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Publication ready Martini images
- Rajat Desikan
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10 years 5 months ago #2651
by Rajat Desikan
Publication ready Martini images was created by Rajat Desikan
Hi All,
I want to know how to generate publication quality Martini images using vmd/pymol. Some of the Martini images in previous publications are stunning! I have a protein channel embedded in a membrane. Are there any tricks that the pundits here would like to share? :)
I want to know how to generate publication quality Martini images using vmd/pymol. Some of the Martini images in previous publications are stunning! I have a protein channel embedded in a membrane. Are there any tricks that the pundits here would like to share? :)
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- Clement
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10 years 5 months ago #2652
by Clement
Replied by Clement on topic Publication ready Martini images
That's... a wide question.
It depends on your tastes, what you want to show, ... What paper(s) are you referring to?
It depends on your tastes, what you want to show, ... What paper(s) are you referring to?
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- xavier
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10 years 5 months ago #2653
by xavier
Replied by xavier on topic Publication ready Martini images
This is indeed a question difficult to answer to.
We mainly use VMD for rendering where the play with Shadows and Ambiance Occlusion are important, but also the type rendering.
There are also a few tools available in the website that Clement wrote to help visualising the CG systems. In particular cg_bonds.tcl help VMD to define the topology of a system by reading the CG topology.
We mainly use VMD for rendering where the play with Shadows and Ambiance Occlusion are important, but also the type rendering.
There are also a few tools available in the website that Clement wrote to help visualising the CG systems. In particular cg_bonds.tcl help VMD to define the topology of a system by reading the CG topology.
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- Rajat Desikan
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10 years 5 months ago #2654
by Rajat Desikan
Replied by Rajat Desikan on topic Publication ready Martini images
The picture in the gating of the mechanosensitive protein channel in a liposome was stunning. Can you share your thoughts on how you managed to accomplish that?
www.ncbi.nlm.nih.gov/pmc/articles/PMC2993341/figure/F3/
www.ncbi.nlm.nih.gov/pmc/articles/PMC2993341/figure/F3/
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10 years 5 months ago #2655
by xavier
Replied by xavier on topic Publication ready Martini images
This one is indeed not bad!
Martti Louhivuori is responsible for the rendering. You first have to actually have a system with a small liposome with a channel imbedded (and equilibrated is better). Then the inside water is represented as spheres with Amb. Occl. on and potentially diffuse rendering. The lipids are small liquorice with a transparent surface in orange probably restructured to the phosphate atoms. The channel itself is rendered with sticks on the trace (white) and tubes (cylinders defined in VMD) help following the helices direction. The channel also has a transparent white surface to occult its features.
This is simply a lot of playing around with the options of VMD added to some personal taste … that probably took a couple of weeks to get the final rendering done although once you know what you want it is much easier.
Martti Louhivuori is responsible for the rendering. You first have to actually have a system with a small liposome with a channel imbedded (and equilibrated is better). Then the inside water is represented as spheres with Amb. Occl. on and potentially diffuse rendering. The lipids are small liquorice with a transparent surface in orange probably restructured to the phosphate atoms. The channel itself is rendered with sticks on the trace (white) and tubes (cylinders defined in VMD) help following the helices direction. The channel also has a transparent white surface to occult its features.
This is simply a lot of playing around with the options of VMD added to some personal taste … that probably took a couple of weeks to get the final rendering done although once you know what you want it is much easier.
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- Rajat Desikan
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10 years 5 months ago #2656
by Rajat Desikan
Replied by Rajat Desikan on topic Publication ready Martini images
Interesting. So many layers!
I will check it out:) I am in the final stages of writing up a manuscript. I have a couple of questions.
How was the liposome made partially transparent?
Was cg_bonds used at all?
"The channel itself is rendered with sticks on the trace (white) and tubes (cylinders defined in VMD) help following the helices direction."
Does VMD read a protein like that? Or was cg_bonds used?
I have never used occlusion and ambience. I need to play around these features.
I will check it out:) I am in the final stages of writing up a manuscript. I have a couple of questions.
How was the liposome made partially transparent?
Was cg_bonds used at all?
"The channel itself is rendered with sticks on the trace (white) and tubes (cylinders defined in VMD) help following the helices direction."
Does VMD read a protein like that? Or was cg_bonds used?
I have never used occlusion and ambience. I need to play around these features.
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- Clement
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10 years 5 months ago - 10 years 5 months ago #2657
by Clement
Replied by Clement on topic Publication ready Martini images
The picture you link to was done with VMD. Sticks (lipids and helices; DynamicBonds probably, since the cg_bonds.tcl script did not exist at the time), densities (the transparent thingies you're asking about; densities of phosphatidyl moeity rendered with Surf), colors and materials (something like AOChalky for the sticks and balls, Glass1 for the densities). The whole thing rendered with Tachyon (it will slightly change compared to whatever you have on your screen). As Xavier mentioned the main thing here is to play with the Materials and the percentage of Ambient Occlusion and light you impose on your image, as well as finding the right orientation. One picture like that takes time to do; and is entirely function of your tastes.
If you want to get the proper bonds and some enhanced representation of your protein you can check this page (two scripts there: cg_bonds.tcl and cg_secondary_structure.tcl). It's primitive, but sufficient for most of the images you want to do I think. If you have further questions and comments on that, please share... We'll try to find a way to improve these scripts.
If you want to get the proper bonds and some enhanced representation of your protein you can check this page (two scripts there: cg_bonds.tcl and cg_secondary_structure.tcl). It's primitive, but sufficient for most of the images you want to do I think. If you have further questions and comments on that, please share... We'll try to find a way to improve these scripts.
Last edit: 10 years 5 months ago by Clement.
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10 years 5 months ago #2658
by xavier
Replied by xavier on topic Publication ready Martini images
I believe cg_bonds was users but dynamic bonds could be ask used although the liquorice do not show ..
You can use clipping plans (Extensinos>Visualization>Clipping Plane Tool) in VMD to hide a section of your system,
Good luck for the figures.
You can use clipping plans (Extensinos>Visualization>Clipping Plane Tool) in VMD to hide a section of your system,
Good luck for the figures.
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- Rajat Desikan
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10 years 5 months ago #2659
by Rajat Desikan
Replied by Rajat Desikan on topic Publication ready Martini images
Thank you Clement, Xavier. I intend to give this a shot.
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