Proteopedia - User contributions [en]

User:Shai Biran/Practice Proteopedia tutorial shai1

2015-06-07T10:01:30Z

Shai Biran:

== HOW TO EDIT A PAGE ==

In your second window Go to http://proteopedia.org .

Use the search box to get to your assigned Sandbox page.
You will need to log in to edit the page. Log in with a student account and password given to you by the instructor.
On your assigned Sandbox page, click on “edit this page” at the top of the page.
Then scroll down and click the “save page” button. This will ‘create’ and save your Sandbox page for further editing.

'''Your page should look like this:''' ↓↓↓↓↓↓↓↓↓↓↓↓

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Practice Proteopedia tutorial shai1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>

== Next ==

*Click on the link [http://proteopedia.org/w/User:Shai_Biran/GFP_test_page GFP Test page] to reach an example page on Green Fluorescent Protein. We will recreate this page in Proteopedia as an example. 
keep this page open throughout the workshop.

[[User:Shai Biran/Practice Proteopedia tutorial shai|Previous page (1)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai2|Next page (3)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai

2015-06-03T06:46:16Z

Shai Biran:

=='''Creating a page in Proteopedia is easy and fun!'''==
The first step, before you can start editing and creating Proteopedia pages, you must attain a '''user''' ID. Press the link on your upper right corner whee it says '''Log in / request account''' and follow the instructions. For this tutorial, you can use the student account given by the instructor.

<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
<scene name='65/651279/1stp_color/1'>Scenes</scene> are easy to create.

You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Adding and changing structures in your page ==

*In a new page:
#go to http://proteopedia.org and type ‘Hemoglobin’ in the empty white search box on the left-hand toolbar, then press ‘Go’.
#Explore the first section. Press the <scene name='65/651279/1stp_color2/1'>green links</scene>. Stop before ‘Hemoglobin subunit binding O2’

*Now type ‘Peptide’ in the search box and press ‘Go’. Explore this page. again, see what the green links do.

*Navigate back to the [[http://proteopedia.org/wiki/index.php/Main_Page Main Page]] by clicking the link ‘Main Page’ on the left-hand toolbar.
#Scroll down to ‘What can Proteopedia do for me’ and in the ‘Educators’ column, click on the link ‘tutorials or molecular scenes’, you will be taken to a new page.
#Now click on the link titled ‘Structural_Templates’
#Scroll down to the section titled ‘Secondary structure elements’.
#Explore this section, but stop before the section titled ‘Turns and loops’

== STOP here ==

</StructureSection>

'''''What are we going to learn?'''''

How to create your own pages in Proteopedia, including '''3D''' structures and <scene name='65/651279/1stp_color3/2'>green links</scene>.

[[User:Shai Biran/Practice Proteopedia tutorial shai1|Next page (2)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai1

2015-06-02T12:05:28Z

Shai Biran:

== HOW TO EDIT A PAGE ==

In your second window Go to http://proteopedia.org .

Use the search box to get to your assigned Sandbox page.
You will need to log in to edit the page. Log in with a guest account.
On your assigned Sandbox page, click on “edit this page” at the top of the page.
Then scroll down and click the “save page” button. This will ‘create’ and save your Sandbox page for further editing.

'''Your page should look like this:''' ↓↓↓↓↓↓↓↓↓↓↓↓

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Practice Proteopedia tutorial shai1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>

== Next ==

*Click on the link [http://proteopedia.org/w/User:Shai_Biran/GFP_test_page GFP Test page] to reach an example page on Green Fluorescent Protein. We will recreate this page in Proteopedia as an example. 
keep this page open throughout the workshop.

[[User:Shai Biran/Practice Proteopedia tutorial shai|Previous page (1)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai2|Next page (3)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai

2015-06-02T12:02:03Z

Shai Biran:

=='''Creating a page in Proteopedia is easy and fun!'''==
The first step, before you can start editing and creating Proteopedia pages, you must attain a '''user''' ID. Press the link on your upper right corner whee it says '''Log in / request account''' and follow the instructions.

