How to make a mesh protein

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Graham Mills
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How to make a mesh protein

Post by Graham Mills » Sat Jan 18, 2014 5:04 pm

If you are interested in making molecular meshes, the basics are below. You can see some examples here: https://files.app.net/gld0WNhw

We will start with an easy one, 1rez (lysozyme). I suggest you use a sandbox region in case anything goes awry.
Firstly, you need to install a couple of applications:
UCSF Chimera: http://www.cgl.ucsf.edu/chimera/download.html (opt to precompile scripts)
MeshLab: http://sourceforge.net/projects/meshlab ... %20v1.3.2/
I use Kokua as viewer for import but any should work.

1. Run UCSF Chimera. Select File|Fetch by ID and with the PDB option selected enter 1rez in the adjacent field and click Fetch. You need to be connected to the internet for this to work.
2. The molecule is displayed. This is a simplified cartoon-style representation by default but this is probably the most common style for teaching as it makes the features obvious. You can click and drag the molecule around to change perspective.
3. There are various different ways to style and colour the molecule but sadly most do not play nicely with MeshLab as far as I know so we will simply select File|Export Scene and enter the file name 1rez with VRML (WRL) as the file format. You may need to scroll the file dialog back to the left if you want to change folder. Click Save and wait for the export to complete (it opens a new window while processing and closes it when finished).
4. Close Chimera and start MeshLab.
5. Select File|Import Mesh and select the file you just created and click OK. The molecule loads and again you can drag it around.
6. Select Filters|Remeshing etc|Quadric Edge Collapse Decimation and in the dialog enter 21000 for the number of faces required (top field), click Apply, wait for the progress bar to complete, and then click Close.
7. Select File|Export Mesh As, select Collada as the file type and then click OK. Accept the defaults in the next dialog and the DAE (COLLADA) file is created.
8. Start Kokua, select Build|Upload|Model, select the DAE file and wait for it to load and all red cross warning symbols to change to green ticks. Swap to the Upload Options tab and enter a scaling factor of 0.1 and press Enter (important or you may find the mesh too large to easily work with), click Calculate Weights & Fee and wait for the button text to change to Upload. Click Upload.
9. The model is uploaded and the inventory is opened automatically. Unless you name it in the upload dialog, the mesh is called shape0. Drag it inworld to rez it. Then edit and colour (presently this is restricted to one colour per mesh under most circumstances). You may also want to set it to phantom to reduce lag.

You can find additional proteins at http://www.rcsb.org/ -- 4AHL, for example, is a visually interesting toxin that has a very obvious cap region that stays on the membrane surface as well as an associated tube that punches a hole through the membrane. MeshLab will also work directly with protein structure (PDB) files; these can be downloaded from the above site and are available from a link at the top right of the page as PDB File (text).

Suitable files may also be sourced from http://www.ebi.ac.uk/pdbe/emdb/ and structures combined to create, for example, a bacterial flagellum.
Last edited by Graham Mills on Sat Jan 18, 2014 6:40 pm, edited 2 times in total.
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Re: How to make a mesh protein

Post by Graham Mills » Sat Jan 18, 2014 6:23 pm

You can add a coloured texture to a hydrophobicity surface for small, single chain proteins as follows:

10. In Chimera, select Presets|3. Interactive (hydrophobicity surface) and export as VRML.
11. In MeshLab, reduce the face count as before then select the following under the Filters|Texture sub-menu:
a. Parametrization: Trivial Per-Triangle
b. Project active rasters color to texture etc
c. Vertex color to texture (enable the first two options, Overwrite and Assign, in addition to the others)
12. This time when you export you should see the assigned texture listed.
13. In Kokua make sure you enable the Include textures option on the Upload options tab.

That should work OK with 1rez.

Bear in mind that I'm a microbiologist rather than a structural biologist but I do feel these are aspects my students should appreciate. I look forward to the days ahead when we will be able variously to walk among such models (preferably animated) as well as hold virtual (or 3D printed) representations in our hands and see the two connect.
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Re: How to make a mesh protein

Post by Graham Mills » Sat Jan 18, 2014 9:26 pm

I left full perms copies of two of the proteins on my region Stuff. They are set to be copyable so if anyone wants one, they're in front of the Scripting exhibit. http://www.kitely.com/virtual-world/Gra ... ls-2/Stuff

You can also download the mesh for one of the proteins here https://files.app.net/bp8ttzbl. Don't forget to resize it during import as the default is ~90 metres!
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Re: How to make a mesh protein

Post by Graham Mills » Sun Jan 19, 2014 10:15 pm

It turns out that the MeshLab z-painting tool in flood fill mode does a good job of highlighting the protein structure.

https://files.app.net/b4mf23GB
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Re: How to make a mesh protein

Post by Graham Mills » Fri Oct 10, 2014 10:58 pm

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