This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Getting 3D model

Hi everyone! I am trying to download 3D model of Oxaloacetate.
Which I can present as animation.
Is there is a simple way to do it? (for free of course)
Thanks a lot!!

3d oxaloacetate
• 3,347 views • link
updated by Kevin Blighe Kevin Blighe • written by elisheva elisheva

1 answer

Use Jmol and load the PDB ID for your protein of interest directly from Jmol (File->Get PDB).

Here's an example: http://www.rcsb.org/pdb/explore.do?structureId=3lye

jmol
upload pic

• 0 views • link
written by Kevin Blighe Kevin Blighe

Thanks a lot.
But as I mentioned:
I'm looking for a molecule, not a protein.
What makes PDB irrelevant I think.
And another remark: I woul'd like to presemt the animation on ppt.

• 0 views • link
written by elisheva elisheva

Yes, the PDB is for protein - it does have oxaloacetate but always complexed with a protein.

However, Jmol can be used to load molecules, too, including oxaloacetate / oxaloacetic acid. To get it, load Jmol and then go to File->Get MOL, and then type in 'oxaloacetate' (or other IDs for the molecule), as shown in my screenshot:

jmol
image host

To integrate this into Powerpoint®, you could load Jmol from a button in Powerpoint® or just take screenshots (or a movie) of the molecule. Another approach is to insert the Jmol appet as an object into Powerpoint® (Insert->Object).

In the past, as a quantum chemist, I used Spartan for modeling molecules, but it is commercial.

Good luck

Kevin

• 0 views • link
written by Kevin Blighe Kevin Blighe

Thanks!!
That was very helpful.
Is there is a simple way to save it as a movie?

• 0 views • link
written by elisheva elisheva

Certainly, here's a test that I've done just now to show you how it could work. This is a MOV file that would be easily inserted into Powerpoint®: https://app.box.com/s/enhtpwcv4j8gq19qxtwjlmn1npqsvpen

To run Jmol itself, just download the JAR files and run with java -jar Jmol.jar

To record the video, I used SimpleScreenRecorder on Linux Ubuntu. I'm guessing that you are using Mac or Windows? There appear to be a few options:

Or you can just use the one that I've created - no licence; no warranty!

Kevin

• 0 views • link
written by Kevin Blighe Kevin Blighe

Log in to answer this question.

More posts like this