James, it's just the C centring: (1/2,y,1/2) + (1/2,1/2,0) = (0,1/2+y,1/2) which is the alternate origin so you will indeed get the same F's and different phases (don't forget that shifts along y are arbitrary!).
Cheers -- Ian On Tue, Mar 2, 2010 at 11:13 PM, James Holton <[email protected]> wrote: > Apologies for bringing back an old thread, but I recently returned home to > my dear copy of the ITC vol. B, and decided to double-check that my > "personal" list of origin shifts matches the one found in there. To my > surprise, there seems to be at least one real difference: C2 > > The "allowed origins" listed in my copy (1999 edition) for C2 are: > (0,y,0) > (0,y,1/2) > > However, if I take a random bunch of atoms: > http://bl831.als.lbl.gov/~jamesh/pickup/C2_origin_ref.pdb > which has unit cell a=50 b=70 c=123 beta=123 > > and move all these atoms by a fractional shift: 0.5 0 0.5 > > I get a new PDB file: > http://bl831.als.lbl.gov/~jamesh/pickup/C2_origin_shifted.pdb > > which, upon calculating structure factors with SFALL, gives the same Fs as > the "ref" pdb file above. Albeit with different phases. > > Now, (1/2,y,1/2) is not an "allowed origin", but could it be an allowed > origin shift? > > -James Holton > MAD Scientist > > George M. Sheldrick wrote: >> >> Dear Ian, >> >> Although these tables are indeed very useful, on closer perusal I have >> found a typo in my edition (which appears to be the same as yours but >> slightly different to the on-line edition) - in the 3rd column of table >> 2.2.3.2, "P6" should obviously have a bar over the "6", though this is >> unlikely to cause problems for most readers of CCP4bb. Less satisfactory >> from our point of view is that R3 and R32 are only given for the primitive >> rhombohedral setting, not for the hexagonal cell with three times the volume >> (H3 or H32) that protein crystallographers seem to prefer. >> >> Best wishes, George >> Prof. George M. Sheldrick FRS >> Dept. Structural Chemistry, >> University of Goettingen, >> Tammannstr. 4, >> D37077 Goettingen, Germany >> Tel. +49-551-39-3021 or -3068 >> Fax. +49-551-39-22582 >> >> >> On Mon, 8 Feb 2010, Ian Tickle wrote: >> >> >>> >>> Yes, thanks! I wish I had spotted that before! >>> >>> As you say Tables 2.2.3.2 (pp 212-213 in my ed.) & 2.2.3.4 (pp 214-215), >>> for non-centrosymmetric primitive & centred space groups respectively, >>> contain all the authoritative information you need to define the allowed >>> origin shifts (as well as info on semi-invariants etc). I think it >>> would be useful if all documentation/scripts/programs which claim to >>> specify alternate origins etc referenced (and of course were consistent >>> with!) these tables. >>> >>> Cheers >>> >>> -- Ian >>> >>> >>>> >>>> -----Original Message----- >>>> From: George M. Sheldrick [mailto:[email protected]] >>>> Sent: 05 February 2010 23:08 >>>> To: Ian Tickle >>>> Cc: [email protected] >>>> Subject: Re: [ccp4bb] reforigin on 2FKA >>>> >>>> >>>> I have just noticed that there is a definitive table of equivalent >>>> origins for all 230 space groups in volume B of International >>>> Tables (in Chapter 2.2 by Carmelo Giacovazzo). This appears to >>>> agree with Ian's last email in this thread for the space groups >>>> discussed there. It gives the origins directly rather than the >>>> Cheshire groups so may be slightly easier to use. >>>> >>>> George >>>> >>>> Prof. George M. Sheldrick FRS >>>> Dept. Structural Chemistry, >>>> University of Goettingen, >>>> Tammannstr. 