CAVEAT
The procedure discussed in previous email to try to simply import one set of Rfree flags from on mtz to the other, however, would required a very carefully choice of "matching" unit cells origins ...
This problem would be overcome by expanding the orthorombic lattice to the primitive monoclinic, as you were originally thinking of do it. However, as discussed below by others, that procedure is not really valid/correct, as you will get a "virtual" monoclinic lattice with a=c and beta=120, which is indeed a real centered orthorombic lattice.
D
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Dom Bellini [[log in to unmask]]
Sent: 03 October 2013 08:21
To: ccp4bb
Subject: Re: [ccp4bb] Fwd: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21
QUICK ERRATUM
Sorry W, I forgot a very important bit (I was half asleep ;-)). As the unit cells are, it would not be correct to import one set of Rfree flags from one dataset to the other in sftools as the axes are moved around and the indexing is no longer consistent between the two mtzs.
First you would need to swap around the b and c axes in the orthorhombic crystal, to give
C2221 a=37, b=126, c=72
since the pseudo orthorombic non-90 angle is the one between the two shorter axes (as revealed by your monoclinic b axis).
P21 a=37, b=126, c=40 beta=117
This should give you the necessary indexing consistency between the two to import one set of Rfree flags to the other using sftools. However, when importing the Rfree flags from one to another with sftools, I would first generate them for the C2221 dataset and import these ones to the P21 mtz files (as the other way around will cause you to go in manually and change some of the P21 flags with indices no longer present in the C2221 after having been merged, as you now have only 1/4 of the monoclinic reflections).
I think this should work, hopefully :-)
D
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From: CCP4 bulletin board [[log in to unmask]] on behalf of Ethan A Merritt [[log in to unmask]]
Sent: 03 October 2013 00:53
To: ccp4bb
Subject: Re: [ccp4bb] Fwd: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21
On Wednesday, 02 October, 2013 17:31:06 wtempel wrote:
> Tim,
> I agree with your statement.
> Consider this situation:
> Macromolecular sample MA produces crystal CA. Data scale well in C2221 and
> refinement proceeds smoothly to give stuctural model SA.
> Slightly modified macromolecular sample MA* crystallizes to yield crystal
> CA*. Data scale well in C2221 with cell dimensions virtually identical to
> those of CA. I attempt, without spatial transformation, to solve the
> structure by refining SA using CA* data and for each HKL in CA* assign the
> same flag value as in same HKL of CA. I am not aware of any alternative
> equivalent indexing issue in this space group and am surprised to learn
> that SA does not refine well against data from CA*, Rfree does not drop
> from 48%, while Rcryst drops from 46 to 44%. Modifying SA to better
> correspond to MA* does not help. I scale data from CA* in P21. Over 10
> cycles of refinement, Rcryst, Rfree drop from 35 -> 29%, 34 -> 33%. As I
> assigned a new Rfree set, I am not surprised about Rfree < Rcryst,
> initially. Neither does the modest reduction in Rfree convince me that
> symmetry reduction yielded a true improvement in the model.
If I understand correctly, your starting Rfree (prior to refinement) was
48% if the model was placed in a C2221 cell and 34% if the same model
was placed in a P21 cell. That seems more than a "modest reduction".
However, based solely on your description above it remains a formal
possibility that the CA* structure really is orthorhombic but is not
isomorphous to the CA structure even though the two unit cells are
virtually identical. Perhaps the molecule sits differently in the asymmetric
unit. Did you try treating it as a fresh molecular replacement problem?
Ethan
> For that
> purpose, I would prefer a comparison of refinement in C2221 and P21 with
> properly transfered free flags. I just do not know how to accomplish that
> transfer.
> W.
