RMSD is root mean square deviation. That's what you did?
x = {1.1}
y = {2.1}[1][17]
s = 0.0
for (var i = 1; i <= 17; i++) { d = (x[i].xyz - y[i].xyz).distance(0); s +=
d * d }
print Sqrt(s / 17)
0.09403623
or
x = {1.1}.xyz.all
y = {2.1}[1][17].xyz.all
d2 = (x.sub(y)).mul(x.sub(y))
script inline @{"print sqrt((" + d2.join("+") +")/17)"}
0.09403623
Right?
On Tue, Feb 11, 2014 at 4:41 PM, jiayi.zhou <jiayi.z...@mun.ca> wrote:
> To whom it may concern:
>
> I load the following 2 xyz files to Jmol:
> one is :
> 17
> ! Z X Y Z
> 6 0.71255210 -0.00198305 -0.00038352
> 6 -0.71255210 -0.00198305 -0.00038352
> 1 1.21161832 0.18106610 -0.95074020
> 1 -1.21161832 0.18106610 -0.95074020
> 6 1.46675482 0.00032949 1.14700560
> 6 -1.46675482 0.00032949 1.14700560
> 1 2.54646693 0.11331346 1.09224163
> 1 -2.54646693 0.11331346 1.09224163
> 1 1.08622161 -0.39776285 2.08112697
> 1 -1.08622161 -0.39776285 2.08112697
> 6 0.67118625 2.01435437 2.13503804
> 6 -0.67118625 2.01435437 2.13503804
> 6 0.00000000 2.84303299 1.08839760
> 1 1.52119718 2.05013757 2.79982503
> 1 -1.52119718 2.05013757 2.79982503
> 1 0.00000000 2.45945232 0.05743608
> 1 0.00000000 3.93573820 1.14965666
>
> The other is
>
> 18
> ! Z X Y Z
> 6 0.70278691 0.00014763 -0.00008885
> 6 -0.70283130 0.00011551 0.00005579
> 1 1.20540366 0.21486646 -0.92795273
> 1 -1.20578976 0.21177870 -0.92847329
> 6 1.43671821 0.00003416 1.15847654
> 6 -1.43721538 -0.00051139 1.15914169
> 1 2.50370092 0.12922702 1.11059239
> 1 -2.50496728 0.12304603 1.11006957
> 1 1.08008477 -0.48901903 2.04407291
> 1 -1.08072573 -0.49287434 2.04301717
> 6 0.66693737 1.82383282 2.19972392
> 6 -0.68099663 1.81770231 2.20659332
> 6 -0.00260321 2.75871804 1.30056176
> 1 1.47088200 1.86272007 2.90329829
> 1 -1.47312945 1.84287565 2.92443313
> 1 -0.00414384 2.54881018 0.23702931
> 8 0.06066504 4.12302196 1.58495019
> 1 -0.60337264 4.58301869 1.08939537
>
> Then I ran the script compare {1.1} {2.1} rotate translate 2
> The RMSD is 0.09 Angstroms.
>
> However, I captured coordinates of each atom one by one after rotation
> from Jmol.
> The first structure's coordinates is as following
> x y z
> 0.712552100 -0.001983050 -0.000383520 -0.712552100 -0.001983050
> -0.000383520 1.211618300 0.181066100 -0.950740160 -1.211618300
> 0.181066100 -0.950740160 1.466754800 0.000329490 1.147005600
> -1.466754800 0.000329490 1.147005600 2.546466800 0.113313460 1.092241600
> -2.546466800 0.113313460 1.092241600 1.086221600 -0.397762840 2.081127000
> -1.086221600 -0.397762840 2.081127000 0.671186300 2.014354500 2.135038100
> -0.671186300 2.014354500 2.135038100 0.000000000 2.843032800 1.088397600
> 1.521197200 2.050137500 2.799825000 -1.521197200 2.050137500 2.799825000
> 0.000000000 2.459452400 0.057436080 0.000000000 3.935738000 1.149656700 The
> second structure's coordinates are as following:
> x y z
> 0.702808560 -0.043177366 0.002896905 -0.702807550 -0.045481680
> 0.002591014 1.205491000 0.103391530 -0.938106400 -1.205694100
> 0.096357524 -0.939174300 1.436228400 0.043286085 1.158556200
> -1.437700500 0.038123070 1.158334500 2.503024000 0.170331480 1.101624400
> -2.505626400 0.155993580 1.099946000 1.079985600 -0.379748700 2.077672000
> -1.080815100 -0.387181040 2.076207600 0.663078800 1.937610600 2.062311600
> -0.684846600 1.929813900 2.069180300 -0.007556678 2.802598000 1.096479200
> 1.466650000 2.029550300 2.761365700 -1.477334900 2.006536000 2.782957800
> -0.008293512 2.514878300 0.051308513 0.053408604 4.184252300 1.279566500
> -0.611143900 4.605397000 0.751244370
> Then I calculated the RMSD manually, I got the value is
> 1.250598150
> The way I calculated the RMSD is the sum of all the distances between
> paired atoms.(17 atoms got paired in this case)
>
> So I was confused how did Jmol get 0.09?
>
> Thank you.
>
> --
> Aiden/Jiayi Zhou
>
> Office Tel: 709-864-4891
> Master Candidate
> Dept. of Computer Science
> Memorial University of Newfoundland
> St. John's, NL, Canada, A1B 3X5
>
> P I*f you decide to print this...*
>
> * then you'll need to find a place to file it...!*
>
>
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