4, >>>> D37077 Goettingen, Germany >>>> Tel. +49-551-39-3021 or -3068 >>>> Fax. +49-551-39-22582 >>>> >>>> >>>> On Wed, 27 Jan 2010, Ian Tickle wrote: >>>> >>>> >>>>> >>>>> Correction: my apologies, I see now that the table of Cheshire >>>>> >>> >>> groups >>> >>>>> >>>>> that I referred to originally came from: Hirshfeld (1968), Acta >>>>> >>> >>> Cryst. >>> >>>>> >>>>> A24, 301-311. I got it from Jorge: it's still good to know that it >>>>> >>> >>> has >>> >>>>> >>>>> Jorge's seal of approval! >>>>> >>>>> Cheers >>>>> >>>>> -- Ian >>>>> >>>>> >>>>>> >>>>>> -----Original Message----- >>>>>> From: [email protected] >>>>>> [mailto:[email protected]] On Behalf Of Ian Tickle >>>>>> Sent: 27 January 2010 22:25 >>>>>> To: James Holton; Francois Berenger >>>>>> Cc: [email protected] >>>>>> Subject: RE: [ccp4bb] reforigin on 2FKA >>>>>> >>>>>> ... and I was assuming that since it was clear that there are >>>>>> omissions >>>>>> for F222 and F23 on the CCP4 'alternate origins' page, that >>>>>> James' page >>>>>> was 100% correct! But I think we have both made the same mistake >>>>>> >>> >>> of >>> >>>>>> >>>>>> assuming that F222, F23 and F432 all behave identically as >>>>>> far as origin >>>>>> shifts are concerned. >>>>>> >>>>>> According to this document: >>>>>> http://www.ccp4.ac.uk/dist/html/cheshirecell.html which I >>>>>> have no reason >>>>>> to question since it comes from an excellent authority (Jorge >>>>>> >>> >>> Navaza), >>> >>>>>> >>>>>> the Cheshire space group and cell for both F222 and F23 is I >>>>>> >>> >>> centred >>> >>>>>> >>>>>> (Immm & Im3m resp) with cell lengths a/2, b/2, c/2. This implies >>>>>> >>> >>> the >>> >>>>>> >>>>>> origin shift (1/4,1/4,1/4), and therefore by unit translations in >>>>>> >>> >>> the >>> >>>>>> >>>>>> Cheshire lattice (3/4,3/4,3/4) also, is a non-equivalent origin. >>>>>> >>> >>> For >>> >>>>>> >>>>>> F432 the Cheshire cell is the same as for F222 & F23 but the >>>>>> >>> >>> Cheshire >>> >>>>>> >>>>>> space group is primitive (Pm3m), which implies that (1/4,1/4,1/4) >>>>>> >>> >>> is >>> >>>>>> >>>>>> *not* an allowed origin shift, i.e. 'disallowed' in the sense that >>>>>> >>> >>> you >>> >>>>>> >>>>>> can't use the same SF calculation formula and still expect to get >>>>>> >>> >>> the >>> >>>>>> >>>>>> right answer: if you're willing to use a different formula >>>>>> then anything >>>>>> (including completely arbitrary origin shifts, i.e. as in P1) is >>>>>> allowed! >>>>>> >>>>>> So the one redeeming factor from all this is that reforigin at >>>>>> >>> >>> least >>> >>>>>> >>>>>> appears to give the right answer. >>>>>> >>>>>> Cheers >>>>>> >>>>>> -- Ian >>>>>> >>>>>> >>>>>>> >>>>>>> -----Original Message----- >>>>>>> From: [email protected] >>>>>>> [mailto:[email protected]] On Behalf Of James Holton >>>>>>> Sent: 27 January 2010 21:35 >>>>>>> To: Francois Berenger >>>>>>> Cc: [email protected] >>>>>>> Subject: Re: [ccp4bb] reforigin on 2FKA >>>>>>> >>>>>>> Francois Berenger wrote: >>>>>>> >>>>>>>> >>>>>>>> It correspond to what is found at the end of James Holton's >>>>>>>> origins.com script >>>>>>>> http://bl831.als.lbl.gov/~jamesh/pickup/origins.com >>>>>>>> so I guess it should be correct. >>>>>>>> >>>>>>> >>>>>>> Uhhh... >>>>>>> >>>>>>>> >>>>>>>> He also says how he found them: >>>>>>>> <origins.com snippet> >>>>>>>> # TABLE OF ALLOWED ORIGIN SHIFTS >>>>>>>> These origin shifts were determined emprirically using 100 >>>>>>>> randomly-placed atoms >>>>>>>> that were shifted around with pdbset and