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Multiple Molecule Visualization
- luongsh
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8 years 7 months ago #4888
by luongsh
Multiple Molecule Visualization was created by luongsh
Hello,
I am using Martini to run a 50 identical molecule simulation. I used VMD to visualize the system. In order to distinguish different molecules, I had to create 50 representation with different color for each molecule.
My question is that is there any other methods or tool that I can use for a system consisting of multiple identical molecules?
Thank you
I am using Martini to run a 50 identical molecule simulation. I used VMD to visualize the system. In order to distinguish different molecules, I had to create 50 representation with different color for each molecule.
My question is that is there any other methods or tool that I can use for a system consisting of multiple identical molecules?
Thank you
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8 years 6 months ago #4989
by mnmelo
Replied by mnmelo on topic Multiple Molecule Visualization
Hi,
I believe with VMD you can color by residue. If your molecules are one residue each, then this should already solve your problem.
(The most obvious way would be to color by fragment, which VMD also does, but since it typically can't detect Martini-length bonds this fails).
If you have multi-residue molecules you can make an .itp just for visualization purposes where all atoms in a molecule belong to residue 1. If you then generate a .tpr and extract a .gro from that (using editconf) again you should have your problem solvable by coloring by residue.
(This solution applies to GROMACS. You'll have to adapt to other simulation software).
Finally, VMD can be scripted in either tcl or python, and generating multiple representations doesn't seem a very hard task to script.
I'm not entirely sure if you'll be limited by the number of available colors, but you can also use the occupancy or beta fields of a PDB file to convey molecule number, which will then be colored on a color gradient (tune it in Graphics->Colors->Color Scale). You need only generate a suitable PDB file (maybe even from converting a .gro file and copying over the resnumber column to the beta or occupancy one).
If you go the scripting route VMD also allows you to assign values to a 'user' variable, which will also be colored on a gradient.
I believe with VMD you can color by residue. If your molecules are one residue each, then this should already solve your problem.
(The most obvious way would be to color by fragment, which VMD also does, but since it typically can't detect Martini-length bonds this fails).
If you have multi-residue molecules you can make an .itp just for visualization purposes where all atoms in a molecule belong to residue 1. If you then generate a .tpr and extract a .gro from that (using editconf) again you should have your problem solvable by coloring by residue.
(This solution applies to GROMACS. You'll have to adapt to other simulation software).
Finally, VMD can be scripted in either tcl or python, and generating multiple representations doesn't seem a very hard task to script.
I'm not entirely sure if you'll be limited by the number of available colors, but you can also use the occupancy or beta fields of a PDB file to convey molecule number, which will then be colored on a color gradient (tune it in Graphics->Colors->Color Scale). You need only generate a suitable PDB file (maybe even from converting a .gro file and copying over the resnumber column to the beta or occupancy one).
If you go the scripting route VMD also allows you to assign values to a 'user' variable, which will also be colored on a gradient.
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8 years 6 months ago #5019
by luongsh
Replied by luongsh on topic Multiple Molecule Visualization
Thanks,
I was able to write a tcl script to create 50 representations, each contain 1 molecular with different color
I was able to write a tcl script to create 50 representations, each contain 1 molecular with different color
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8 years 6 months ago #5028
by mnmelo
Replied by mnmelo on topic Multiple Molecule Visualization
That's great!
If it's not too much trouble, could you post here your code snippet, for future reference?
Cheers,
Manel
If it's not too much trouble, could you post here your code snippet, for future reference?
Cheers,
Manel
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8 years 6 months ago - 8 years 6 months ago #5034
by luongsh
Replied by luongsh on topic Multiple Molecule Visualization
This is the description and the script I wrote:
I want to investigate how 50 protein molecules assemble so I use gromacs to create 50 copies of a protein in a box. Each molecule contain 65 coarse grain atoms after using "martinized script". For better visualization, I wrote a tcl script to color each molecule with a different color. Basically, the script creates 50 representations. In each representation, it display the specific index for a single molecule and choose a color for it. We can manually do it but it take lots of time if we have multiple simulations.
I am only 3 months old in gromacs so please don't laugh if I do something not so intelligent.
I want to investigate how 50 protein molecules assemble so I use gromacs to create 50 copies of a protein in a box. Each molecule contain 65 coarse grain atoms after using "martinized script". For better visualization, I wrote a tcl script to color each molecule with a different color. Basically, the script creates 50 representations. In each representation, it display the specific index for a single molecule and choose a color for it. We can manually do it but it take lots of time if we have multiple simulations.
I am only 3 months old in gromacs so please don't laugh if I do something not so intelligent.
set color 0 ; # initiate the index of color
set index 1 ; # initiate the index of each representation
set begin 0 ; # initiate the index of the first residue of a molecule
set end 64 ; # initiate the index of the last residue of a molecule
for {set i 0} {$i < 50} {incr i} {
mol color ColorID $color ; # choose a color for a representation
mol addrep top ; # add a representation
mol modselect $index top "index $begin to $end" ; # choose to display only selected atoms for each representation
mol modstyle $index top VDW ; # change the drawing style to VDW
set begin [expr {$begin + 65}] ; # reassign the index for the first residue for the next molecule
set end [expr {$end + 65}] ; # reassign the index for the last residue for the next molecule
set index [expr {$index + 1}]
if {$color < 32} {set color [expr {$color + 1}]} else {set color 0}
}
mol delrep 0 top
Last edit: 8 years 6 months ago by mnmelo. Reason: Code formatting
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8 years 6 months ago #5041
by mnmelo
Replied by mnmelo on topic Multiple Molecule Visualization
Big thanks!
(I edited your reply to have neatly formatted code.)
Cheers,
Manel
(I edited your reply to have neatly formatted code.)
Cheers,
Manel
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