How do I make a scene in PyMOL?

Simply setup each view and then when ready you can do Scene->Store from the PyMOL menus (or scene auto, store on the command line or the third method Ctrl+PgDn (Fn+Ctrl+DownArrow on the Mac)). Do this for each view you setup. Once done, you can scroll through your scenes by pushing PgUp/PgDn.

What can you do with PyMOL?

PyMOL allows you to save movies you’ve created, too. You can automatically save the MPEG or save a series of PNG files–for stitching together later. This is a new command, and I don’t know too much about it. Use File=>Save Movie.

Is PyMOL hard to use?

In this lab, we will be using the program PyMOL to visualize and analyze protein structures. PyMOL is a powerful utility for studying proteins, DNA, and other biological molecules. The software itself is well written and easy to use, and in the past 10 years it has become very popular with structural biologists.

Is PyMOL free?

Open-Source PyMOL is available free of charge. It also allows sponsors to create highly customized PyMOL installations which might not be possible with the MSI installer. Pre-compiled Open-Source PyMOL is available free from Christoph Gohlke of the Laboratory for Fluorescence Dynamics, University of California, Irvine.

How do you morph in PyMOL?

Morphing Between Objects

  1. Align your two structures.
  2. Select A > Action > Generate > Morph > To Molecule > …
  3. Choose your target molecule.

Which is better PyMOL or chimera?

Chimera is easier to use than PyMOL to do sophisticated structure analyses, so it would be more appropriate for an advanced course protein structure analysis.

Does PyMOL use Python?

General Scripts. General PyMOL scripting is done in Python. It’s really quite simple, just write your function (following a couple simple rules) and then let PyMOL know about it by using the cmd.

Why is PyMOL used?

PyMOL is a cross-platform molecular graphic tool and has been widely used for 3D visualization of macromolecules. The utilities of PyMOL have been extensively enhanced by various plugins, including macromolecular analysis, homology modeling, protein–ligand docking, pharmacophore modeling, VS, and MD simulations.

Does PyMOL cost money?

Order PyMOL and AxPyMOL Online Educational subscriptions to PyMOL are available at no cost to full-time students and educators teaching full-time students.

What language does PyMOL use?

PyMol is written in Python (hence the name) an extendible scripting language. This language is also popular with the group that develops PHENIX and CCTBX. This means that PyMol can access the powerful scripting features of Python (i.e. you can use Python syntax within PyMol).

What is morphing feature in PyMOL?

The morph command is an incentive PyMOL feature (not available in open-source version). Given two or more conformations, either as two objects or one multi-state object, morph can create an interpolated trajectory from the first to the second conformation.

How do you make a movie in PyMOL?

PyMOL’s concept of moviemaking is to store snapshot information with so called “key frames” on a movie storyboard, and to interpolate that information between the key frames, if applicable. Storable information: PyMOL displays a movie panel with a frame slider at the bottom of the window. Right click on the panel to insert or delete key frames.

What do you need to know about the PyMOL?

PyMOL has a powerful and unique molecular movie-making capability. In order to use it, you first need to understand a few key concepts: States:States most directly correspond to particular arrangements of atoms at a point in time.

How to change transition times in A PyMOL movie?

Using the movie from the previous exercise, modify transition times by inserting or deleting frames, and by moving key frames. Trajectory movie

What does the MDO command do in PyMOL?

The “mdo” command allows you to bind a particular series of PyMOL commands to a frame in the movie. For instance, you can perform a rotation about the axis at each frame of the movie in order to sweep the camera about the object. See “help mdo” or the reference section for more information.