Pymol tutorial español how to#
Pymol tutorial español software#

From the z-buffer the protein outline can be obtained using, for example, the Sobel operator in GIMP (Filters ‣ Edge-Detect ‣ Edge) or the Find Edges filter in Photoshop (Filter ‣ Stylize ‣ Find Edges).This step is optional: Gaussian blur is applied on the shadows layer and then it is clipped to the alpha mask of the whole protein.The alpha mask from the whole protein, the nitrogens and oxygens are transformed into a quick mask and filled with the chosen color.These have to be opened as layers in Photoshop, GIMP, etc. With them the following images are obtained: color black, polymerĪnd finally the z-buffer 4. The alpha mask of nitrogen and oxygen atoms. First load the structure and prepare the scene: hide all In this instance I’m creating the image of an antifreeze protein from the beetle Rhagium inquisitor (PDB ID: 4DT5). This method is more cumbersome than the previous one, but allows more control over the end result. Both approaches consist in rendering colors, shadows and outlines separately, and then merging them using a graphics editor such as Photoshop. One uses Chimera, while the other uses a combination of ePMV and Cinema4D. A more complex methodīonnie Scott published a while ago a tutorial where she uses two methods to achieve Goodsell’s style. 3 Besides, depending on the render size, ray_trace_gain has to be modified to alter the thickness of the borders. It may be necessary to adjust the ambient variable to get rid of the shading on the spheres. Once the scene is prepared, a simple way to get the figure is using the following commands: unset specularĪfter rendering with ray, something like this appears: 2 color whiteĬolor blue, resn ARG+LYS and sidechain and name N*Ĭolor red, resn GLU+ASP and sidechain and name O*

Then remove the water molecules with remove solvent, display the protein as CPK spheres with show spheres, put a white background with bg_color white and color the atoms by element according to the classical scheme (carbon in white, nitrogen, oxygen and sulfur in blue, red and yellow, respectively). To begin with, I will reproduce the figure that appears on the September 2000 entry of MotM, corresponding to hen egg white lysozyme (PDB ID: 2LYZ).įirst load the structure of 2LYZ (for example by using fetch 2lyz),

Pymol tutorial español how to#

At first I just wanted to get an idea of how to do some figures with Goodsell’s style, but it became kind of an obsession. However, I took some ideas from them and managed to develop two methods using PyMOL.

There are several tutorials and tools to emulate his rendering style 1, but none of these fully convince me.

Pymol tutorial español software#

To generate the figures in MoTM Goodsell uses some software he developed (apparently in Fortran, according to this German link). However, reproducing the way he renders molecules is not a straightforward task. Like many people, I like the unique style in which David Goodsell illustrates the structures of the Molecule of the Month (MotM) section in the Protein Data Bank. In particular, I am fascinated by the various ways of representing three-dimensional structures of biological macromolecules, either by computer graphics, animations, or tangible, physical models. Versión en español: Aplicando ingeniería reversa a David Goodsell DecemReverse engineering David Goodsell Introductionįor some time I have been interested in the relationship between art and structural biology.