How do I download a movie from PyMOL?

How do I download a movie from PyMOL?

You can save the movie using the “mpng” command, or you can save it from the “File” menu.

How do you store scenes in PyMOL?

Scenes as Movies 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)).

How do you make a morph in PyMOL?

PyMOL now offers the morphing menu: A > Action > Generate > Morph > ……The options are to morph:

  1. first state to second.
  2. first state directly to last.
  3. first state to last, visiting each intervening state.
  4. first state to last, visiting each intervening state and then back to the first.

How do I use PyMOL software?

The PyMOL Interface

  1. When PyMOL is opened, two windows appear.
  2. The lower-right corner of the Viewer contains a guide to using the mouse, as well as a powerful selection tool.
  3. To run any text command, type it in at a PyMOL> command line and hit [Enter].

What is Sele PyMOL?

sele. Named selection or object “sele”, but only if it doesn’t conflict with the name of another operator.

How do you mutate residue in PyMOL?

To mutate a residue follow these easy steps:

  1. Load a PDB file.
  2. Under the Wizard menu select Mutagenesis.
  3. In the PyMol viewer window select a residue.
  4. Select No Mutation and select resultant residue.
  5. Selecting the rotamer you think better fits your structure.
  6. Select Apply.
  7. Select Done.

What is morphing in PyMOL?

From PyMOLWiki. 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 chimera morph?

In a nutshell, activate Tools->Structure Comparison->Morph conformations, add the start and end structures (should be loaded into chimera first; if you want the morph movie run in a loop add the start model as the third item) and change the number of steps to 40 for smoother motion.

Why is PyMOL useful?

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.

Which programming language is the interpreter of PyMOL?

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).

How do I learn PyMOL?

Getting started: explore a protein

  1. Obtain a PDB coordinates file for your favorite protein.
  2. Open the PDB file using File => Open… from the menu bar.
  3. The right side of the Viewer shows the loaded PDB as an object, as well as its command buttons.

What amino acid is R?

Arginine
Amino Acid Codes

Abbreviation 1 letter abbreviation Amino acid name
Arg R Arginine
Asn N Asparagine
Asp D Aspartic acid
Cys C Cysteine

How do you find N C and terminus in PyMOL?

If you’re looking at a protein molecule in a graphics programme like pymol, then the amino acid with the lowest residue number is the “visible” N-terminus and the one with the highest residue number is the “visible” C-terminus.

How do you rotate a structure in PyMOL?

Holding the left mouse button while the pointer is inside the molecule will cause the camera to rotate along the X and Y axes. If however the pointer is outside the molecule, the camera will rotate along the Z axis. In the PyMOL Viewing Window molecules can be viewed and directly interacted with.