PyMOL Tutorial 10 Answer: Aligning Molecules in PyMOL

In this tutorial, we will explore the alignment functionality of PyMOL, a popular molecular visualization tool. Alignment is an essential step in structural biology and computational chemistry, allowing researchers to compare and analyze the similarities between different molecules.

At the American Chemical Society Meeting, Lead PyMOL Developer 'Mail address for international postal services', announced that Scientific LLC is moving its office to 'new office address'. For those interested in using PyMOL for educational purposes, updated builds are now available upon approval at no cost. The open-source code for PyMOL 0.99rev8 can be accessed through revision 2805 of branch.

Now, let's dive into the world of alignment! By default, PyMOL considers all states (like in NMR structures or trajectories) as a single object. However, this might not yield optimal results. To avoid this issue, we can create a temporary object and align our original molecule with the copy using the `mobile_state` and `target_state` arguments.

Here are some essential tips to keep in mind when aligning molecules:

* Make sure your molecules are in separate objects.

* The number of aligned atoms before refinement (cycles=0) will be reported, as well as after refinement.

* PyMOL provides various options for alignment, including the ability to save the results to a ClustalW sequence alignment file or create a graphical representation of aligned atom pairs.

The `align` function is used to align two molecules. The basic syntax is:

```python

align(string mobile, string target, 'float cutoff = 2.0, int cycles = 5, float gap = -10.0, float extend = -0.5, int max_gap = 50, string object = None, string matrix = 'BLOSUM62', int mobile_state = 0, int target_state = 0, int quiet = 1, int max_skip = 0, int transform = 1, int reset = 0')

```

Some notable parameters include:

* `cutoff`: The outlier rejection cutoff in RMS.

* `cycles`: The number of refinement cycles (default is 5).

* `gap`: The maximum allowed gap between the two molecules (default is -10.0).

The output will display the 'RMS' value, but it's actually the Root Mean Square Deviation (RMSD) in Angstroms.

In conclusion, PyMOL provides a powerful tool for aligning molecules. By following these simple steps and understanding the available options, researchers can easily compare and analyze molecular structures.

Pymol tutorial 10 answer