[Proteopedia] Structural alignment? and other oddities when using multiple models in Proteopedia

Wayne Decatur wdecatur at yahoo.com
Tue Feb 16 14:51:56 EST 2010

Hi Dan,

You can certainly display more than one model in a single Proteopedia applet (when all goes well [see the end]).
For example, see

last green link = "Overall superposition of LepA and EF-G"

Fifth green link = "Showing the structure of DDX19 with ADP bound along with the structure where RNA and an ATP analog are bound. "

I do the superposition in other visualization software and then save the information and make a multi-model pdb file. 

MODEL    1
...your model info...
MODEL    2
...your model info...

Then I upload to Proteopedia. And then load the molecule into the Scene Authoring Tools from within Proteopedia. Leave off the 'Image:" at the front for the upload.

When it loads in the Jmol window to the right, you will only seeone model. Open the Jmol console and enter the command 'model all;'. Then save the file.
Not paste the green link in your article and when you run it, you should see all the models. However, NOTE that if you view the scene in Proteopedia's Scene Authoring tool it will not show all the models even though it does on the actual page.

This is similar to how you can run morphs in Proteopedia except there you usually tell it to animate using the check box in the Scene Authoring Tools when saving and do not need to use the console.

Be sure to do the model number information correctly in the pdb file or it won't work on the Proteopedia page even though you see multiple models when you enter 'model all;' in the console. I just had it frustratingly not work while I was testing what I was describing for you using a file I had uploaded from a morph (see User:Wayne Decatur/3ewsSLASH3g0h Morph methods). The default format of the Yale Morph sever either doesn't work for 'model all;' on a Proteopedia page (it does work for the animation mode though) or if you use more than 3 models there is a problem. A file I tested that I had made had three models (of substantial size) and it worked, as well as a file where I redid the model numbers for a few frames of one I had obtained from the Yale Morph server. Again, I am considering 'work' to be that it shows all models on the Proteopedia page. It shows when you actually enter the command in the console using the files from the Yale Morph server; it
 is subsequent views in the actual Proteopedia page that fail to show more than one model. Maybe others can comment on this.


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