On 06/21/2018 03:34 PM, John Berrisford wrote:
From a PDB deposition point of view, I echo Paul’s comment. If possible,
please move your molecule closer to the origin. It helps with the curation
process and is easier for users of your entry as some software struggles with
such extreme transformations.
Regards
John
Now that we've all read the manual :),
Since the origin shift in question here is always integral: { 1 0 1 }
It seems this is not about _where_ in the unit cell, but in _which_ unit cell.
As I understand it the symop: -X, Y+1/2, Z + (0 -1 1)
is what would work if you were in the first cell { 0 0 0 }
So you need to
Take the current coordinate X =x,y,z
subtract the origin translation O = { 1 0 1 },
apply the symop S = -X, Y+1/2, Z + (0 -1 1) = -X,Y,Z +(0,-1/2,1)
add back the origin translation O
something like X' = S(X-O) + O
which could take three runs of pdbset.
But you could really work out an operator that would do it in one run:
the symop S consists of a rotation and translation
S(x) = M(x) + T
S(X-O) = M(X-O) +T
S(X-O) = M(X) - M(O) +T
X' = S(X-O) + O = M(X) - M(O) + T + O
In the example given, M = -X,Y,Z; T = (0,-1/2,1); O = (1 0 1)
M(O) = -1,0,1
-M(O) = 1,0,-1
add T gives 1,-1/2,0
add O gives 2,-1/2,1
so the operator should be
-X+2,Y-1/2,Z+1
or something like that, which you could use in pdbset.
Matrix inverts along x, coordinates are way positive in x, result way negative,
need to add 2 unit cell translations to position it adjacent to orig
coordinates
Would something like that work?
*From:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of *Paul Emsley
*Sent:* 21 June 2018 17:30
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Regarding symmetry notion in coot
On 20/06/18 20:49, Anurag Misra wrote:
What is the meaning of the last field — the one in curly brackets -- that
describes the symmetry transformation of a given molecule in coot?
See Section 4.11 of Coot User Manual: "Symmetry"
For example, for
a given X Y Z, coot displays the symmetry transformation of an equivalent
position as " -X, Y+1/2, Z + (0 -1 1) & { 1 0 1 }”.
Can the symmetry molecule be written like bellow by summing respective
values?
In the general case, no. Move your molecule closer to the origin - so that the
pre-translation is (0,0,0) - then coot will report "conventional" symmetry.
Regards,
Paul.
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