You may want to pull down the Favorites menu and select ‘ Add to Favorites ’. Browse to your directory and find the file. Finished with that? Then use the ``Browse'' button A file browser will pop up. You should have downloaded these files already if you have not, take the time now to do that. This file is located in the first set of class files. (this has the ascession code ‘103d’ from the RCSB/Protein Data Bank, which we will investigate later). To begin, let's load a relatively well-known molecule: a strand of DNA In the following, text you can type into a VMD form is blue. VMD will open a number of windows,and it will look something like this: The goals of this segment of the class are to enable you to render nice representations of your molecular systems, pull Protein Data Bank files off the Internet and see them quickly, and begin to understand structure and function through the visualization tools. THIS LECTURE ASSUMES YOU HAVE DOWNLOADED ALL OF FILESET1! There are many tutorials and user guides out there (see this link, and this link, for example), from which I'm borrowing heavily. In this lecture we will learn how to use VMD, a powerful and free molecular visualization program available from the folks at Theoretical and Computational Biophysics Group at UIUC. Menu and other descriptions are in GREEN. Example output from the terminal, tkcon or vmd are in BLUE. (You should be able to access these files individually under the "Files" tab on the right of the page(s), too.)ĬONVENTION: In the Laboratory pages, things you will have to type in the terminal, tkcon, or into a VMD input box are in RED. Download them to your Projects folder, mentioned above. You should be able to do this by right-clicking the link with your mouse, or -clicking if you are not using a mouse.įiles: various files will be listed here, as well as on the sections they are required. Save this file to your computer - the best place is the previously mentioned " bin " directory. Packmol : We will use the ' packmol ' program later on in the semester. Again, you may need to enter your password to move NAMD to Applications. You should put this in your "Applications" folder and rename the folder "NAMD" (removing everything after the first four characters). Your email address/password from the VMD step can be used here, also. Open System Preferences -> Security and Privacy, and a box should be there which will allow you to open VMD. When you open it for the first time, you will get a warning from OSX that it is from an unknown developer. This is an academic site so your email won’t end up in any spam lists. You must choose your operating system, and register your email address. Choose the latest version (currently 1.9.4). In addition, it is useful to create a directory called "bin" under your home directory (for example, /Users/mccallum/bin ). Each succeeding project should get its own sub-folder under this one. The first thing you should do is create a “Projects” folder on your computer for this class.
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