On 12/13/2015 11:32 AM, luzuok wrote:
> Dear Warren,
>
> Thank you for your reply.
> I still don't understand how a two-digit number can represent a symmetry operation.
> There must be a table to index?
I think that is about right. The symops for every spacegroup are listed and numbered in Int. Tables Volume A.
Assuming no space group has more than 99 symops, two decimal digits would suffice to identify the operator. CCP4 programs get their list of symops from a machine-readable (and also human-readable) file $CCP4/lib/data/symop.lib (maybe also accessible as $SYMOP). I haven't checked, but i assume these are in the same order as in International Tables. So if the space group is 'F 4 3 2' and the symop 2-digit number is 95, you just find the corresponding entry and count down to number 95. At least that would be my guess.
4 2 2 P21 PG2 MONOCLINIC 'P 1 21 1'
X,Y,Z
-X,Y+1/2,-Z
~~~~~~~
209 96 24 F432 PG432 CUBIC 'F 4 3 2'
X,Y,Z
-X,-Y,Z
-X,Y,-Z
X,-Y,-Z
Z,X,Y
Z,-X,-Y
-Z,-X,Y
-Z,X,-Y
Y,Z,X
-Y,Z,-X
Y,-Z,-X
-Y,-Z,X
Y,X,-Z
-Y,-X,-Z
Y,-X,Z
-Y,X,Z
X,Z,-Y
-X,Z,Y
-X,-Z,-Y
X,-Z,Y
Z,Y,-X
Z,-Y,X
-Z,Y,X
-Z,-Y,-X
X,1/2+Y,1/2+Z
-X,1/2-Y,1/2+Z
-X,1/2+Y,1/2-Z
X,1/2-Y,1/2-Z
Z,1/2+X,1/2+Y
Z,1/2-X,1/2-Y
-Z,1/2-X,1/2+Y
-Z,1/2+X,1/2-Y
Y,1/2+Z,1/2+X
-Y,1/2+Z,1/2-X
Y,1/2-Z,1/2-X
-Y,1/2-Z,1/2+X
Y,1/2+X,1/2-Z
-Y,1/2-X,1/2-Z
Y,1/2-X,1/2+Z
-Y,1/2+X,1/2+Z
X,1/2+Z,1/2-Y
-X,1/2+Z,1/2+Y
-X,1/2-Z,1/2-Y
X,1/2-Z,1/2+Y
Z,1/2+Y,1/2-X
Z,1/2-Y,1/2+X
-Z,1/2+Y,1/2+X
-Z,1/2-Y,1/2-X
1/2+X,Y,1/2+Z
1/2-X,-Y,1/2+Z
1/2-X,Y,1/2-Z
1/2+X,-Y,1/2-Z
1/2+Z,X,1/2+Y
1/2+Z,-X,1/2-Y
1/2-Z,-X,1/2+Y
1/2-Z,X,1/2-Y
1/2+Y,Z,1/2+X
1/2-Y,Z,1/2-X
1/2+Y,-Z,1/2-X
1/2-Y,-Z,1/2+X
1/2+Y,X,1/2-Z
1/2-Y,-X,1/2-Z
1/2+Y,-X,1/2+Z
1/2-Y,X,1/2+Z
1/2+X,Z,1/2-Y
1/2-X,Z,1/2+Y
1/2-X,-Z,1/2-Y
1/2+X,-Z,1/2+Y
1/2+Z,Y,1/2-X
1/2+Z,-Y,1/2+X
1/2-Z,Y,1/2+X
1/2-Z,-Y,1/2-X
1/2+X,1/2+Y,Z
1/2-X,1/2-Y,Z
1/2-X,1/2+Y,-Z
1/2+X,1/2-Y,-Z
1/2+Z,1/2+X,Y
1/2+Z,1/2-X,-Y
1/2-Z,1/2-X,Y
1/2-Z,1/2+X,-Y
1/2+Y,1/2+Z,X
1/2-Y,1/2+Z,-X
1/2+Y,1/2-Z,-X
1/2-Y,1/2-Z,X
1/2+Y,1/2+X,-Z
1/2-Y,1/2-X,-Z
1/2+Y,1/2-X,Z
1/2-Y,1/2+X,Z
1/2+X,1/2+Z,-Y
1/2-X,1/2+Z,Y
1/2-X,1/2-Z,-Y
1/2+X,1/2-Z,Y
1/2+Z,1/2+Y,-X
1/2+Z,1/2-Y,X
1/2-Z,1/2+Y,X
1/2-Z,1/2-Y,-X
>
> Best wishes!
> Lu
>
>
>
> --
> 卢作焜
> 南开大学新生物站A202
>
> Lu Zuokun, Ph.D. Candidate
> College of Life Science, Nankai University
>
> 在 2015-12-13 03:18:33,"Schubert, Carsten [JRDUS]" <[log in to unmask]> 写道:
>
> Lu,
>
> here is a post from Warren which explains this:
>
> Alex,
>
> Symexp creates object with names of the form:
>
> prefixSSXXYYZZ
>
> After the prefix, the first two digits SS are the symmetry operation. The next six digits correspond to the relative integral unit cell translation XXYYZZ *after* an initial unit cell translation intended to bring the translated atoms back into closest adjacency.
>
> In other words, the exact XXYYZZ will depend on the atoms in the object, since that will determine the initial "origin" 000000 translation. Nevertheless, the actual symmetry mates displayed should be equivalent, even if their names differ slightly.
>
> Are you finding otherwise?
>
> Cheers,
>
> Warren
>
> *From:*CCP4 bulletin board [mailto:[log in to unmask] <mailto:[log in to unmask]>] *On Behalf Of *luzuok
> *Sent:* Saturday, December 12, 2015 2:46 AM
> *To:* [log in to unmask] <mailto:[log in to unmask]>
> *Subject:* [ccp4bb] pymol symexp
>
> Hi,
> Can anyone tell me what does the eight digits mean after pymol command "symexp". How can I transform it into symmetry operator, as the program "contact" needs it.
> eg. after running "symexp ...", I got the object "sym01000000".
>
> Have a good weekend!
> Lu
>
>
>
>
> --
>
> 卢作焜
>
> 南开大学新生物站A202
>
> Lu Zuokun, Ph.D. Candidate
>
> College of Life Science, Nankai University
>
>
>
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