Proteopedia - User contributions [en]

Sandbox3

2009-03-03T16:01:52Z

Kaitie Sniffen:

'''This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!'''

L Thompson 3/1/09
:Start by finding a protein with a known structure that interests you (see assignment sheet instructions). Determine whether anyone else in the class has already started a sandbox page for your protein (see list below). If so, join their page. If not, start a new sandbox page (you can use any unused ones listed below, or search for available numbers) and add a link to your page to our class list below (use editing button above (Ab) or follow my model).
'''Chem490a Sandbox pages:'''
[[Sandbox4]] [[sandbox5]] [[sandbox7]] [[sandbox8]] [[sandbox9]] [[sandbox10]] [[sandbox11]]

Copy the message at the top into your sandbox page to "reserve" this sandbox for this course (others can still edit it but there is a way to go back -- not sure how yet).

Give "credit" for all your entries: add your name (like mine above) and also the source of anything that you got from another source.

Look for the pdb id for your protein in the Protein Data Bank. I looked for the earliest GFP structure I could find in the protein data bank and found 1ema, then followed the directions below to pull up a rotating GFP on this page.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_1ema | PDB=1ema | SCENE= }}

Wow -- you can start exploring your structure now!

Task#1 (Due Wed 3/4 in the workshop). Describe the overall structure of your protein in words and make a "greenlink" illustration to go along with your description. Use the scene authoring tools and watch video 7 for instructions.
Example: (L Thompson)
The <scene name='Sandbox3/Secondary_structure/1'>overall structure</scene> of green fluorescent protein is an 11-stranded beta barrel (yellow) surrounding a central helix (pink). The chromophore is part of the central helix. Information from [[1ema]].

Sandbox11

2009-03-03T16:00:23Z

Kaitie Sniffen:

<B>This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!</B>

K Sniffen 3/3/09

{{STRUCTURE_1lds | PDB=1lds | SCENE= }}

This protein consists of seven <scene name='Sandbox11/Beta-2-microglobulin/1'>Beta-sheets</scene> shown here in purple. It also has a small <scene name='Sandbox11/Beta_2_microglobulin/1'>alpha-helix</scene> on the surface of the protein shown in teal.

Sandbox11

2009-03-03T15:58:17Z

Kaitie Sniffen:

This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!

K Sniffen 3/3/09

{{STRUCTURE_1lds | PDB=1lds | SCENE= }}

This protein consists of seven <scene name='Sandbox11/Beta-2-microglobulin/1'>Beta-sheets</scene> shown here in purple. It also has a small <scene name='Sandbox11/Beta_2_microglobulin/1'>alpha-helix</scene> on the surface of the protein shown in teal.

Sandbox11

2009-03-03T15:57:38Z

Kaitie Sniffen:

This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!

K Sniffen 3/3/09

==This is a placeholder==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_1lds | PDB=1lds | SCENE= }}

This protein consists of seven <scene name='Sandbox11/Beta-2-microglobulin/1'>Beta-sheets</scene> shown here in purple. It also has a small <scene name='Sandbox11/Beta_2_microglobulin/1'>alpha-helix</scene> on the surface of the protein shown in teal.

Sandbox11

2009-03-03T15:57:15Z

Kaitie Sniffen:

Sandbox11

2009-03-03T15:52:25Z

Kaitie Sniffen:

Sandbox11

2009-03-03T15:47:44Z

Kaitie Sniffen: New page: This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks! K Sniffen 3/3/09 ==This is a placeholder== This is a placeholder text ...

This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!

K Sniffen 3/3/09

==This is a placeholder==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_1lds | PDB=1lds | SCENE= }}

This protein consists of seven <scene name='Sandbox11/Β2_microglobulin/1'>Beta-sheets</scene> shown here in purple.