Re: [phenixbb] individual anisotropic adps
Currently phenix.refine does not support refinement of individual anisotropic ADP and TLS for the same set of atoms (see my previous email). However, in phenix.refine you can refine TLS and individual anisotropic ADP for non-overlapping set of atoms. Pavel. On 12/11/2008 8:34 AM, gerwald jogl wrote:
Thanks, that's roughly what I thought. How about tls and individual anisotropic together? same strategy, just observe Rfree?
Hi all- I'm hoping for some guidance on how to determine the correct twin law, or possibly re-index my data to allow proper refinement. The crystal appears to be R32, R3, or C2. Maps seem best in C2, even though it merges equally well in all these spacegroup options, but R stays high (~0.36/0.4) and a un-modelled helix visible in an untwinned 3.3 A dataset has no difference density in this set. My attempt to treat the twinning have not worked (see output, including cell dimensions, below). Thanks in advance for any help! James phenix.xtriage flags it as most likely twinned with the following output: ... Unit cell: (185.85, 120.972, 111.05, 90, 119.157, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 1784 Resolution range: 28.8717 2.51224 Completeness in resolution range: 0.952773 ... Using data between 10.00 to 3.24 Angstrom. Determining possible twin laws. The following twin laws have been found: ---------------------------------------------------------------------------------------------------------------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ---------------------------------------------------------------------------------------------------------------- | PM | 2-fold | 0.345 | 0.219 | 0.003 | -1/2*h+1/2*k+l,1/2*h-1/2*k+l,1/2*h+1/2*k | | PM | 2-fold | 0.345 | 0.219 | 0.003 | -1/2*h-1/2*k+l,-1/2*h-1/2*k-l,1/2*h-1/2*k | ---------------------------------------------------------------------------------------------------------------- M: Merohedral twin law PM: Pseudomerohedral twin law 0 merohedral twin operators found 2 pseudo-merohedral twin operators found In total, 2 twin operator were found The present crystal symmetry does not allow to have the its lattice symmetry expressed in the setting desired. Becasue of this, a full coset table cannot be produced. Working with the data in the reduced cell will solve this. Splitting data in centrics and acentrics Number of centrics : 961 Number of acentrics : 30683 phenix.refine with twinning { twin_law = "-1/2*h-1/2*k+l,-1/2*h-1/2*k-l,1/2*h-1/2*k" } results in the error: Traceback (most recent call last): File "/usr/local/phenix-1.3- final/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3- final/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/driver.py", line 1081, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3- final/phenix/phenix/refinement/strategies.py", line 190, in refinement_machine twin_law = sgtbx.rt_mx( params.twinning.twin_law ) RuntimeError: cctbx Internal Error: /net/anaconda/scratch1/phenix/phenix-1.3- final/cctbx/sgtbx/rt_mx.cpp(230): Unsuitable value for rational rotation matrix.
Hi,
Thgis is very unfortunate. I have to provide a fix.
P
2008/12/12, whittle
Hi all-
I'm hoping for some guidance on how to determine the correct twin law, or possibly re-index my data to allow proper refinement.
The crystal appears to be R32, R3, or C2. Maps seem best in C2, even though it merges equally well in all these spacegroup options, but R stays high (~0.36/0.4) and a un-modelled helix visible in an untwinned 3.3 A dataset has no difference density in this set.
My attempt to treat the twinning have not worked (see output, including cell dimensions, below).
Thanks in advance for any help!
James
phenix.xtriage flags it as most likely twinned with the following output:
...
Unit cell: (185.85, 120.972, 111.05, 90, 119.157, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 1784 Resolution range: 28.8717 2.51224 Completeness in resolution range: 0.952773
...
Using data between 10.00 to 3.24 Angstrom.
Determining possible twin laws.
The following twin laws have been found:
---------------------------------------------------------------------------------------------------------------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ---------------------------------------------------------------------------------------------------------------- | PM | 2-fold | 0.345 | 0.219 | 0.003 | -1/2*h+1/2*k+l,1/2*h-1/2*k+l,1/2*h+1/2*k | | PM | 2-fold | 0.345 | 0.219 | 0.003 | -1/2*h-1/2*k+l,-1/2*h-1/2*k-l,1/2*h-1/2*k | ---------------------------------------------------------------------------------------------------------------- M: Merohedral twin law PM: Pseudomerohedral twin law
0 merohedral twin operators found 2 pseudo-merohedral twin operators found In total, 2 twin operator were found
The present crystal symmetry does not allow to have the its lattice symmetry expressed in the setting desired. Becasue of this, a full coset table cannot be produced. Working with the data in the reduced cell will solve this.
Splitting data in centrics and acentrics Number of centrics : 961 Number of acentrics : 30683
phenix.refine with
twinning { twin_law = "-1/2*h-1/2*k+l,-1/2*h-1/2*k-l,1/2*h-1/2*k" }
results in the error:
Traceback (most recent call last): File "/usr/local/phenix-1.3- final/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3- final/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/driver.py", line 1081, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3- final/phenix/phenix/refinement/strategies.py", line 190, in refinement_machine twin_law = sgtbx.rt_mx( params.twinning.twin_law ) RuntimeError: cctbx Internal Error: /net/anaconda/scratch1/phenix/phenix-1.3- final/cctbx/sgtbx/rt_mx.cpp(230): Unsuitable value for rational rotation matrix.
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-- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------
participants (3)
-
Pavel Afonine -
Peter Zwart -
whittle