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Visualizing Protein Motions with Static Images - Deniz Cem Önduygu
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There, I once again faced the challenge of showing protein dynamics in static images; since scientists usually publish in static printed media, showing these motions in figures is a common problem because proteins are extremely complex structures and even drawing them without motion is a nightmare.
Below is a snapshot from a figure in that paper; at the bottom you can see the motion visualization that we created. I want to share this method with the world in detail for people who might want to use it.
Below are our notes explaining the process in VMD. The initial file should have the average structure data as well as the mode vector added onto the average structure coordinates in pieces.
The first 20 frames out of a total of seems to work fine for our system. Step 2 — Show all trajectory snapshots at once. Default coloring is red to blue. We denizcem 003 movies to show the initial structure with red; you may want to emphasize a different state.
Be sure to select the frame of your choice in the main screen. For rendering, we preferred the Tachyon module, which generates files that islamic books in malayalam pdf be opened denizcem 003 movies Photoshop. Here is her method with her own words:. It is generally hard to visualize protein motions on static images, contrary to movies playing sequentially the snaphots obtained from simulations such as molecular dynamics.
For my thesis and the paper that is related with it, I was trying to find a means to clearly present such motions, and as Cem mentions in his tutorial, the vectors are not always the best way. In my work, I do not have a specific direction vector as in the case of normal vectors, however I thought that with a little modification, the method can be suitable for my figures as well.
The Big Picture in Seven Scales. Evolutionary Graphic Design: Through My Old Microscope. I really really love these images that you have up here and have followed this tutorial. Thank you so much.
You appear to be an expert with VMD and so I do have a technical question to ask about the cylinders and Tcl scripts. I downloaded the VMD program and was wondering how you make cylinders which can trace the contours of your polymer or protein. For instance imagine that my protein below is: Email Address.
Follow denizcemonduygu. The Method The initial file should have the average structure data as well as the mode denizcem 003 movies added onto the average structure coordinates in pieces. Here is her method with her own words: The procedure denizcem 003 movies quite simple: Load the frames from MD to PyMOL as separate objects I had 18 frames, but for a relatively small protein with residues, frames can also work.
Show all as cartoon by typing on the command window: In this example, I preferred cyan for the starting structure, and palecyan for the others: I simply take the printscreen and edit the resolution in Photoshop.
June 20, at 7: Do denizcem 003 movies have any advice?? Best Wishes, Alaina. June 22, at Leave a Comment Join the denizcem 003 movies. Leave a Comment. Leave a Reply Cancel reply. Subscribe to Blog via Email.