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> -----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<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 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----- -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
