From: Klaas Decanniere
Date: 11 October 2011 22:29
Hi,
I have two solutions from the ShelX C/D/E pipeline I would like to compare (different datasets, same protein). They seem to have different origins.
Space group is I222, with a choice of 8 origins.
How can I find and apply the correct shift to have the phase sets on a common origin?
The information on http://www.ccp4.ac.uk/html/alternate_origins.html and http://www.ccp4.ac.uk/html/non-centro_origins.html explain it very well, but thy don't point to the tools to use.
Is it a matter of reindex and trying all 8 possibilities?
thanks for your help,
Klaas Decanniere
----------
From: George M. Sheldrick
There are 4 possible origins in I222. There is a simple but inelegant way to
check. Run the SHELXE job for the second dataset four times, first with no MOVE
instruction, then with one of the following MOVE instructions inserted between
UNIT and the first atom in the *_fa.res file from SHELXD:
MOVE 0.5 0 0
MOVE 0 0.5 0
MOVE 0.5 0.5 0
one of these should give you phases with the same origin as your first dataset,
so if you display both maps from the .phs files in COOT they will superimpose.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
----------
From: James Holton
I wrote a little jiffy program for doing things like this:
http://bl831.als.lbl.gov/~jamesh/pickup/origins.com
you run it like this:
origins.com rigthorigin.pdb wrongorigin.pdb I222 correlate
This will shift "wrongorigin.pdb" by each of what I think are the
"allowed origin shifts", calculate an electron density map using
SFALL, and compare that map to the one made from "rightorigin.pdb".
The shift that gives the best correlation coefficient will then be
applied to "wrongorigin.pdb" and output as "neworigin.pdb". There are
plenty of faster ways to do this, such as phenix.emma, but I still
like to use this script when I feel like being puerile (which is
often).
Now, the list of origins (at the bottom of the script) is something I
derived empirically by generating random atoms in a random cell and
applying random fractional shifts, searching for cases where the
structure factors are the same as the no-shift case. Again, I did it
this way to avoid thinking about it. My list has 8 different allowed
shifts for I222, but I assume this is because the 0,0,1/2 shift is
part of a symmetry operator. I guess it is a matter of semantics as
to wether or not that is an "allowed shift"?
-James Holton
MAD Scientist
----------
From: Ian Tickle
----------
From: Eleanor Dodson
If you have two pdb files - one for each ha solution, you can use csymmatch -pdbin-ref soln1.pdb -pdbin soln2.pdb -origin-hand -connetivity-radius 1
Eleanor
----------
From: Francois Berenger
Hello,
The more I read this mailing list, the more I feel
the crystallographer is a very special human being:
- he lives in the Fourier space
- when he goes to the Cartesian space, he restricts
himself to a small box that is replicated to the infinity
using symmetry operators and origin shifts
That being said, some live in a world made of zero and ones...
Regards,
F.
----------
From: Boaz Shaanan
Hi Francois,
As for point 2 in your list: There are crystallographers (those who deal with quasi-crystals, such as the recent Nobel laurate Dan Shechtman) who live, so to speak, outside the box that you're referring to. There is no periodicity in their quasi-crystals and even the unit cell is hard to define if at all.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Date: 11 October 2011 22:29
Hi,
I have two solutions from the ShelX C/D/E pipeline I would like to compare (different datasets, same protein). They seem to have different origins.
Space group is I222, with a choice of 8 origins.
How can I find and apply the correct shift to have the phase sets on a common origin?
The information on http://www.ccp4.ac.uk/html/alternate_origins.html and http://www.ccp4.ac.uk/html/non-centro_origins.html explain it very well, but thy don't point to the tools to use.
Is it a matter of reindex and trying all 8 possibilities?
thanks for your help,
Klaas Decanniere
----------
From: George M. Sheldrick
There are 4 possible origins in I222. There is a simple but inelegant way to
check. Run the SHELXE job for the second dataset four times, first with no MOVE
instruction, then with one of the following MOVE instructions inserted between
UNIT and the first atom in the *_fa.res file from SHELXD:
MOVE 0.5 0 0
MOVE 0 0.5 0
MOVE 0.5 0.5 0
one of these should give you phases with the same origin as your first dataset,
so if you display both maps from the .phs files in COOT they will superimpose.
