These commands are entered as text commands on the Tcl command line. But it is not difficult to expand the script. Advanced: setting labels with Tcl commands¶ VMD comes with a full-blown scripting language, namely Tcl with VMD-specific extensions (which are described in the VMD Users Guide). At the moment, the selected fragments can be saved only as pdb and no inverse selection is possible. Till you don't decide to save the fragments, you can change the radius and the center of the selection as much as you need without reload the script. Select /S: update view and make the selection Shift: change the center of the spherical selection Rad: change/set the radius of the spherical selection Type: choose between spherical or cylindrical region The selection is based on the fragment definition, so to avoid to break molecules. tkcon works on all platforms where Tcl/Tk is available. The console itself provides manymore features than the standard console. The classic Tcl books include documentation on the popular Tk extensions. What I really wanted was a menu item or an icon to bring up a simple UI to accept parameters and run the thing I wanted to do, like in KDE on Linux. The region is selected given a radius (10 ang by default) and a center (0,0,0 by default). tkcon is a replacement for the standard console that comes with Tk (on Windows/Mac, but also works on Unix). Type a long command with options to start the desired automation I use macOS on a daily basis. Here a tcl script useful to select all the fragments that are in a particular spherical region of your system, and save them as pdb file. (top) select.tcl: select fragments in a spherical or cylindrical region Plus, there is the bonus of interactively see what we are going to remove… which is not bad at all ) You may ask why not to do a perl or python script instead: to be honest I have tried if, but those scripts are slow with loops of hundreds of thousands of atoms, while with VMD everything is already loaded in ram, so fast fast fast (more than 160000 atoms have been used in the video tutorial). Here a small video tutorial on what you can do with the script: reprompt the initial questions (fragment, radius and index file name) Look at the VMD console for the information about the molecule loaded protein structure file crystal coordinates (frame 0) MD trajectory (frames 1-3600). I: inverse the selection: displays only the atoms that will be removed.Furthermore, there are a number of commands available: files that indicate position specific properties of your protein or molecule of interest. The script will ask for the CNT fragment number, the radius of the selection and the name of the index file. In order to uses plugins, you normally have to use the tkconsole, load the file, and then issue commands to extract the functionality. VMD is great for visualizing grid files, i.e. Source /the/path/of/the/script/nosolincnt.tcl
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