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Visualizing atoms in XYZ file with colors representing partial charges
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I have a file containing the atomic coordinates (in XYZ format) of a structure, and I also have a list of the partial atomic charges for each atom. I'd like to create an image of the structure where the colors of the atoms correspond to the computed charges. What are some good ways for doing this?
quantum-chemistry computational-chemistry theoretical-chemistry
asked 3 hours ago
Argon
828517
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up vote
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I have a file containing the atomic coordinates (in XYZ format) of a structure, and I also have a list of the partial atomic charges for each atom. I'd like to create an image of the structure where the colors of the atoms correspond to the computed charges. What are some good ways for doing this?
quantum-chemistry computational-chemistry theoretical-chemistry
asked 3 hours ago
Argon
828517
(In reply to a deleted comment). I'd be happy if it helps, but I see no benefit in doing so. The XYZ coordinates are a simple $ntimes3$ matrix, and the charges are stored as a $ntimes1$ vector. The filetype is irrelevant (I can freely convert to any format of your choosing -- CIF, *CAR, XYZ, JMol, etc.).
– Argon
2 hours ago
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up vote
3
down vote
favorite
up vote
3
down vote
favorite
I have a file containing the atomic coordinates (in XYZ format) of a structure, and I also have a list of the partial atomic charges for each atom. I'd like to create an image of the structure where the colors of the atoms correspond to the computed charges. What are some good ways for doing this?
quantum-chemistry computational-chemistry theoretical-chemistry
asked 3 hours ago
Argon
828517
I have a file containing the atomic coordinates (in XYZ format) of a structure, and I also have a list of the partial atomic charges for each atom. I'd like to create an image of the structure where the colors of the atoms correspond to the computed charges. What are some good ways for doing this?
quantum-chemistry computational-chemistry theoretical-chemistry
quantum-chemistry computational-chemistry theoretical-chemistry
asked 3 hours ago
Argon
828517
asked 3 hours ago
Argon
828517
edited 22 mins ago
asked 3 hours ago
Argon
828517
asked 3 hours ago
Argon
828517
asked 3 hours ago
Argon
828517
828517
(In reply to a deleted comment). I'd be happy if it helps, but I see no benefit in doing so. The XYZ coordinates are a simple $ntimes3$ matrix, and the charges are stored as a $ntimes1$ vector. The filetype is irrelevant (I can freely convert to any format of your choosing -- CIF, *CAR, XYZ, JMol, etc.).
– Argon
2 hours ago
add a comment |Â
(In reply to a deleted comment). I'd be happy if it helps, but I see no benefit in doing so. The XYZ coordinates are a simple $ntimes3$ matrix, and the charges are stored as a $ntimes1$ vector. The filetype is irrelevant (I can freely convert to any format of your choosing -- CIF, *CAR, XYZ, JMol, etc.).
– Argon
2 hours ago
(In reply to a deleted comment). I'd be happy if it helps, but I see no benefit in doing so. The XYZ coordinates are a simple $ntimes3$ matrix, and the charges are stored as a $ntimes1$ vector. The filetype is irrelevant (I can freely convert to any format of your choosing -- CIF, *CAR, XYZ, JMol, etc.).
– Argon
2 hours ago
(In reply to a deleted comment). I'd be happy if it helps, but I see no benefit in doing so. The XYZ coordinates are a simple $ntimes3$ matrix, and the charges are stored as a $ntimes1$ vector. The filetype is irrelevant (I can freely convert to any format of your choosing -- CIF, *CAR, XYZ, JMol, etc.).
– Argon
2 hours ago
add a comment |Â
2 Answers
2
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up vote
2
down vote
Have you tried VMD link? It's free, up-to-date, will work with .xyz format files, and would allow you to set charge (or other property) as a color-sensitive characteristic. Here's an example using the bonding coordination (number of nearest neighbors) in a crystal (although only the surface is loaded to conserve memory)
answered 2 hours ago
Rolf
974
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up vote
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As far as I know, no software can do this right away but with some work, this should be possible.
Use CYLview to create a povray file, change the atoms to the desired color and render it with Povray. The problem here is that the coordinates of the xyz file and the povray are not the same. But as far as I can tell the numbering stays the same. So if the 3rd atom in your xyz is this:
N -1.227679000 0.558365000 0.000000000
the 3rd sphere in the povray file would look like that:
sphere {<-1.9762436, 0.9491377, 0.0000000> 0.2812500
pigmentcolor rgbt <0.4,0.4,1.0,0.00>
finishF_normal
All you need to do is change the color here. It should also be pretty easy to automate this color change with some lines of code.