George
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
----------
From: James Holton
I wrote a little jiffy program for doing things like this:
http://bl831.als.lbl.gov/~jamesh/pickup/origins.com
you run it like this:
origins.com rigthorigin.pdb wrongorigin.pdb I222 correlate
This will shift "wrongorigin.pdb" by each of what I think are the
"allowed origin shifts", calculate an electron density map using
SFALL, and compare that map to the one made from "rightorigin.pdb".
The shift that gives the best correlation coefficient will then be
applied to "wrongorigin.pdb" and output as "neworigin.pdb". There are
plenty of faster ways to do this, such as phenix.emma, but I still
like to use this script when I feel like being puerile (which is
often).
Now, the list of origins (at the bottom of the script) is something I
derived empirically by generating random atoms in a random cell and
applying random fractional shifts, searching for cases where the
structure factors are the same as the no-shift case. Again, I did it
this way to avoid thinking about it. My list has 8 different allowed
shifts for I222, but I assume this is because the 0,0,1/2 shift is
part of a symmetry operator. I guess it is a matter of semantics as
to wether or not that is an "allowed shift"?
-James Holton
MAD Scientist
----------
From: Ian Tickle
James, the (0,0,1/2) shift is not "part of" any symmetry operator in I222, but I'm sure you knew that! - whereas the (1/2,1/2,1/2) shift _is_ a symmetry operator: the I centring operator in fact. This means that the lattice repeating units of the crystal structures (i.e. the set of atomic positions in the unit cell) will be identical in pairs, so in I222 (or indeed any I-centred space group) the crystal structure obtaining by shifting by (0,0,1/2) is identical in all respects to the one obtained from the (1/2,1/2,0) shift. In contrast, the structures obtained from all the other pairs, e,g, (0,0,0) and (0,0,1/2), are different in all respects, excepting that their sets of calculated amplitudes will be identical.
In your terminology a "non-allowed" origin shift is one which would cause even the |Fc|s to differ, which is practice would mean that you would have to use a different space-group specific formula for the structure factor (so it's "non-allowed" only in the sense that you are "not allowed" to use the same structure factor formula, but you "are allowed" to use a different one).
I prefer to call it "non-equivalent origin shift" (as opposed to equivalent origin or centring shift) - it's not really a question of whether it's "allowed" or not, it's whether it has any effect on the crystal structure. In practical terms of course it makes absolutely no difference to the result if you choose to do things that have absolutely no effect!
Cheers
-- Ian
In your terminology a "non-allowed" origin shift is one which would cause even the |Fc|s to differ, which is practice would mean that you would have to use a different space-group specific formula for the structure factor (so it's "non-allowed" only in the sense that you are "not allowed" to use the same structure factor formula, but you "are allowed" to use a different one).
I prefer to call it "non-equivalent origin shift" (as opposed to equivalent origin or centring shift) - it's not really a question of whether it's "allowed" or not, it's whether it has any effect on the crystal structure. In practical terms of course it makes absolutely no difference to the result if you choose to do things that have absolutely no effect!
Cheers
-- Ian
----------
From: Eleanor Dodson
If you have two pdb files - one for each ha solution, you can use csymmatch -pdbin-ref soln1.pdb -pdbin soln2.pdb -origin-hand -connetivity-radius 1
Eleanor
----------
From: Francois Berenger
Hello,
The more I read this mailing list, the more I feel
the crystallographer is a very special human being:
- he lives in the Fourier space
- when he goes to the Cartesian space, he restricts
himself to a small box that is replicated to the infinity
using symmetry operators and origin shifts
That being said, some live in a world made of zero and ones...
Regards,
F.
----------
From: Boaz Shaanan
Hi Francois,
As for point 2 in your list: There are crystallographers (those who deal with quasi-crystals, such as the recent Nobel laurate Dan Shechtman) who live, so to speak, outside the box that you're referring to. There is no periodicity in their quasi-crystals and even the unit cell is hard to define if at all.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
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