Chris,
To change the axis ordering for e.g. changing which cell edge is the P21
B axis use an "hkl matrix" command. Probably can do this via the Macros
during scaling but I distrust this and just edit scl.in by hand and run
it as "scalepack < scl.in"
For k,l,h reindexing use "hkl matrix 0 1 0 0 0 1 1 0 0"
For l, h, k reindexing use "hkl matrix 0 0 1 1 0 0 0 1 0"
Systematic absences would be an anecdotal indicator that it is/isn't
P212121. That would show strong systematic absences for (h,0,0),
(0,k,0), (0,0,l) reflections. (Or reflexions if one prefers). While
not impossible I would think it statistically unlikely to observe such
absences if the data was really P1, P2 or P21. Going back to the images
to eyeball the actual reflections on the display can be pretty illuminating.
I don't remember Scalepack giving much detail in postrefinement but
paying attention to the positional chi^2 values during integration might
give clues about how far from 90 those unit cell axes are wandering if
you try integrating in different space groups. There's also a method
(or was, last time I tried it) to change the way Scalepack postrefines
unit cell dimensions (value per frame or value per crystal) which might
also help. More hacking of scl.in might be required.
However I'm usually pretty happy if my R-free drops 12% at 2.0 Angstrom
resolution when going from P21 to P1. I would look for legitimate
deviations between previously identical monomers in the map and probably
consider using NCS to reduce the random deviation between monomers that
actually are identical by symmetry. You may have assigned the
crystallographic 21 down the wrong unit cell axis in that P21 test case.
Phil Jeffrey
Princeton
On 7/11/14 7:33 PM, Chris Fage wrote:
Nat and Misha,
Thank you for the suggestions.
Xtriage does indeed detect twinning in P1, reporting similar values
for <|L|>, <L^2>, and twin fraction as in P212121.
The unit cell dimensions for the 2.0-A structure (P1) are:
72.050 105.987 201.142 89.97 89.98 89.94 P 1
The unit cell dimensions for the 2.8-A structure (P212121) are:
75.456 115.154 202.022 90.00 90.00 90.00 P 21 21 21
I have been processing in HKL2000, which only recognizes one set of
unit cell parameters for each Bravais lattice (does anyone know how to
change this?). Specifically, for a primitive monoclinic unit cell it estimates:
104.53 71.82 200.99 89.86 91.80 91.16
This is the unit cell which refined to Rwork/Rfree ~ 27%/34%.
Indexing in mosflm gives three options for primitive monoclinic:
105.6 71.7 200.9 90.0 90.1 90.0
71.7 105.6 201.0 90.0 89.9 90.0
71.7 200.9 105.6 90.0 90.3 90.0
Attempting to integrate in any of these space groups leads to a fatal
error in subroutine "MASKIT". I can also use the "index multiple
lattices" feature to get a
whole slew of potential space group; however, integrating reflections
leads to the same fatal error.
Finally, Zanuda tells me that P212121 is the best space group,
according to R-factors. However, I do not believe P212121 is the
correct assignment.
Best,
Chris
On 7/10/14, Isupov, Michail <m.isu...@exeter.ac.uk> wrote:
I would recommend to run ZANUDA in the default mode from ccp4i or on CCP4
web server.
ZANUDA has resolved several similar cases for me.
Misha
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Chris Fage
[cdf...@gmail.com]
Sent: 10 July 2014 01:14
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Proper detwinning?
Hi Everyone,
Despite modelling completely into great electron density, Rwork/Rfree
stalled at ~38%/44% during refinement of my 2.0-angstrom structure
(P212121, 4 monomers per asymmetric unit). Xtriage suggested twinning,
with <|L|> = 0.419, <L^2> = 0.245, and twin fraction = 0.415-0.447.
However, there are no twin laws in this space group. I reprocessed the
dataset in P21 (8 monomers/AU), which did not alter Rwork/Rfree, and
in P1 (16 monomers/AU), which dropped Rwork/Rfree to ~27%/32%. Xtriage
reported the pseudo-merohedral twin laws below.
P21:
h, -k, -l
P1:
h, -k, -l;
-h, k, -l;
-h, -k, l
Performing intensity-based twin refinement in Refmac5 dropped
Rwork/Rfree to ~27%/34% (P21) and ~18%/22% (P1). Would it be
appropriate to continue with twin refinement in space group P1? How do
I know I'm taking the right approach?
Interestingly, I solved the structure of the same protein in P212121
at 2.8 angstroms from a different crystal. Rwork/Rfree bottomed out at
~21%/26%. One unit cell dimension is 9 angstroms greater in the
"twinned" dataset than in the "untwinned".
Thank you for any suggestions!
Regards,
Chris
