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:gshe...@shelx.uni-ac.gwdg.de]
Sent: 05 February 2010 23:08
To: Ian Tickle
Cc: CCP4BB@JISCMAIL.AC.UK
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: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle
Sent: 27 January 2010 22:25
To: James Holton; Francois Berenger
Cc: CCP4BB@jiscmail.ac.uk
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: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton
Sent: 27 January 2010 21:35
To: Francois Berenger
Cc: CCP4BB@jiscmail.ac.uk
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: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Francois Berenger
Sent: 27 January 2010 06:50
To: CCP4BB@JISCMAIL.AC.UK
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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