checked with SFALL >>>>>>>> >>>>>>> >>>>>>> for identical >>>>>>> >>>>>>>> >>>>>>>> amplitudes to the 0 0 0 origin. They should be correct for >>>>>>>> >>>>>>> >>>>>>> the CCP4 >>>>>>> >>>>>>>> >>>>>>>> convention >>>>>>>> of symmetry. (I.E. R3 and R32 have hexagonal indexing) >>>>>>>> </origins.com snippet> >>>>>>>> >>>>>>> >>>>>>> Okay, I just went back to my notes on this. I should admit >>>>>>> that in my >>>>>>> completely brain-dead allowed-origin-shift search described >>>>>>> >>> >>> above I >>> >>>>>>> >>>>>>> originally found no "allowed" shifts for F432 (not sure why, >>>>>>> but maybe >>>>>>> because it was last on my list). Years later, I think it was >>>>>>> Peter Zwart >>>>>>> who pointed out to me that I was missing a few of what ought to >>>>>>> >>> >>> be >>> >>>>>>> >>>>>>> allowed origins. As I recall, at least one of them passed my >>>>>>> pdbset/sfall test, so I just assumed I must have done >>>>>>> >>>>>> >>>>>> something wrong >>>>>> >>>>>>> >>>>>>> and added everything in the CCP4 document and ITC Vol B to >>>>>>> >>>>>> >>>>>> the list. >>>>>> >>>>>>> >>>>>>> For purposes of the origins.com script, I decided to err on >>>>>>> the side of >>>>>>> having it try things that may or may not work. If it finds >>>>>>> >>>>>> >>>>>> a match, >>>>>> >>>>>>> >>>>>>> then great! Right? >>>>>>> >>>>>>> Perhaps this was not wise of me. I just tried shifting the >>>>>>> >>>>>> >>>>>> 2fka PDB >>>>>> >>>>>>> >>>>>>> file by "SHIFT FRAC 0.25 0.25 0.25" with pdbset and comparing >>>>>>> >>> >>> the >>> >>>>>>> >>>>>>> resulting Fs from sfall to those of the un-shifted PDB. They >>>>>>> are ~30% >>>>>>> different. It could be that this is a bug in sfall or pdbset >>>>>>> (doubtful), but I would say that pragmatically, this is not >>>>>>> an "allowed >>>>>>> origin shift" for F432. However, 0,0,0.5 and 0,0.5,0.5 and all >>>>>>> >>> >>> the >>> >>>>>>> >>>>>>> other half-cell combinations do work! Guess I missed those! >>>>>>> I have now >>>>>>> updated my origins.com script. It appears that the allowed >>>>>>> >>> >>> origin >>> >>>>>>> >>>>>>> shifts for F432 and F23 are not the same, as I had >>>>>>> >>>>>> >>>>>> previously thought. >>>>>> >>>>>>>>> >>>>>>>>> plus of course the symmetry-equivalent origins generated >>>>>>>>> >>>>>>> >>>>>>> from these 4 by >>>>>>> >>>>>>>>> >>>>>>>>> the space-group centring (F) translations: >>>>>>>>> >>>>>>>>> 0.0000 0.5000 0.5000 >>>>>>>>> 0.5000 0.0000 0.5000 >>>>>>>>> 0.5000 0.5000 0.0000 >>>>>>>>> >>>>>>>> >>>>>>>> I can see these in syminfo.lib. >>>>>>>> >>>>>>>> However, from what you say, I understand that only 2x3 >>>>>>>> >>> >>> possible >>> >>>>>>>> >>>>>>>> origins with each coordinate being 0 or .5 should be accepted >>>>>>>> >>> >>> by >>> >>>>>>>> >>>>>>>> reforigin. >>>>>>>> But in my test it accepted all 8 possible combinations of 0 >>>>>>>> >>> >>> and .5 >>> >>>>>>>> >>>>>>>> that I artificially introduced in my translated test PDBs: >>>>>>>> >>>>>>>> m...@myps:2fka# grep Frac run.log | sort | uniq >>>>>>>> Fractional origin shift: 0.0000 0.0000 0.0000 >>>>>>>> Fractional origin shift: 0.0000 0.0000 0.5000 >>>>>>>> Fractional origin shift: 0.0000 0.5000 0.0000 >>>>>>>> Fractional origin shift: 0.0000 0.5000 0.5000 >>>>>>>> Fractional origin shift: 0.5000 0.0000 0.0000 >>>>>>>> Fractional origin shift: 0.5000 0.0000 0.5000 >>>>>>>> Fractional origin shift: 0.5000 0.5000 0.0000 >>>>>>>> Fractional origin shift: 0.5000 0.5000 0.5000 >>>>>>>> >>>>>>>> Should I be worried? >>>>>>>> >>>>>>> >>>>>>> At