>
> ---------- Forwarded message ----------
> From: Tim Gruene <[log in to unmask]>
> Date: Wed, Oct 2, 2013 at 4:13 PM
> Subject: Re: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21
> To: wtempel <[log in to unmask]>
> Cc: [log in to unmask]
>
>
> Dear W.,
>
> if P21 is a proper subgroup of C2221, scaling a P21 data set in C2221
> would try to make non-equivalent reflections equal, would it not? I
> would reintegrate the data in the correct point group and scale in the
> correct space group.
>
> Best,
> Tim
>
> On 10/02/2013 08:32 PM, wtempel wrote:
> > Hello Appu and Boaz, my suspicion arises from failure to refine (as
> > in reducing crystallographic R-factor from the 40%s) a related,
> > virtually isomorphous crystal structure in the original C2221
> > setting. Scaling statistics are very nice even in C2221. If I drop
> > the symmetry to P21, the R-factor drops to a little more than 0.3
> > and the maps look significantly cleaner. Caveat: because I am not
> > using a consistent free set between the C2221 and P21 settings, I
> > do not trust Rfree as a reliable progress indicator in this case.
> > P21 is a subgroup (or superset) of C2221, per "the tables". And as
> > there is a transformation between them, should not that
> > transformation be applicable to the "lattice sampling"? I would
> > therefore like to cleanly expand my free set from C2221 to P21.
> > Using REINDEX following Appu's suggestion, with specification of
> > the new space group again gets me the familiar P21 cell dimensions,
> > but the unique reflection count remains unchanged when I would
> > expect it to approximately double. Now I do not know how to best
> > generate the other half of the data set or even if something is
> > wrong at this point already. W.
> >
> > ---------- Forwarded message ---------- From: Appu kumar
> > <[log in to unmask]> Date: Wed, Oct 2, 2013 at 1:29 PM Subject:
> > Re: [ccp4bb] expanding reflections from C2221 to P21 To: wtempel
> > <[log in to unmask]>, CCP4BB <[log in to unmask]>
> >
> >
> > How do you suspect that C2221 is 'pseudo' and P21 is 'real'? You
> > can use the reindex programme incorporated in ccp4 suit. Reindex
> > programme can expand symmetry from C2221 to P21.I Hope you will get
> > the result. Thank you Appu
> >
> >
> > On 2 October 2013 21:43, wtempel <[log in to unmask]> wrote:
> >
> >> Hello, I would like to expand a reflection data set in mtz format
> >> from C2221 to P21. The purpose is to obtain consistent R-free
> >> flags based on a structure already refined in C2221 for a related
> >> data set that I suspect is pseudo-C2221 but "real" P21.
> >>
> >> Primitive cell dimensions are: 37.6 126.1 40.61 89.99 117.6
> >> 90.01, C-centered: 37.6 71.99 126.1 90 89.99 90.01 pointless
> >> provides the following matrix: <pointless> Reindex operator from
> >> input cell to lattice cell: [h,h+2l,-k]
> >>
> >> h' = ( h k l ) ( 1 1 0 ) ( 0 0
> >> -1 ) ( 0 2 0 )
> >>
> >> </pointless> In sftools, I loaded the C2221 data set and did
> >>
> >> sftools$ reindex matrix 1 0 0 0 0 -1 -.5 .5 0
> >>
> >> with the transposed (to account for the presumably inverted order
> >> of factors in the program?) inverse matrix of the one listed
> >> above with the aim of restoring the primitive asymmetric unit. I
> >> was encouraged seeing sftools report new cell dimensions matching
> >> the expected primitive cell. Then I did
> >>
> >> sftools$ expand 4
> >>
> >> I expected now to have a "workable" P21 version of my C2221 data
> >> set, but molecular replacement (MOLREP) with my C2221 model
> >> failed to place even a single copy of the model. Thus, I must
> >> have misused sftools by issuing commands that were either wrong
> >> or in the wrong order or my application of linear algebra was
> >> mistaken. Any ideas out there? Thanking you in advance, Wolfram
> >> Tempel
> >>
> >
>
> --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
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