The last two options are essentially the same, and save the raw data for the graph to a text file that you can then easily load up into a spreadsheet. If you want to save this graph, you can use the “File” menu at the top-left of the graph window itself to export the graph either to postscript (for printing), Xmgrace (a graphing package) or to an “ASCII matrix” or “ASCII vector”.
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Use the “scrubber” movie control in the VMD main window to scan through your movie to see what is happening at these three frames. However, there are three occasions then the distance jumped to higher values (frame 155, frame 299 and frame 329). You can graph this distance across the entire movie by clicking “Graph” in the “Labels” window, and then clicking the “Graph…” button that will appear below, e.g.įrom this graph, you can see that the distance between the oxygen of oseltamivir and nitrogen of arginine 292 mostly fluctuated between 2.75 and 3.75 angstroms. In this case, for frame 500, the distance is 3.024 angstroms). This shows the distance between these two atoms in the “Value” box in the bottom right of the window (this distance will depend on which frame of the movie you are viewing. To get information about the bond you have selected, go to the “Labels” window and select “Bonds” from the top-right menu. This will add a label to both of these atoms, and will also draw a (still barely visible!) white line between these two atoms. the oxygen on oseltamivir that is closest to Arginine 292, and the nitrogen on Arginine 292 that is closest to oseltamivir. Then click on two atoms (one after another), e.g. Switch into bond selecting mode by clicking “Mouse | Label | Bonds” in the VMD main window. This will delete and remove all atom labels.Īs well as labelling atoms, VMD can also be used to label “bonds”, which in VMD-speak, are actually just pairs of atoms. You can do this by selecting all of the atoms in the “Labels” window (left click on the top label in the list, then press shift and left click on the bottom label in the list - this will select all of the labels in the list) and then click the delete button on the top right of the window, e.g. Once you have finished selecting atoms, you should remove all of the labels.
If you want to remove this label, then you can click on the selected atom a second time. Every atom you click on will be highlighted in the VMD graphics window with a (barely visible) green text label.
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The residue that contains this atom is also shown (ARG, short for arginine), as is the name of the selected atom (in this case NH1), and the residue ID number (212).įeel free to click on as many atoms as you want, looking at their information as it appears in the “Labels” window. The “Labels” window shows you the molecule file to which the atom belongs (h7n9.pdb), the X, Y and Z coordinates of the atom (the exact values will depend on the frame of the movie that you are viewing. Do this by clicking “Graphics | Labels…”.
You can get more detail by opening the “Labels” window.
In this case, the literature number is 292, for Arginine 292, but the PDB residue number is 212) Ĭlicking on the atom adds a (barely visible!) green label to that atom. It is common that the PDB file residue number does not match up with the “canonical” residue number that is used in the literature. Make sure that you are ready to select atoms (you have clicked “Mouse | Label | Atoms”) and then click on one of the atoms of Arginine 292 as shown in the below picture (note that the residue ID number is the number given in the PDB file.
This residue is to the bottom right of oseltamivir. We will now use the “select atoms” feature to label the Arginine 292 residue in the wild type H7N9 neuraminidase that you have loaded into VMD. For example, in the original paper on which this workshop is based it was noted that there were two variants of H7N9 neuraminidase the wild type form, and a mutant form in which the arginine (R) residue at position 292 was mutated to lysine (K). You can do this by clicking “Mouse | Label | Atoms” in the VMD main window, and then clicking on individual atoms in the VMD graphics window. Part 1: Molecular Visualisation Picking AtomsĪs well as allowing you to view molecules, VMD also allows to you select atoms.
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