<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
<scene name='65/651279/1stp_color/1'>Scenes</scene> are easy to create.

You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Adding and changing structures in your page ==

*In a new page:
#go to http://proteopedia.org and type ‘Hemoglobin’ in the empty white search box on the left-hand toolbar, then press ‘Go’.
#Explore the first section. Press the <scene name='65/651279/1stp_color2/1'>green links</scene>. Stop before ‘Hemoglobin subunit binding O2’

*Now type ‘Peptide’ in the search box and press ‘Go’. Explore this page. again, see what the green links do.

*Navigate back to the [[http://proteopedia.org/wiki/index.php/Main_Page Main Page]] by clicking the link ‘Main Page’ on the left-hand toolbar.
#Scroll down to ‘What can Proteopedia do for me’ and in the ‘Educators’ column, click on the link ‘tutorials or molecular scenes’, you will be taken to a new page.
#Now click on the link titled ‘Structural_Templates’
#Scroll down to the section titled ‘Secondary structure elements’.
#Explore this section, but stop before the section titled ‘Turns and loops’

== STOP here ==

</StructureSection>

'''''What are we going to learn?'''''

How to create your own pages in Proteopedia, including '''3D''' structures and <scene name='65/651279/1stp_color3/2'>green links</scene>.

[[User:Shai Biran/Practice Proteopedia tutorial shai1|Next page (2)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai

2015-06-02T09:19:30Z

Shai Biran:

=='''Creating a page in Proteopedia is easy and fun!'''==
The first step, before you can start editing and creating Proteopedia pages, you must attain a '''user''' ID. Press the link on your upper right corner whee it says '''Log in / request account''' and follow the instructions.

<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
<scene name='65/651279/1stp_color/1'>Scenes</scene> are easy to create.

You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Adding and changing structures in your page ==

*In a new page:
#go to http://proteopedia.org and type ‘Hemoglobin’ in the empty white search box on the left-hand toolbar, then press ‘Go’.
#Explore the first section. Press the <scene name='65/651279/1stp_color2/1'>green links</scene>. Stop before ‘Hemoglobin subunit binding O2’

*Now type ‘Peptide’ in the search box and press ‘Go’. Explore this page. again, see what the green links do.

*Navigate back to the [[http://proteopedia.org/wiki/index.php/Main_Page Main Page]] by clicking the link ‘Main Page’ on the left-hand toolbar.
#Scroll down to ‘What can Proteopedia do for me’ and in the ‘Educators’ column, click on the link ‘tutorials or molecular scenes’, you will be taken to a new page.
#Now click on the link titled ‘Structural_Templates’
#Scroll down to the section titled ‘Secondary structure elements’.
#Explore this section, but stop before the section titled ‘Turns and loops’

== STOP here ==

</StructureSection>

'''''What are we going to learn?'''''

How to create your own pages in Proteopedia, including '''3D''' structures and <scene name='65/651279/1stp_color3/2'>green links</scene>.

[[User:Shai Biran/Practice Proteopedia tutorial shai1|Next page (2)]]

User:Shai Biran/Practice Proteopedia tutorial shai

2015-06-02T09:16:59Z

Shai Biran:

=='''Creating a page in Proteopedia is easy and fun!'''==
The first step, before you can start editing and creating Proteopedia pages, you must attain a '''user''' ID. Press the link on your upper right corner whee it says '''Log in / request account''' and follow the instructions.

<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
<scene name='65/651279/1stp_color/1'>Scenes</scene> are easy to create.

You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Adding and changing structures in your page ==

*In a new page:
#go to http://proteopedia.org and type ‘Hemoglobin’ in the empty white search box on the left-hand toolbar, then press ‘Go’.
#Explore the first section. Press the <scene name='65/651279/1stp_color2/1'>green links</scene>. Stop before ‘Hemoglobin subunit binding O2’

*Now type ‘Peptide’ in the search box and press ‘Go’. Explore this page. again, see what the green links do.

