Animated Gifs

Animated Gifs

Some methods offer the user already some animated gifs, but some methods only provide pymol skripts. Here we explain how to create animated gifs for each method.

Webnma

We did not find any method the visualize the VMD or DCD file. Therefore we created the pictures manually.

1) right click on the animation to see the menue
2) Animation -> Framerate einstellen -> 5
3) Animation -> Anhalten
4) Datei -> exportiere Gif Abbild
5) Animation -> Nächster Frame
6) Repeat step 4 and 5 until you made pictures of the whole motion
7) Now search for a program which allows you the create animated gifs (we used http://www.createagif.net/ but this site only allows to upload 20 pictures, but the site accepts gif and png files; an alternative is GIMP, if you open the first picture and add the following as "Ebenen" you can save it as a gif-animation)
8) Save the gif and upload it to the wiki

Anisotropic Network Model web server

1) Create Pymol Scripts for each Model you want to visualize
2) Download the three files. The files have to be in the same directory
3) Start pymol and load the pml file with Run into Pymol
4) Start the animation (click on the play button on the lower right side to see the visualisation
5) Save movie as PNG Images
6) Continue as on Webnma at step 7

NOMAD-Ref

• Download multiple model PDB-file
• Split multiple model PDB-file into individual models (find scripts here)
• Load individual models with pymol and save snapshots of each model
• Create animated gif

Now we found a simpler way:

• replace the "HEADER Frame generated by pdbio.c" in your pdb-files by "MODEL"
• start it in pymol
• continue on Anisotropic Network Model web server, step 4

All-atom NMA using Gromacs on the NOMAD-Ref server

1) Download different modes
2) Load it in pymol
3) Continue on Anisotropic Network Model web server, step 4