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Re: [ccp4bb]: find_ncs
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Jim Naismith wrote:
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> Interpreting find_ncs
Very difficult!
Have you used polarrfn to identify the direction of the 3 fold?
It is probably R32 - C2 often is, and if you run axissearch on the C2
cell you find:
axis
Reciprocal lattice vector and Length: 0 0 1 0.005438
Reciprocal lattice vector and Length: 1 1 0 0.015378
Reciprocal lattice vector and Length: 1 -1 0 0.015378
Reciprocal lattice vector and Length: 0 2 0 0.015494
Angles:
0 0 1 0.005438
.....
1 1 0 0.015378 90.00
1 -1 0 0.015378 90.00
0 2 0 0.015494 90.00
.....
1 1 0 0.015378
1 -1 0 0.015378 60.50
0 -2 0 0.015494 120.25
0 2 0 0.015494 59.75
...
1 -1 0 0.015378
0 -2 0 0.015494 59.75
0 2 0 0.015494 120.25
Have I been here before? Yes I have!!
You reindex:
REIN 1.5h-0.5k+l , k,l to convert to R32
Eleanor
> Does anyone use this program?
>
> I always get lost trying to fathom what it tells me.
>
> I fairly certain I am looking for a three fold ncs axis in C2221
>
> I will find it by eye on the graphics but I thought I should learn to do it
> automagically. Ironic that it has taken much longer to do this way than by hand.
>
>
> Is this match #7 a 6 fold axis? If so why does 1 map to 14 and 14 to 1? Is not
> this a characteristic of a 2-fold. I cannot have a 6 fold axis but is this an
> interaction of crystallographic 2-fold with a ncs 3-fold? (I see the 2-fold is
> match #9). It looks like match #12 is the 3-fold but why does 1 match 6 and 6
> match 1?
>
> I have poured over the manual, its clear what a 2-fold looks like and the
> authors web site is down. So any help gratefully received.
>
> Best
> Jim
>
>
> MATCH # 7 with matching pairs 10
> 21 389 85 119 257 417 213 225 307 321
> 448 300 288 256 78 14 352 106 414 206
> Real match pairs 10
> 1 13 3 4 9 14 7 8 10 11
> 14 10 9 8 3 1 11 4 13 7
> NCS matrix:
> 0.43929 -0.86093 -0.25655
> 0.86093 0.48502 -0.15346
> 0.25655 -0.15346 0.95427
> 4.70989 -17.29215 84.45421
> RMS of this NCS: 0.405801982
> Polar angles: psi1, phi1,kappa1 -- psi2,phi2,kappa2
> 163.41 90.00 63.94 16.59 -90.00 -63.94
> Screwing along the axis -85.88 Angstrom
>
> MATCH # 10 with matching pairs 9
> 1 307 65 115 145 177 209 321 385
> 177 385 145 225 65 1 321 209 307
> Real match pairs 9
> 1 10 3 4 5 6 7 11 13
> 6 13 5 8 3 1 11 7 10
> NCS matrix:
> 0.46244 -0.85036 -0.25106
> -0.85042 -0.50550 0.14576
> -0.25086 0.14610 -0.95693
> 42.53104 48.22172 84.64629
> RMS of this NCS: 0.508555889
> Polar angles: psi1, phi1,kappa1 -- psi2,phi2,kappa2
> 81.56 149.82 179.98 98.44 -30.18 -179.98
> Screwing along the axis 0.03 Angstrom
>
> MATCH # 12 with matching pairs 10
> 17 49 257 115 145 161 193 449 385 337
> 177 401 129 465 273 1 321 101 33 209
> Real match pairs 10
> 1 2 9 4 5 6 7 15 13 11
> 6 13 5 15 9 1 11 4 2 7
> NCS matrix:
> -0.45038 -0.85787 0.24743
> 0.85787 -0.49259 -0.14635
> 0.24743 0.14635 0.95779
> -42.69761 47.79170 7.34895
> RMS of this NCS: 0.391739368
> Polar angles: psi1, phi1,kappa1 -- psi2,phi2,kappa2
> 170.32 180.00 119.51 9.68 0.00 -119.51
> Screwing along the axis -0.06 Angstrom
>
> James H. Naismith | Research mailto:naismith@st-and.ac.uk
> Professor of Chemical Biology | Teaching mailto:jhn@st-and.ac.uk
> BBSRC Career Development Fellow |
> Centre for Biomolecular Sciences | Office: 1334-463792 (24 hr)
> The North Haugh | Fax : 1334-467229
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> Fife Scotland, U.K., KY16 9ST | www http://speedy.st-and.ac.uk/
>
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