison if I run the detect_twin routine of CNS it tells me that they are no merohedral twin laws for the point group 222 (using the statistical method of Yeates) ? This is confusing me quite a bit.
Assuming that the twinning law suggested by Phenix is correct how should I proceed? I have noticed the section concerning refinement using twinned data in Phenix phenix.refine data.hkl model.pdb twin_law="-k,-h,-l" detwin.map_types.aniso_correct=true
but It seems I only have a MR solution in P2(1) but not in P222(1) so how can I refine in P222(1)
I will greatly appreciate your input, many thanks.
Pascal F. Egea, PhD University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (4)
-
Pascal EGEA -
Paul Adams -
Peter Zwart -
Randy J. Read