David Goodsell like images

Almost all of us visiting PDB would have looked at the image shown below that attract us like moths attracted to a light. I am talking about the aesthetically pleasing protein images created by David Goodsell.

p53 Tumor Suppresor.
Image Courtesy: http://dx.doi.org/10.2210/rcsb_pdb/mom_2002_7

In case you didn’t know, he is the author of Molecule of the Month series. Since the images look anything like the ones we usually keep looking at, one is attracted to the level of abstraction the image projects due to which, the reader understands the big picture. And, of course, they come in all cute colors!

To quote him about the artwork’s intention, that is to give

a pictorial overview of the molecules that orchestrate the process of life. [2]

Some history about David Goodsell can be found in his website and here.

So, you have correctly guessed that this post is about how to make such “David Goodsell-sque” images of your protein. For consistency, I used 2BEM, a CBM33 polysaccharide monooxygenase enzyme [3]. The view is looking at the protein’s active site, which is quite planar.

Using Python Molecule Viewer

PMV [4] is good tool to run AutoDock, and manipulating structures. This link explains in basically two steps of getting such images. Here is my try with PMV

Using Python Molecule Viewer (PMV) surface

Using Python Molecule Viewer (PMV) CPK

Using PyMOL

Can PyMOL be far behind in implementing this? I didn’t think so. Fortunately, there are at least two alternate ways of doing this in PyMOL.

1. Using a couple of commands. After loading the protein, type in the following commands as given here [5]

• unset specular
• set ray_trace_gain, 0
• set ray_trace_mode, 3
• bg_color white
• set ray_trace_color, black
• unset depth_cue
• ray

In surface,

If you want to change the colors to David Goodsell-sque, then it comes out like this. The important commands are the “specular” and “ray_trace_mode, 3”.

2. Are you thinking “Meh!, Close enough. But, not what I was looking for.”? Then, with some small tweaking in PyMOL you could get like this, using GLSL shaders [6, 7]

Using VMD

If you are using VMD version 1.8.7 or 1.8.6, then you can follow this link [8]

After loading the molecule, this is what I did to get the following image

• Main Menu->Graphics-> Representations
• Coloring method->Element
• Drawing Method->VDW
• Material->Goodsell
• Main Menu->Display->Rendermode->GLSL
• Main Menu->Display->Light 3
• Main Menu->Graphics-Materials->Goodsell->I played around with the diff parameters given under that
• Main Menu->Graphics->Colors->Categories->Element->C->white
• Main Menu->Display->Axes->Off

Using VMD and Blender

In case, you need to make such images to make a great impression, you can learn how to use Blender. It is a open-source 3D tool that can create models and has huge applications in animated movies, interior designing and other non-science stuff.  See this link for more details: http://chemistry.stackexchange.com/questions/484/what-software-is-used-to-generate-the-pdb-molecule-of-the-month-images

I did not use VMD or Blender for 2BEM so using one of the images given in the above link. [9]

Using QuteMol

This is probably the ONE-CLICK David-Goodsell-sque image making tool. Download it from here. After loading the molecule, just click on the “Molecule of the Month” button. Voila!

A downside was I was unable to change the carbons to white. Sigh!

Anyway, I hope you had fun making images like I did. Enjoy! 🙂

References:

1. http://mgl.scripps.edu/people/goodsell/
2. http://www.asbmb.org/asbmbtoday/asbmbtoday_article.aspx?id=13702&page_id=2
3. http://dx.doi.org/10.1074/jbc.M407175200
4. Sanner MF (1999). Python: a programming language for software integration and development. Journal of molecular graphics & modelling, 17 (1), 57-61 PMID: 10660911
5. http://www.pymolwiki.org/index.php/Gallery
6. http://pymolwiki.org/index.php/GLSL_Shaders
7. http://kpwu.wordpress.com/2012/06/28/pymol-draw-goodsell-like-view-using-glsl/
8. http://www.ks.uiuc.edu/Research/vmd/minitutorials/glsloutline/
9. http://chemistry.stackexchange.com/questions/484/what-software-is-used-to-generate-the-pdb-molecule-of-the-month-images
10. http://pmvbase.blogspot.com/2010/04/making-david-goodsell-like.html
11. http://www.researchgate.net/post/How_can_I_draw_proteins_like_in_PDB_Molecules_of_the_Month
12. http://biostumblematic.wordpress.com/2009/12/02/rendering-proteins-in-pymol/
13. Sanner MF, Olson AJ, & Spehner JC (1996). Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, 38 (3), 305-20 PMID: 8906967
14. Goodsell, D. (2002). p53 RCSB Protein Data Bank DOI: 10.2210/rcsb_pdb/mom_2002_7

say SMILES!

Recently, Babel (in my system) was not working and I needed to convert my .sdf files to smiles format. I troubleshooted the error was able to run successfully. But, this made me think, what about a web-based application to do this format conversion? That’s how I found these three amazing tools based at the National Cancer Institute’s CADD Chemoinformatics group.

1. Online SMILES Translator and Structure File Generator

http://cactus.nci.nih.gov/translate/

Upload your .sdf file and get the SMILES format in Kekule or Aromatic format. Also, converts .sdf file to .pdb, .smiles, and .mol. Although, it does not have all the file formats listed in Babel. For a quick conversion, this is amazing site.

2. Create image files without any molecular visualization tool.

http://cactus.nci.nih.gov/gifcreator/

This was a cool site. Just put a smiles format and see the many colorful images you can make with your structure. Not only that. If you wanted to know what atom number is that Carbon next to the Nitrogen, make sure to have the “Image Map Style” to “Atoms”, similarly to see the connectivity by selecting “Bonds”. Simultaneously, if the generation of an HTML image map associated with the image is desired, just copy the code below. See details here

3. Image-to-Structure file-conversion

Found a cool structure in a book and tired of drawing that on a structure editor? This is the site for you, then. Scan the page and upload the image and see the transformation happening! And click on the “Show 3D” to see the image on paper coming as a 3D structure that you could download it as a .sdf file.

http://cactus.nci.nih.gov/cgi-bin/osra/index.cgi

See the screenshot of the image to above image to the structure

Click to see full-size

References:

Weininger, D. (1988). SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules Journal of Chemical Information and Modeling, 28 (1), 31-36 DOI: 10.1021/ci00057a005