PYMOL TUTORIAL REACTION MOVIE
PYMOL TUTORIAL REACTION CODE
PYMOL TUTORIAL REACTION DOWNLOAD

This exercise is similar to the previous one, but we will add style information with scenes.

PYMOL TUTORIAL REACTION MOVIE

The movie should play in a loop and the camera bounce between the two views. Store another key frame at (or near) frame 30 by right clicking on the middle of the movie panel, or type:

Move or rotate the molecule (actually: the camera) with the mouse in the 3D window to get a different view.

Store the first key frame by right-clicking on the movie panel > store, or type:ДЄ blue button should appear at the current frame.

Note that 2 seconds correspond to 60 frames, since the movie plays with 30 fps (frames per second).

The movie panel should appear at the bottom of the viewing window. Add time to the movie with Movie > Append > 2 seconds, or type:.

PYMOL TUTORIAL REACTION DOWNLOAD

, or download one from the PDB by typing into the PyMOL command line:

Load a PDB file of your choice with File > Open >.

at least two key frames with different camera orientation.

In this exercise we create a movie which pans between different camera views.

movie_auto_interpolate=on/off: immediately reinterpolate when adding a key frame (Movie > Auto Interpolate).

movie_loop=on/off: connect the last and first frame when interpolating (Movie > Loop Frames).

mdo and mappend: Storing commands with frames.

The Motions Mouse Mode is used to store object specific key frames. Right click on the panel to insert or delete key frames. PyMOL displays a movie panel with a frame slider at the bottom of the window.

18.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.

18.3 Coarse-grained MD simulation of TBP-DNA Sequence-Specific Recognition.

18.2 Coarse-grained MD simulation of DNA with the 3SPN.2C model.

18.1 Coarse-grained MD simulation of protein with the AICG2+ model.

Simulations with recent residue-level coarse-grained models.

17.3 Flexible fitting refinement for de novo models.

17.2 Multi-scale cryo-EM flexible fitting.

17.1 GGBP using a simulated density map.

The enzyme reaction 2: Free-energy calculation

16.5 The enzyme reaction 1: Reaction path search.

16.4 Vibrational analysis of phosphate ion in solution.

15.1 Relative protein-ligand binding affinity.

Replica-exchange solute tempering (gREST).

Replica-exchange umbrella sampling (REUS).

Replica-exchange molecular dynamics simulation (REMD).

9.1 Target MD and steered MD simulations of Ribose Binding Protein in water.

MD simulations with the implicit solvent model.

7.1 Protein G with the Karanicolas-Brooks Go model.

MD simulations with the coarse-grained model.

6.1 POPC lipid bilayers with the CHARMM force field.

MD simulations of various biomolecules with the all-atom model.

5.2 Creating input files for the AMBER force field.

5.1 Creating input files for the CHARMM force field.

Preparation of the input files for various systems.

4.2 Analysis of the statistics of the trajectory data.

4.1 Analysis of DCD file by the userвЂ™s Fortran programming.

MD simulations of peptides and proteins with the all-atom CHARMM force field.

2.3 Building the initial structure of the target system.

2.2 Preparation of the force field parameters.

2.1 3D structure of biological molecules.

Preparation of the input files for GENESIS.

PYMOL TUTORIAL REACTION CODE

1.2 LetвЂ™s take a quick look at the source code of GENESIS.

1.1 Installation of GENESIS for Tutorials.

: Suitable for cluster machine or super-computer (spdyn, more than 64 CPU cores).

: Suitable for workstation or GPU machine (spdyn, ~16 CPU cores).

: Suitable for laptop or small desktop machine (atdyn, less than 4 CPU cores).

The tutorials are mainly composed of three levels according to the required computational resource. However, most tutorials at the intermediate and advanced levels require parallel computation with many cores, because their calculations are heavy. The GENESIS beginners may first start the basic tutorial, which can be mainly performed on a few CPU cores. If you do not know their basic usage, learn them in advance. WeВ will use various linux commands such as grep, cut, paste, tail, sed, and tee. Before starting the tutorials, the users are recommended to get VMD to visualize the obtained MD trajectories, and also gnuplot to plot the data. We show basic, intermediate, and advanced tutorials for GENESIS.

Pymol tutorial reaction