*Navigate back to the [[http://proteopedia.org/wiki/index.php/Main_Page Main Page]] by clicking the link ‘Main Page’ on the left-hand toolbar.
#Scroll down to ‘What can Proteopedia do for me’ and in the ‘Educators’ column, click on the link ‘tutorials or molecular scenes’, you will be taken to a new page.
#Now click on the link titled ‘Structural_Templates’
#Scroll down to the section titled ‘Secondary structure elements’.
#Explore this section, but stop before the section titled ‘Turns and loops’

== STOP here ==

'''''What are we going to learn?'''''

How to create your own pages in Proteopedia, including '''3D''' structures and <scene name='65/651279/1stp_color3/2'>green links</scene>.

[[User:Shai Biran/Practice Proteopedia tutorial shai1|Next page (2)]]

User:Shai Biran/Practice Proteopedia tutorial shai

2015-06-02T09:16:34Z

Shai Biran:

=='''Creating a page in Proteopedia is easy and fun!'''==
The first step, before you can start editing and creating Proteopedia pages, you must attain a '''user''' ID. Press the link on your upper right corner whee it says '''Log in / request account''' and follow the instructions.

<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
<scene name='65/651279/1stp_color/1'>Scenes</scene> are easy to create.

You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Adding and changing structures in your page ==

*In a new page:
#go to http://proteopedia.org and type ‘Hemoglobin’ in the empty white search box on the left-hand toolbar, then press ‘Go’.
#Explore the first section. Press the <scene name='65/651279/1stp_color2/1'>green links</scene>. Stop before ‘Hemoglobin subunit binding O2’

*Now type ‘Peptide’ in the search box and press ‘Go’. Explore this page. again, see what the green links do.

*Navigate back to the [[http://proteopedia.org/wiki/index.php/Main_Page Main Page]] by clicking the link ‘Main Page’ on the left-hand toolbar.
#Scroll down to ‘What can Proteopedia do for me’ and in the ‘Educators’ column, click on the link ‘tutorials or molecular scenes’, you will be taken to a new page.
#Now click on the link titled ‘Structural_Templates’
#Scroll down to the section titled ‘Secondary structure elements’.
#Explore this section, but stop before the section titled ‘Turns and loops’

== STOP here ==

----

'''''What are we going to learn?'''''

How to create your own pages in Proteopedia, including '''3D''' structures and <scene name='65/651279/1stp_color3/2'>green links</scene>.

[[User:Shai Biran/Practice Proteopedia tutorial shai1|Next page (2)]]

User:Shai Biran/Practice Proteopedia tutorial shai11

2015-06-02T08:40:52Z

Shai Biran: New page: ==Creating Your Own Account== Now that you had a feeling of how easy and fun it is to create Proteopedia <ref>PMID:18673581</ref><ref>PMID: 21536137</ref><ref>Hanson, Prilusky, Renjian, N...

==Creating Your Own Account==

Now that you had a feeling of how easy and fun it is to create Proteopedia <ref>PMID:18673581</ref><ref>PMID: 21536137</ref><ref>Hanson, Prilusky, Renjian, Nakane & Sussman (2013) “JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia” Israel J of Chem 53, 207-216.</ref> pages, you can sign for an account and start adding your own input.

*If you want to use Proteopedia in the future to create your own pages, please request your own account in your own name. You can do this now if you want!
*Request an account in your name by logging out of guest account and clicking “log in / request account” at top right corner of website. Enter the information that is requested, and your account will be approved by Prof. Eric Martz (Univ of Mass).

