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...!*
------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Reply via email to