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I am a newbie to material studio. I have a membrane, coordinates are in pdb format. I am trying to visualize the pores of this membrane. I tried Atoms and Volume surfaces, but the result was that the VdW surfaces were also shown. I also unchecked the VdW surfaces in analysis window, but it still shows. My probe radius is 1 angstrom. Is there anyway that I can just visualize the pores. I am attaching a picture of the settings and my output. This is what I am looking for. Figure 1d in https://www.nature.com/articles/nmat4638

enter image description here

enter image description here

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    $\begingroup$ +1. It might be easier if you take a screenshot with your computer rather than a photograph with your camera! $\endgroup$ Jul 15, 2021 at 13:58
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    $\begingroup$ Could you share the PDB of the membrane? $\endgroup$
    – Camps
    Jul 15, 2021 at 15:16
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    $\begingroup$ @Camps Shared the pdb $\endgroup$
    – Vasista
    Jul 15, 2021 at 17:12
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    $\begingroup$ Is this what you need? $\endgroup$
    – Camps
    Jul 15, 2021 at 21:22
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    $\begingroup$ The black color is the backgroundÅ› color, so, if you see it, it is because your seeing through a porous. I used a 1Angst to create the molecular surface. I did it with MAESTRO. Sorry if I can not help more. $\endgroup$
    – Camps
    Jul 16, 2021 at 12:36

1 Answer 1

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Finally got the solution to visualize pores of a membrane.

The first thing you need to do is to check your lattice parameters. I had a membrane of 110*110*70 angstroms, but the pdb file contains the dimensions as 120*120*100. This is the main issue for me.

Step 1

Change the lattice parameters here, build -> build crystal -> options -> lattice parameters (check your lattice parameters) and click apply and finally build crystal

Step 2

Go to Tools -> Atom Volume and Surfaces -> Task-Solvent Surfaces and change the settings according to your need and create the isosurface.

Step 3

Right click on the image you have generated go to display style -> isosurfaces and increase the Transparency slider.

The resulting image will show the pores of your membrane.

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  • $\begingroup$ Could you share the final image? $\endgroup$
    – Camps
    Jul 20, 2021 at 14:53
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    $\begingroup$ @camps I thought of doing that. But it isn't yet published. So I'm not sure whether to share or not $\endgroup$
    – Vasista
    Jul 20, 2021 at 14:56
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    $\begingroup$ @Camps Here it is: pubs.rsc.org/image/article/2021/TA/d1ta04763a/… $\endgroup$
    – Vasista
    Dec 6, 2022 at 13:10

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