Save C:\Users\John\Desktop\Hemoglobin.obj ![]() Now reset the solvent radius to 1 or so (the default is 1.4, I think).įinally, to save your model as an.obj, type:Īnd PyMOL will export an obj of the model to the directory where the pdb is stored (in this case, since we used the fetch command, it’s in the program directory where PyMOL is installed) You can add a path name to the front of the file name if you like, This changes the size of the balls which represent the atoms of the molecule, and is kind of a “season to taste” thing. The default is “reasonable quality” and is just what it says on the tin.Īnother way to change the model’s appearance is to change the “Solvent Radius” “ Maximum quality” looks nice, but is a super-dense mesh. Try each of the settings and see what it looks like. Under the “Display” menu in the text field, there is a sub-menu for “Quality”. If the model in the viewer is what you want, then you are ready to export, but let me show you a few things first. It doesn’t really matter what color you choose, since the model will be surfaced in Lightwave (or whatever other collection of 3D code you prefer to bang your head against.) a nice gray perhaps? Aaahhh, that’s better. If you want to save your eyes, click the C button for “all” and choose something else. Seriously, the default color scheme is hard to look at. Now click the S and choose Show: surface.Īnd that’s what it looks like if you run a pocketful of skittles through the dryer. You can have a play with them later, for now onward!Ĭlick the H for the “all” entry at the top of the list and choose Hide: everything. The letters stand for Actions, Show, Hide, Label, and Color. ![]() You can toggle the pieces on and off in the list, and each of the letters accesses a drop-down menu of choices. If you don’t want separate parts, you can skip this step, but split_chains is a very useful command, especially when you get to animating and surfacing. In the list on the right side of the viewer, you will see four new entries, corresponding to the separate parts of this structure. PyMOL will fetch the pdb file and display a line version of the molecule. In the command line at the bottom of the text window, type the following command Two windows will open: a viewer and a text window, with a bunch of menus and buttons. Open PyMOL (if you need to install PyMOL, follow the instructions, here). ![]() For the purpose of this tutorial, we will be making hemoglobin from the file: There are thousands (millions?) of known structures available in the PDB Database, and figuring out which one to use, or which parts of it to use is a dark art unto itself. ![]() There is a subscription version, which includes support and some extra features, but for just exporting models for use in Lightwave, the pre-compiled open source version (described here) will work just fine. PyMOL is a molecular visualization viewer, built on open-source software. Until we get access to ePMV the options for Lightwave users are Sean Moyer’s PDB reader (which, unfortunately, inverts models on their Z axis), or an external molecular viewing software. Medical and scientific animations frequently require the display of molecular models from PDB (Protein Data Bank) files.
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