So you can go from this
to for example this
by simply changing the color value shown above to
pigmentcolor rgbt <0.2,0.8,1.0,0.00>
answered 2 hours ago
DSVA
4,55011335
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2 Answers
2
active
oldest
votes
2 Answers
2
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
2
down vote
Have you tried VMD link? It's free, up-to-date, will work with .xyz format files, and would allow you to set charge (or other property) as a color-sensitive characteristic. Here's an example using the bonding coordination (number of nearest neighbors) in a crystal (although only the surface is loaded to conserve memory)
answered 2 hours ago
Rolf
974
New contributor
Rolf is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |Â
up vote
2
down vote
Have you tried VMD link? It's free, up-to-date, will work with .xyz format files, and would allow you to set charge (or other property) as a color-sensitive characteristic. Here's an example using the bonding coordination (number of nearest neighbors) in a crystal (although only the surface is loaded to conserve memory)
answered 2 hours ago
Rolf
974
New contributor
Rolf is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |Â
up vote
2
down vote
up vote
2
down vote
Have you tried VMD link? It's free, up-to-date, will work with .xyz format files, and would allow you to set charge (or other property) as a color-sensitive characteristic. Here's an example using the bonding coordination (number of nearest neighbors) in a crystal (although only the surface is loaded to conserve memory)
answered 2 hours ago
Rolf
974
New contributor
Rolf is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Have you tried VMD link? It's free, up-to-date, will work with .xyz format files, and would allow you to set charge (or other property) as a color-sensitive characteristic. Here's an example using the bonding coordination (number of nearest neighbors) in a crystal (although only the surface is loaded to conserve memory)
answered 2 hours ago
Rolf
974
New contributor
Rolf is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
answered 2 hours ago
Rolf
974
New contributor
Rolf is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
answered 2 hours ago
Rolf
974
answered 2 hours ago
Rolf
974
974
New contributor
Rolf is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
Rolf is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Rolf is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |Â
add a comment |Â
up vote
1
down vote
As far as I know, no software can do this right away but with some work, this should be possible.
Use CYLview to create a povray file, change the atoms to the desired color and render it with Povray. The problem here is that the coordinates of the xyz file and the povray are not the same. But as far as I can tell the numbering stays the same. So if the 3rd atom in your xyz is this:
N -1.227679000 0.558365000 0.000000000
the 3rd sphere in the povray file would look like that:
sphere {<-1.9762436, 0.9491377, 0.0000000> 0.2812500
pigmentcolor rgbt <0.4,0.4,1.0,0.00>
finishF_normal
All you need to do is change the color here. It should also be pretty easy to automate this color change with some lines of code.
So you can go from this
to for example this
by simply changing the color value shown above to
pigmentcolor rgbt <0.2,0.8,1.0,0.00>
answered 2 hours ago
DSVA
4,55011335
add a comment |Â
up vote
1
down vote
As far as I know, no software can do this right away but with some work, this should be possible.
Use CYLview to create a povray file, change the atoms to the desired color and render it with Povray. The problem here is that the coordinates of the xyz file and the povray are not the same. But as far as I can tell the numbering stays the same. So if the 3rd atom in your xyz is this:
N -1.227679000 0.558365000 0.000000000
the 3rd sphere in the povray file would look like that:
sphere {<-1.9762436, 0.9491377, 0.0000000> 0.2812500
pigmentcolor rgbt <0.4,0.4,1.0,0.00>
finishF_normal
All you need to do is change the color here. It should also be pretty easy to automate this color change with some lines of code.
So you can go from this
to for example this
by simply changing the color value shown above to
pigmentcolor rgbt <0.2,0.8,1.0,0.00>
answered 2 hours ago
DSVA
4,55011335
add a comment |Â
up vote
1
down vote
up vote
1
down vote
As far as I know, no software can do this right away but with some work, this should be possible.
Use CYLview to create a povray file, change the atoms to the desired color and render it with Povray. The problem here is that the coordinates of the xyz file and the povray are not the same. But as far as I can tell the numbering stays the same. So if the 3rd atom in your xyz is this:
N -1.227679000 0.558365000 0.000000000
the 3rd sphere in the povray file would look like that:
sphere {<-1.9762436, 0.9491377, 0.0000000> 0.2812500
pigmentcolor rgbt <0.4,0.4,1.0,0.00>
finishF_normal
All you need to do is change the color here. It should also be pretty easy to automate this color change with some lines of code.
So you can go from this
to for example this
by simply changing the color value shown above to
pigmentcolor rgbt <0.2,0.8,1.0,0.00>
answered 2 hours ago
DSVA
4,55011335
As far as I know, no software can do this right away but with some work, this should be possible.
Use CYLview to create a povray file, change the atoms to the desired color and render it with Povray. The problem here is that the coordinates of the xyz file and the povray are not the same. But as far as I can tell the numbering stays the same. So if the 3rd atom in your xyz is this:
N -1.227679000 0.558365000 0.000000000
the 3rd sphere in the povray file would look like that:
sphere {<-1.9762436, 0.9491377, 0.0000000> 0.2812500
pigmentcolor rgbt <0.4,0.4,1.0,0.00>
finishF_normal
All you need to do is change the color here. It should also be pretty easy to automate this color change with some lines of code.
So you can go from this
to for example this
by simply changing the color value shown above to
pigmentcolor rgbt <0.2,0.8,1.0,0.00>
answered 2 hours ago
DSVA
4,55011335
answered 2 hours ago
DSVA
4,55011335
answered 2 hours ago
DSVA
4,55011335
answered 2 hours ago
DSVA
4,55011335
4,55011335
add a comment |Â
add a comment |Â
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(In reply to a deleted comment). I'd be happy if it helps, but I see no benefit in doing so. The XYZ coordinates are a simple $ntimes3$ matrix, and the charges are stored as a $ntimes1$ vector. The filetype is irrelevant (I can freely convert to any format of your choosing -- CIF, *CAR, XYZ, JMol, etc.).
– Argon
2 hours ago