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> 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> Cc: CCP4BB@jiscmail.ac.uk -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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> Date: Wed, Oct 2, 2013 at 1:29 PM Subject: > Re: [ccp4bb] expanding reflections from C2221 to P21 To: wtempel > <wtem...@gmail.com>, CCP4BB <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> 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSTH5mUxlJ7aRr7hoRAg7/AJ4wYtkv2Wx/t6lf0GUXbFjepeZ8eACeK6eX YpZwzT6XAtVtPtkp3sI32pM= =yKT3 -----END PGP SIGNATURE-----
