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 <[log in to unmask]> 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:[log in to unmask]]
>>>> Sent: 05 February 2010 23:08
>>>> To: Ian Tickle
>>>> Cc: [log in to unmask]
>>>> 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: [log in to unmask]
>>>>>> [mailto:[log in to unmask]] On Behalf Of Ian Tickle
>>>>>> Sent: 27 January 2010 22:25
>>>>>> To: James Holton; Francois Berenger
>>>>>> Cc: [log in to unmask]
>>>>>> 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: [log in to unmask]
>>>>>>> [mailto:[log in to unmask]] On Behalf Of James Holton
>>>>>>> Sent: 27 January 2010 21:35
>>>>>>> To: Francois Berenger
>>>>>>> Cc: [log in to unmask]
>>>>>>> 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: [log in to unmask]
>>>>>>>>>>
>>>>>>>
>>>>>>> [mailto:[log in to unmask]]
>>>>>>>
>>>>>>>>>
>>>>>>>>> On
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Behalf Of Francois Berenger
>>>>>>>>>> Sent: 27 January 2010 06:50
>>>>>>>>>> To: [log in to unmask]
>>>>>>>>>> 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.
>>>>>>>>>>
>>>>>>>>>
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