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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