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 >
