Dear W.,


If you really want to do a comparison on the Rfree, the only way would be to 
start off how described by Tim, i.e., rescaling your images to create a P21 mtz 
and then further reducing them to create a second higher symmetry C2221 mtz. 
Then you could create a set of Rfree flags for one dataset and then import the 
same set of flags in the second dataset using sftools. However, a comparison of 
how well the Rfree refines between two datasets scaled in different spacegroups 
it seems to me quite pointless, as the Rfactor should tell you everything you 
need to know, and in your case it seems to indicate that your new CA* crystal 
has truly changed to P21.



Expanding the C2221 mtz to a P21 mtz is probably not a good idea for two main 
reasons:



1- once you merged the reflections all the information about each single 
reflection value is lost.

2- I am not sure how you can decide how much to degenerate the C2221 gamma 
angle to obtain the new non-90 degree beta angle for the P21 lattice. Perhaps 
you could empirically calculate it by knowing that your P21 beta angle should 
be approximately 117 degrees, but personally I am not aware of a program that 
would let you do this.



HTH



D

________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel 
[wtem...@gmail.com]
Sent: 02 October 2013 22:31
To: ccp4bb
Subject: [ccp4bb] Fwd: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 
to P21

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. 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 <t...@shelx.uni-ac.gwdg.de<mailto:t...@shelx.uni-ac.gwdg.de>>
Date: Wed, Oct 2, 2013 at 4:13 PM
Subject: Re: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21
To: wtempel <wtem...@gmail.com<mailto:wtem...@gmail.com>>
Cc: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>


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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
> <appu.kum...@gmail.com<mailto:appu.kum...@gmail.com>> Date: Wed, Oct 2, 2013 
> at 1:29 PM Subject:
> Re: [ccp4bb] expanding reflections from C2221 to P21 To: wtempel
> <wtem...@gmail.com<mailto:wtem...@gmail.com>>, CCP4BB 
> <CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>>
>
>
> 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 
> <wtem...@gmail.com<mailto:wtem...@gmail.com>> 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

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