# How to visualize pores using material studio?

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

• +1. It might be easier if you take a screenshot with your computer rather than a photograph with your camera! Jul 15 at 13:58
• Could you share the PDB of the membrane?
– Camps
Jul 15 at 15:16
• @Camps Shared the pdb Jul 15 at 17:12
• Is this what you need?
– Camps
Jul 15 at 21:22
• The black color is the backgroundś 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.
– Camps
Jul 16 at 12:36

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.

• Could you share the final image?
– Camps
Jul 20 at 14:53
• @camps I thought of doing that. But it isn't yet published. So I'm not sure whether to share or not Jul 20 at 14:56