Opening a file from downloads in pymol

PyMOL is a powerful program, and everyone uses it for something different. The remainder of this guide is devoted to common tasks that come in handy. You've found the perfect view, and you'd like to Save it? Tip: Using the ray command before saving an image will create a higher quality version with shadows, etc. This can take time, depending on the size of the image and speed of the computer, but the images created after ray tracing are usually spectacular.

However, the ray tracing disappears if the view is changed in any way. Sometimes it might be useful to select part of an object and modify it directly; for example, selecting active-site residues in a protein to highlight them in another color. In the lower-right corner of the Viewer, next to the animation controls, is an S button not to be confused with the S how button in the object control panel that activates the selection tool.

The selection tool can be changed to select atoms or residues by clicking Selecting Residues or whatever until the right mode appears. Once selecting is activated, a list of parts to select appears at the top of the Viewer.

Select things clicking or dragging across a range. Selections can be controlled individually in the object control panel, just like any other object. To save a selection, select rename from the A menu. PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common problems:. PyMOL supports saving your work in various formats. You can save, images, molecules, sessions, movies, etc.

You can save the session to disk and reload it later. A dialog box will appear from which you can select your molecule to save. You can also save an object or selection using the Save command.

It's very easy:. For example, to save just the waters to disk do:. You can save images to disk, through the command line, by using the Png command. PyMOL allows you to save movies you've created, too. This is a new command, and I don't know too much about it. Scripting in PyMOL ranges from very simple to very intricate. You can make a simple loop say rotating a molecule one-degree at a time or execute full featured scripts. Once you've got the basics of PyMOL down, learning scripting will greatly enhance your productivity and capabilities.

This is a very handy feature--you essentially have a live Python interpreter you can interact with, which makes your life much easier. Take the following for example:. Did you notice that f on line 1 and for and x on line 2 are not PyMOL commands or symbols? Alternatively, if you want to change the default directory for data, you can just put the path to the new default directory in the "Start In" field of the "shortcut link" that is used to launch Pymol.

To do this, right click on the "shortcut link" that is used to launch Pymol, click on "Properties" and then, in the "Start In" field, type in the path to the new default data directory. Then click "OK" and the changes are complete. You might wish to make an alias :.

It uses OS X Here is one example of a MacOSX-specific. A couple of simple lines to put in your. The recommended approach is to just use PyMOL as your python interpreter:. Is enough. Of course, the file script. Asynchronous means, that a new Python thread is started:. Jump to: navigation , search. Category : Launching.