Re: [Jmol-users] Some question about RMSD calculation
better:
x = {1.1}.xyz.all
y = {2.1}[1][17].xyz.all
print sqrt(x.sub(y).mul(x.sub(y)).sum/17)
(Iforgot about array.sum)
On Tue, Feb 11, 2014 at 8:35 PM, Robert Hanson wrote:
> 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 wrote:
>
>> To whom it may concern:
>>
>> I load the following 2 xyz files to Jmol:
>> one is :
>> 17
>> !ZX Y Z
>> 60.71255210 -0.00198305 -0.00038352
>> 6 -0.71255210 -0.00198305 -0.00038352
>> 11.211618320.18106610 -0.95074020
>> 1 -1.211618320.18106610 -0.95074020
>> 61.466754820.000329491.14700560
>> 6 -1.466754820.000329491.14700560
>> 12.546466930.113313461.09224163
>> 1 -2.546466930.113313461.09224163
>> 11.08622161 -0.397762852.08112697
>> 1 -1.08622161 -0.397762852.08112697
>> 60.671186252.014354372.13503804
>> 6 -0.671186252.014354372.13503804
>> 60.2.843032991.08839760
>> 11.521197182.050137572.79982503
>> 1 -1.521197182.050137572.79982503
>> 10.2.459452320.05743608
>> 10.3.935738201.14965666
>>
>> The other is
>>
>> 18
>> !ZX Y Z
>> 60.702786910.00014763 -0.8885
>> 6 -0.702831300.000115510.5579
>> 11.205403660.21486646 -0.92795273
>> 1 -1.205789760.21177870 -0.92847329
>> 61.436718210.34161.15847654
>> 6 -1.43721538 -0.000511391.15914169
>> 12.503700920.129227021.11059239
>> 1 -2.504967280.123046031.11006957
>> 11.08008477 -0.489019032.04407291
>> 1 -1.08072573 -0.492874342.04301717
>> 60.666937371.823832822.19972392
>> 6 -0.680996631.817702312.20659332
>> 6 -0.002603212.758718041.30056176
>> 11.470882001.862720072.90329829
>> 1 -1.473129451.842875652.92443313
>> 1 -0.004143842.548810180.23702931
>> 80.060665044.123021961.58495019
>> 1 -0.603372644.583018691.08939537
>>
>> 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
>> 0.0 2.843032800 1.088397600 1.521197200 2.050137500 2.799825000
>> -1.521197200 2.050137500 2.799825000 0.0 2.459452400 0.057436080
>> 0.0 3.935738000 1.149656700 The second structure's coordinates
>> are as following:
>>xyz
>> 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 1.46665 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...!*
>>
>>
>> --
Re: [Jmol-users] Some question about RMSD calculation
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 wrote:
> To whom it may concern:
>
> I load the following 2 xyz files to Jmol:
> one is :
> 17
> !ZX Y Z
> 60.71255210 -0.00198305 -0.00038352
> 6 -0.71255210 -0.00198305 -0.00038352
> 11.211618320.18106610 -0.95074020
> 1 -1.211618320.18106610 -0.95074020
> 61.466754820.000329491.14700560
> 6 -1.466754820.000329491.14700560
> 12.546466930.113313461.09224163
> 1 -2.546466930.113313461.09224163
> 11.08622161 -0.397762852.08112697
> 1 -1.08622161 -0.397762852.08112697
> 60.671186252.014354372.13503804
> 6 -0.671186252.014354372.13503804
> 60.2.843032991.08839760
> 11.521197182.050137572.79982503
> 1 -1.521197182.050137572.79982503
> 10.2.459452320.05743608
> 10.3.935738201.14965666
>
> The other is
>
> 18
> !ZX Y Z
> 60.702786910.00014763 -0.8885
> 6 -0.702831300.000115510.5579
> 11.205403660.21486646 -0.92795273
> 1 -1.205789760.21177870 -0.92847329
> 61.436718210.34161.15847654
> 6 -1.43721538 -0.000511391.15914169
> 12.503700920.129227021.11059239
> 1 -2.504967280.123046031.11006957
> 11.08008477 -0.489019032.04407291
> 1 -1.08072573 -0.492874342.04301717
> 60.666937371.823832822.19972392
> 6 -0.680996631.817702312.20659332
> 6 -0.002603212.758718041.30056176
> 11.470882001.862720072.90329829
> 1 -1.473129451.842875652.92443313
> 1 -0.004143842.548810180.23702931
> 80.060665044.123021961.58495019
> 1 -0.603372644.583018691.08939537
>
> 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 0.0 2.843032800 1.088397600
> 1.521197200 2.050137500 2.799825000 -1.521197200 2.050137500 2.799825000
> 0.0 2.459452400 0.057436080 0.0 3.935738000 1.149656700 The
> second structure's coordinates are as following:
>xyz
> 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
> 1.46665 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
[Jmol-users] Some question about RMSD calculation
To whom it may concern:
I load the following 2 xyz files to Jmol:
one is :
17
!ZX Y Z
60.71255210 -0.00198305 -0.00038352
6 -0.71255210 -0.00198305 -0.00038352
11.211618320.18106610 -0.95074020
1 -1.211618320.18106610 -0.95074020
61.466754820.000329491.14700560
6 -1.466754820.000329491.14700560
12.546466930.113313461.09224163
1 -2.546466930.113313461.09224163
