User talk:Karl Oberholser

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Hi Karl, I see your email is written so that crawlers won't be able to read it from the page and spam you. May I suggest a more attractive feature recently introduced to Proteopedia? Simply surround your email in the following tags: <email> </email>. As an example, those tags make my email look like this . It converts the email to an image. Best, Eran

P.S. We showed Emily's page on Photosystem II here at the International School on Crystallography for Drug Design in Erice, Italy. We used it as an example of assigning Proteopedia pages as class projects, as well as an example of a Jmol novice successfully creating a Proteopedia page. People were certainly impressed, and we gave you and Emily full credit for the initiative and the page.

Eran, Thanks for the information and thanks for showing Emily's page. It is good to get such a positive response.



Ramachandran page

Hi Karl,

I noticed you're working on a page on Ramachandran plots. Are you using the Scene authoring tools or just opening the Jmol console to create your scenes? If there is anything you would like to have simplified or any features that you find are missing, let me know.

Eran Hodis 17:47, 11 June 2008 (IDT)

Eran, Am I using this discussion page in the way that it is intended? I am still discovering my way around.

I am using both the Scene authoring tools and the Jmol console. You can help with a problem that I encountered. I want the background of the applet black so when I inserted it I set color=black, but that has no effect on the background color.

Karl Oberholser

Hi Karl, Well, the idea is that you leave messages for me on my user talk page, and I leave them for you on yours. That way we are each notified of "new messages". I found this message you left me simply because I frequently check "recent changes" on Proteopedia.

To make the background of the applet black, you can use the "colors" tab of the Scene Authoring Tools (SAT). Just change the radio button from "selection" to "background" and then click on the black color square. Does that work?

Best, Eran Hodis 22:03, 11 June 2008 (IDT)


Hi Karl,

You can insert your signature (Your name linked to your Userpage, as well as a timestamp) by typing ~~~~ (4 tildas in a row). It is also a button above the text editing area (where you find Bold and Italic buttons), 2 buttons to the left of the 3D button. I usually just use the 4 tildas. The effect is of course: Eran Hodis 23:50, 11 June 2008 (IDT)

Scenes with non-alphabetical characters

Hi Karl,

The problem is one we've been alerted to for some time: Unfortunately there is a problem in having the green links displaying characters that are non-alphabetical like ampersands and greek letters. For the time being, try to use only alphabetical characters.

Best, Eran Hodis 17:27, 12 June 2008 (IDT)

Dihedral angles

Dear Karl,

Did you know that you can make measurements in Jmol? For example, to make a dihedral angle measurement, click twice on the first atom, once on the second, once on the third, and twice on the fourth.

For a standard angle measurement, click twice on the first atom, once on the second, and twice on the third. For a distance measurement, click twice on the first atom and twice on the second.

Best,Eran Hodis 13:54, 13 June 2008 (IDT)

User pages

Hi Karl, Just made "Emily Forschler" and "Photosystem II" into links on your userpage. Hope that's okay. If not, just revert it. Best, Eran Hodis 22:49, 17 June 2008 (IDT)

Inserting an initial scene

Dear Karl,

Yes, use this method of insertion <applet load='file.pdb' size='300' frame='true' . Just specify an additional parameter scene='mypage/myscene/myversionnumber'. For more help see this section on the scene parameter in the applet tag.

Best, Eran Hodis 09:40, 18 June 2008 (IDT)

Ramachandran plots

Dear Karl,

I'm following the growth of your Ramachandran Plots page with much interest. I'm glad to see the new version of Jmol is correctly coloring the Ramachandran plots as the latest section you have added (with myoglobin) does a great job of conveying a real example of where amino acids in helices, in sheets, and in loops map to the Ramachandran plot.

Best, Eran Hodis 23:28, 20 June 2008 (IDT)

Deleting scenes

Hi Karl, At the moment, you cannot delete scenes. We have not worked out the way that this should be done yet, but we will worry about it when Proteopedia becomes so widely used that tidying up scenes is necessary.

As I understood from your question, you weren't asking me what went wrong with your scene, but rather how to delete it.

Best, Eran Hodis 18:39, 26 June 2008 (IDT)

Troublesome link

If it's not too crucial for you, I'll let it be and put my focus elsewhere. Should it become crucial, let me know. Eran Hodis 18:54, 26 June 2008 (IDT)

PDBSum site

Dear Karl,

Can you clarify what you mean by "the entry page to this site changes"? And yes, I agree with you that PDBSum is a wonderful resource.

Best, Eran

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