![]() ![]() Note: Since I don’t pay for a PyMOL subscription, I have to compile the code myself. When you are ready to create the frames of the movie, turn ray tracing back on: set ray_trace_frames=1. ![]() To test the movie, turn off ray tracing of frames: paste set ray_trace_frames=0 into the PyMOL command line. The mpng command will write each frame of the movie to a separate file with the specified prefix, in this case, CaM-conf-mov. If the frame cache is turned on, a large amount of memory is used saving the images in RAM. The set cache_frames=0 command tells PyMOL to not save each frame in memory. ![]() Stopping at state 2 allows smooth motion when we loop the resulting exported movie. The mset command tells PyMOL which states get included as frames of a movie. The mclear command tells PyMOL to remove any saved frames from the cache. > mclear > mset 1 - 48 - 2 > set cache_frames = 0 > set ray_trace_frames = 1 > cd ~/ pymol - work / 1 - pymol - movies / CaM - conformation > mpng CaM - conf - mov Just click on the blue area in the outside circle and you get a nice palette of compatible shades. I found a good html color picker online on the website. I want to use a blue color palette for my protein this time. If you are successful, you should have a multi-state file loaded with the name of mov. The "file%05d.pdb" tells PyMOL that the pdb files have a prefix of file followed by a 5-digit number, %05d, and the extension. Setting the range to be range(0,48) results in all 48 files being loaded. The output files from climber are numbered from 0 to 47 (48 files), but PyMOL does not want to use 0 as the first state. The range(0,48) corresponds to the number of pdb files in the directory. The second command loads those files into PyMOL as a movie. The first command changes directories so that PyMOL can find the pdb files created by climber. > cd ~/ climber - work / test03 / 1 QX5_3CLN_050step # path/to/your/pdb-files > for idx in range ( 0, 48 ): cmd. Then login to your account and go to the Climber download page and download the software appropriate for your system. Go to the SimTK website, and create an account. I just changed the filenames, directory names, etc. Note: The steps below were taken from the README.txt file that is downloaded with the software. ![]() Using energy minimization means that the resulting movie is likely to be closer to what really happens when the protein changes shape. The Climber 1 program uses energy minimization in calculating the shape changes rather than only linear interpolation. There are about a zillion calmodulin-related structures, so after a bit of filtering and searching I found the following structures:ġQX5, the crystal structure of apoCalmodulin (without bound calcium) from Rattus norvegicusģCLN, the structure of calmodulin with bound calcium from Rattus rattus Get the Climber software Go to the RCSB protein database and search for calmodulin in the X-ray structures. Here is how I created a movie of calmodulin morphing from the “closed” state (without calcium ions) to the “open” state (with bound calcium ions). Using energy minimization means that the resulting conformational change is likely to be closer to what really happens when the protein changes shape. What I like about the Climber program is that it uses energy minimization in calculating the shape changes rather than only linear interpolation. When combined with PyMOL, the output looks absolutely stunning.ĬaM-conf-vimeo1 from David Oppenheimer on Vimeo. I recently found the Climber program, which can calculate the structural changes necessary to morph one protein conformation into another using the structure files from the RCSB Protein Data Bank. My protein of choice for these demonstrations is calmodulin, which undergoes a large conformational change upon binding calcium ions. When I teach protein structure in introductory biology, I like to show the dramatic shape changes that can occur when proteins bind ions. ![]()
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