Ian Tickle wrote:
Francois, the possible non-equivalent alternate origins for F432 are:
1 0.0000 0.0000 0.0000
2 0.2500 0.2500 0.2500
3 0.5000 0.5000 0.5000
4 0.7500 0.7500 0.7500
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.
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>
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?
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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