this point, I would say no. Reforigin seems to be doing >>>>>>> >>>>>> >>>>>> it right. >>>>>> >>>>>>> >>>>>>> I think some of the confusion might be arising because an >>>>>>> >>>>>> >>>>>> "alternate >>>>>> >>>>>>> >>>>>>> origin" and a fractional coordinate shift that gives you the >>>>>>> >>> >>> same >>> >>>>>>> >>>>>>> structure factor amplitudes may or may not be the same thing. >>>>>>> >>> >>> Some >>> >>>>>>> >>>>>>> shifts change the phase, but not the amplitude so whether >>>>>>> >>>>>> >>>>>> or not they >>>>>> >>>>>>> >>>>>>> are "alternate" depends on what you are trying to do. >>>>>>> >>>>>>> -James Holton >>>>>>> MAD Scientist >>>>>>> >>>>>>> >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Francois. >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> So there will be 12 in all, which I think include the ones >>>>>>>>> >>> >>> you >>> >>>>>>>>> >>>>>>>>> mentioned. >>>>>>>>> >>>>>>>>> If you're going by >>>>>>>>> http://www.ccp4.ac.uk/dist/html/alternate_origins.html >>>>>>>>> >>>>>>> >>>>>>> then you should >>>>>>> >>>>>>>>> >>>>>>>>> be aware of a very recent BB discussion in which it was >>>>>>>>> >>>>>>> >>>>>>> pointed out that >>>>>>> >>>>>>>>> >>>>>>>>> the entries for F222, F23, F432 and possibly others are >>>>>>>>> >>>>>> >>>>>> incomplete. >>>>>> >>>>>>>>> >>>>>>>>> Eleanor has given me the task of checking & correcting >>>>>>>>> >>>>>>> >>>>>>> this particular >>>>>>> >>>>>>>>> >>>>>>>>> documentation, until then don't trust it! >>>>>>>>> >>>>>>>>> Of course you shouldn't trust reforigin either, just as >>>>>>>>> >>>>>>> >>>>>>> you shouldn't >>>>>>> >>>>>>>>> >>>>>>>>> trust any program until you have verified that the results >>>>>>>>> >>>>>>> >>>>>>> are sensible, >>>>>>> >>>>>>>>> >>>>>>>>> but I think in this particular the fault doesn't lie with >>>>>>>>> >>>>>>> >>>>>>> reforigin. >>>>>>> >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> >>>>>>>>> -- Ian >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> -----Original Message----- >>>>>>>>>> From: [email protected] >>>>>>>>>> >>>>>>> >>>>>>> [mailto:[email protected]] >>>>>>> >>>>>>>>> >>>>>>>>> On >>>>>>>>> >>>>>>>>>> >>>>>>>>>> Behalf Of Francois Berenger >>>>>>>>>> Sent: 27 January 2010 06:50 >>>>>>>>>> To: [email protected] >>>>>>>>>> Subject: reforigin on 2FKA >>>>>>>>>> >>>>>>>>>> Hello, >>>>>>>>>> >>>>>>>>>> I am playing with ccp4's reforigin to verify some MR >>>>>>>>>> >>> >>> solutions. >>> >>>>>>>>>> >>>>>>>>>> If I translate a copy of the pdb.org's PDB 2FKA (from >>>>>>>>>> >>>>>>> >>>>>>> spacegroup F432) >>>>>>> >>>>>>>>>> >>>>>>>>>> by +/-0.5 fractional in any unit cell direction, then >>>>>>>>>> >>>>>>> >>>>>>> reforigin will >>>>>>> >>>>>>>>>> >>>>>>>>>> find back this translation and consider it as valid for this >>>>>>>>>> >>>>>>>>> >>>>>>>>> spacegroup. >>>>>>>>> >>>>>>>>>> >>>>>>>>>> But for this spacegroup I should find only (0,0,0) or >>>>>>>>>> >>>>>>> >>>>>>> (1/2,1/2,1/2) >>>>>>> >>>>>>>>>> >>>>>>>>>> as possible alternate origins. >>>>>>>>>> >>>>>>>>>> Does this mean that I can't trust reforigin and that I >>>>>>>>>> >>>>>> >>>>>> must filter >>>>>> >>>>>>>>>> >>>>>>>>>> out its results to retain only the valid ones? >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Francois. >>>>>>>>>> >>>>>>>>> >>>>>>>>> Disclaimer >>>>>>>>> This communication is confidential and may contain privileged >>>>>>>>> information intended solely for the named addressee(s). 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