11.08622161 -0.397762852.08112697
1 -1.08622161 -0.397762852.08112697
60.671186252.014354372.13503804
6 -0.671186252.014354372.13503804
60.2.843032991.08839760
11.521197182.050137572.79982503
1 -1.521197182.050137572.79982503
10.2.459452320.05743608
10.3.935738201.14965666
The other is
18
!ZX Y Z
60.702786910.00014763 -0.8885
6 -0.702831300.000115510.5579
11.205403660.21486646 -0.92795273
1 -1.205789760.21177870 -0.92847329
61.436718210.34161.15847654
6 -1.43721538 -0.000511391.15914169
12.503700920.129227021.11059239
1 -2.504967280.123046031.11006957
11.08008477 -0.489019032.04407291
1 -1.08072573 -0.492874342.04301717
60.666937371.823832822.19972392
6 -0.680996631.817702312.20659332
6 -0.002603212.758718041.30056176
11.470882001.862720072.90329829
1 -1.473129451.842875652.92443313
1 -0.004143842.548810180.23702931
80.060665044.123021961.58495019
1 -0.603372644.583018691.08939537
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 0.0 2.843032800 1.088397600 1.521197200 2.050137500
2.799825000 -1.521197200 2.050137500 2.799825000 0.0 2.459452400
0.057436080 0.0 3.935738000 1.149656700 The second structure's
coordinates are as following:
xyz
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 1.46665 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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Re: [Jmol-users] MEP questions
load nacl.mol
{_Na}.formalcharge = 1
{_Cl}.formalcharge = -1
isosurface ionic
The Spartan reader does not assign formal charges, and you need those for
"ionic"
Bob
On Tue, Feb 11, 2014 at 9:30 AM, Alexander Rose wrote:
> Hi,
>
> there is an "IONIC radius" option for the isosurface comand, have you
> tried that?
>
> http://chemapps.stolaf.edu/jmol/docs/#isosurface
>
>
> Alex
>
> - Ursprüngliche Mail -
> > Von: "Pshemak Maslak"
> > An: jmol-users@lists.sourceforge.net
> > Gesendet: Dienstag, 11. Februar 2014 16:19:44
> > Betreff: [Jmol-users] MEP questions
> >
> >
> > I have visualized MEP for NaCl (molecule) in Spartan and in Jmol). In
> > Spartan, I see MEP mapped on a density surface that correspond to the
> > expectation of ionic sizes (Na+ small, Cl- big). In Jmol, MEP is
> > mapped
> > on what appears to be a molecular surface matching atomic sizes (Na
> > big,
> > Cl small).
> >
> > 1. Can I reproduce the Spartan surface in Jmol? If so, how?
> >
> > 2. can I read the surface from the spartan file? If so, how?
> >
> > Thanks,
> >
> > PM
> >
> >
> --
> > 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
> >
>
>
> --
> 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
> ___
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>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [Jmol-users] MEP questions
Hi, there is an "IONIC radius" option for the isosurface comand, have you tried that? http://chemapps.stolaf.edu/jmol/docs/#isosurface Alex - Ursprüngliche Mail - > Von: "Pshemak Maslak" > An: jmol-users@lists.sourceforge.net > Gesendet: Dienstag, 11. Februar 2014 16:19:44 > Betreff: [Jmol-users] MEP questions > > > I have visualized MEP for NaCl (molecule) in Spartan and in Jmol). In > Spartan, I see MEP mapped on a density surface that correspond to the > expectation of ionic sizes (Na+ small, Cl- big). In Jmol, MEP is > mapped > on what appears to be a molecular surface matching atomic sizes (Na > big, > Cl small). > > 1. Can I reproduce the Spartan surface in Jmol? If so, how? > > 2. can I read the surface from the spartan file? If so, how? > > Thanks, > > PM > > -- > 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 > -- 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
[Jmol-users] jmol-14.1.8_2014.02.11.zip
Alas, this is why we test... http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.8_2014.02.11.zip 2014.02.10b not usable -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- 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
[Jmol-users] MEP questions
I have visualized MEP for NaCl (molecule) in Spartan and in Jmol). In Spartan, I see MEP mapped on a density surface that correspond to the expectation of ionic sizes (Na+ small, Cl- big). In Jmol, MEP is mapped on what appears to be a molecular surface matching atomic sizes (Na big, Cl small). 1. Can I reproduce the Spartan surface in Jmol? If so, how? 2. can I read the surface from the spartan file? If so, how? Thanks, PM -- 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
