Biol 6312

1 May 2018

Lesson 11: Jmol video and HW#8

Download the text file jmol-animation-script.txt

Links to Jmol-WIKI:

Today we will try to make a movie file from a series of Jmol-generated jpg files.

1. Launch Jmol.jar and open a pdb file, then open the console.

2. Make the background white, and render the molecule as you like.

To turn off the Jmol logo, type "frank off"

3. Open the text file linked above: jmol-animation-script.txt

4. In the text file it says: ~fileprefix = "jpg-frames1/“

5. So, you must make a folder named "jpg-frames1" in your jmol folder. That is where the jpg files will be saved.

6. If you make more than one set of jpgs, you should name those folders "jpg-frames2“, etc. Then change the script file to say ~fileprefix = "jpg-frames2/“ , etc. Otherwise Jmol will simply overwrite your files, without any warning.

7. In the text file it also says: rotate y @~degstep

8. You can change the axis of rotation: The y axis is vertical. The x axis is horizontal, and the z axis is coming out at you. Sometimes you might want to rotate around x. Rotation around z does not show you anything.

9. In the text file it also says: ~degstep = 1 # or 2, degrees per step

The 1 indicates it will rotate one degree, then save another image file. You can decrease the size of the rotation to make a smoother, but larger file size. If you use a 2 degree step, final file will be one half the size, but the video will probably look the same.

10. Now go to the text file and select all, and copy. This is the last time to alter the text.

11. Go to the console window of Jmol, and paste.

12. It should start to make the files immediately. It will take a few minutes to make all 360 jpgs.

13. To make the movie file, you will need other software. I will show how to do it in Photoshop CC 2017 for Mac.

14. Launch Photoshop.

15. Under 'File', go to 'Open' and find the first jpg in the folder, e.g. "m1.jpg". Select it, then click the box for Options, and check "Image Sequence", then click open. You have the option to change the frame rate (default 30 is good). Click OK. The first image should appear.

16. Under 'File', 'Export', choose 'Render Video'. In the box you can name the video file, change where it will be saved, alter the quality, and choose which frames to use. When ready, click 'Render'.

17. Go to the file and open it.

18. If you do not have access to Photoshop, other software might be available. Or take your files to an SMU computer that has Photoshop installed.

19. Send me your video, or compress the folder of jpgs and email to me. I will make it for you.

20. Or Download ChimeraX. It's rather easy to make a simple video.

UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE.
Protein Sci. 2018 Jan;27(1):14-25

Comments/questions: email me

Copyright 2018, Steven B. Vik, Southern Methodist University

Last modified May 1, 2018