- Vmd movie trace how to#
- Vmd movie trace software#
- Vmd movie trace download#
You can choose which molecule is used as the reference by clicking and selecting it from this list. By default, this will contain all molecules loaded from all files (so in this case, both h7n9.pdb and h7n9_rk.pdb).
Molecule list : This lists the molecules that will be affected by the alignment request. This means that all frames will be aligned against the molecules loaded from the reference file at frame 0. The number next to “ref:” is the frame number, which is currently 0. Frame selector : The choice of which frame to use to align the molecules. Can either be the “Top” molecule (the last one loaded), the “Average” of all loaded molecules, or the “Selected” molecule (the one picked in the Molecule list below) Reference selector : Chooses which molecule is used as the reference for the alignment (the molecule against which everything will be aligned). May take a while for large trajectories or lots of molecules. Align button : Click this to align every frame from every selected molecule file. Selection modifiers : These provide a quick and easy way to modify the selection so that only the protein backbone is matched (if “Backbone” is ticked), or that only the alpha carbons are matched (if “Trace” is ticked) or that only match non-hydrogen atoms (if “noh” is ticked). The selection string has the same format as that used in the Graphical Representations window. Atom selection box : This is an atom selection string used to pick the atoms that will be used to align the molecules from the two files. This will open up the “RMSD Trajectory Tool” window, which is described in the image below. Open this by clicking “Extensions | Analysis | RMSD Trajectory Tool” in the VMD main window. To align the structures, we need to use the “RMSD Trajectory Tool” that comes with VMD. In this case we will use the backbone of h7n9 neuraminidase. In general, the best frame of reference for any bimolecular alignment is the protein backbone at the start of the trajectory for one of the structures. What we need to do is to ensure that all of the frames from both trajectories are aligned against a common frame of reference. This makes comparison of the two trajectories difficult. You should be able to see that the molecules in h7n9_rk.pdb are not aligned with those in h7n9.pdb, and so oseltamivir in h7n9_rk.pdb appears rotated by about 90 degrees compared to oseltamivir in h7n9.pdb. Once you have done this, zoom in to get a view similar to that in the above picture. To do this, you will need to ensure that the “Selected Molecule” selector at the top of the “Graphical Representations” window is selecting “2: h7n9_rk.pdb”, e.g. Go into the graphical representations window and add representations to match those for h7n9.pdb. The molecules in h7n9_rk.pdb are currently visualised using the “lines” representation. Select this and click “Load” to load this file. Then click “Browse” and find the h7n9_rk.dcd file that you downloaded. To do this, in the “Molecule File Browser” window change the “Load files for:” selector to select “2: h7n9_rk.pdb”. Next, we will load the trajectory in h7n9_rk.dcd into the molecules loaded from h7n9_rk.pdb. Then, ensuring that the “Load files for:” selector is selecting “New Molecule”, click “Browse” and find the h7n9_rk.pdb file that you downloaded. To do this, click “File | New Molecule…” in the VMD main window to open the “Molecule File Browser” window. Next, we will load up the h7n9_rk.pdb file in addition to the h7n9.pdb file that is already loaded into your VMD session. h7n9_rk.dcd : This contains the trajectory from a 50 nanosecond molecular dynamics simulation of oseltamivir bound to the R292K mutant of H7N9 neuraminidase. h7n9_rk.pdb : This is a PDB file containing oseltamivir bound to the R292K mutant of H7N9 neuraminidase. Vmd movie trace download#
Please download the below two files and place them into the same directory as h7n9.pdb and h7n9.dcd
Vmd movie trace how to#
The final thing we will learn in VMD is how to load up and compare the output of two different molecular dynamics trajectories. Part 1: Molecular Visualisation Comparing Trajectories
Molecular Visualisation, Modelling and Dynamics. Sampling the Ligand - Intramolecular Moves. Sampling the Solvent - Rigid Body Moves. Part 2: Parallel Programming Using Intel Threading Building Blocks. Concepts, Default Arguments and Operators. Part 3: Multinode (distributed/cluster) Parallel Programming. Part 2: Multicore (local) Parallel Programming. Vmd movie trace software#
What is good research software engineering?.
0 kommentar(er)
