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.
> > >>
> > >>
> > >>
> > >> Disclaimer
> > >> This communication is confidential and may contain privileged
> > >> information intended solely for the named addressee(s). It
> > may not be
> > >> used or disclosed except for the purpose for which it has
> > been sent.
> > >> If you are not the intended recipient you must not review, use,
> > >> disclose, copy, distribute or take any action in reliance
> > upon it. If
> > >> you have received this communication in error, please
> notify Astex
> > >> Therapeutics Ltd by emailing [log in to unmask] and
> > >> destroy all copies of the message and any attached
> > documents. Astex
> > >> Therapeutics Ltd monitors, controls and protects all its
> messaging
> > >> traffic in compliance with its corporate email policy.
> The Company
> > >> accepts no liability or responsibility for any onward
> > transmission or
> > >> use of emails and attachments having left the Astex Therapeutics
> > >> domain. Unless expressly stated, opinions in this message
> > are those
> > >> of the individual sender and not of Astex Therapeutics Ltd. The
> > >> recipient should check this email and any attachments for the
> > >> presence of computer viruses. Astex Therapeutics Ltd accepts no
> > >> liability for damage caused by any virus transmitted by
> > this email.
> > >> E-mail is susceptible to data corruption, interception,
> > unauthorized
> > >> amendment, and tampering, Astex Therapeutics Ltd only send and
> > >> receive e-mails on the basis that the Company is not
> > liable for any
> > >> such alteration or any consequences thereof.
> > >> Astex Therapeutics Ltd., Registered in England at 436 Cambridge
> > >> Science Park, Cambridge CB4 0QA under number 3751674
> >
> >
>
>
> Disclaimer
> This communication is confidential and may contain privileged
> information intended solely for the named addressee(s). It
> may not be used or disclosed except for the purpose for which
> it has been sent. If you are not the intended recipient you
> must not review, use, disclose, copy, distribute or take any
> action in reliance upon it. If you have received this
> communication in error, please notify Astex Therapeutics Ltd
> by emailing [log in to unmask] and destroy all
> copies of the message and any attached documents.
> Astex Therapeutics Ltd monitors, controls and protects all
> its messaging traffic in compliance with its corporate email
> policy. The Company accepts no liability or responsibility
> for any onward transmission or use of emails and attachments
> having left the Astex Therapeutics domain. Unless expressly
> stated, opinions in this message are those of the individual
> sender and not of Astex Therapeutics Ltd. The recipient
> should check this email and any attachments for the presence
> of computer viruses. Astex Therapeutics Ltd accepts no
> liability for damage caused by any virus transmitted by this
> email. E-mail is susceptible to data corruption,
> interception, unauthorized amendment, and tampering, Astex
> Therapeutics Ltd only send and receive e-mails on the basis
> that the Company is not liable for any such alteration or any
> consequences thereof.
> Astex Therapeutics Ltd., Registered in England at 436
> Cambridge Science Park, Cambridge CB4 0QA under number 3751674
>
>
Disclaimer
This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [log in to unmask] and destroy all copies of the message and any attached documents.
Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
|