----

== Help Resources ==
*General Help: http://www.proteopedia.org/w/Help:Contents
*Editing Help: http://www.proteopedia.org/w/Help:Editing
*Wikitext Cheatsheet: http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet
*Scene Authoring Tools Help: http://www.proteopedia.org/w/Scene_authoring_tools
*Proteopedia Video Guide: http://www.proteopedia.org/w/Proteopedia:Video_Guide

== References ==
<references/>

== Re-read ==

Previous pages [[User:Shai Biran/Practice Proteopedia tutorial shai| (1)]][[User:Shai Biran/Practice Proteopedia tutorial shai1| (2)]][[User:Shai Biran/Practice Proteopedia tutorial shai2| (3)]][[User:Shai Biran/Practice Proteopedia tutorial shai3| (4)]][[User:Shai Biran/Practice Proteopedia tutorial shai4| (5)]][[User:Shai Biran/Practice Proteopedia tutorial shai5| (6)]][[User:Shai Biran/Practice Proteopedia tutorial shai6| (7)]][[User:Shai Biran/Practice Proteopedia tutorial shai7| (8)]][[User:Shai Biran/Practice Proteopedia tutorial shai8| (9)]][[User:Shai Biran/Practice Proteopedia tutorial shai9| (10)]][[User:Shai Biran/Practice Proteopedia tutorial shai10| (11)]]

User:Shai Biran/Practice Proteopedia tutorial shai10

2015-06-02T08:23:54Z

Shai Biran:

==Inserting a Quiz==

We want to add a quiz to the page to test the reader’s comprehension. Click on ‘edit this page’.
Add the following text after the line ‘<references/>’:

*‘==Quiz==’ is a section heading as before.

*< quiz display=simple > is wiki-text for a quiz. Spaces are added so you can see the text.

*The question is between two curly brackets {}.
*Each potential answer is on its own line.
*A wrong answer is preceded by a minus (‘-’) sign and the correct answer by the plus (‘+’) sign.

Open our example page [[User:Shai Biran/GFP test page]] and press edit this page. At the bottom you can see an example for a quiz.

Now create one of your own and '''save''' page.

==Quiz==
<quiz display=simple>
{What do you think about Proteopedia?}
- Nice
- Okay
+ So cool, I can't believe I didn't know about it before!
- informative
</quiz>

----

Next page - creating your own account

[[User:Shai Biran/Practice Proteopedia tutorial shai9|Previous page (10)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai11|Next Page (12)]]

User:Shai Biran/Practice Proteopedia tutorial shai10

2015-06-02T08:21:58Z

Shai Biran: New page: ==Inserting a Quiz== We want to add a quiz to the page to test the reader’s comprehension. Click on ‘edit this page’. Add the following text after the line ‘<references/>’ ‘==...

==Inserting a Quiz==

We want to add a quiz to the page to test the reader’s comprehension. Click on ‘edit this page’.
Add the following text after the line ‘<references/>’
‘==Quiz==’
is a section heading as before.

< quiz display=simple > is wiki-text for a quiz. Spaces are added so you can see the text.

*The question is between two curly brackets {}.
*Each potential answer is on its own line.
*A wrong answer is preceded by a minus (‘-’) sign and the correct answer by the plus (‘+’) sign.

Open our example page [[User:Shai Biran/GFP test page]] and press edit this page. At the bottom you can see an example for a quiz.

Now create one of your own and '''save''' page.

==Quiz==
<quiz display=simple>
{What do you think about Proteopedia?}
- Nice
- Okay
+ So cool, I can't believe I didn't know about it before!
- informative
</quiz>

----

Next page - creating your own account

[[User:Shai Biran/Practice Proteopedia tutorial shai9|Previous page (10)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai11|Next Page (12)]]

User:Shai Biran/Practice Proteopedia tutorial shai9

2015-06-02T08:01:03Z

Shai Biran:

==Adding 2D Images==

Adding 2D images is very easy.
All you need to do is to press the Upload file link in the toolbox on the left side of the screen

[[Image:Upload_file.png]]

Then choose a file to upload. Once you have, copy the name of the file which appears in the 'Destination filename' box.
Now all that's left is to press the icon of image,

[[Image:Icon.png]]

and in the new line that appears, paste your copied image name instead of Example.jpg [ [Image: '''Example.jpg'''] ] into the new wiki-text.
'''Save''' your page and now you have your 2D image.

----

== Let's try this out: ==

*View our example page [[User:Shai Biran/GFP test page]] and save the big picture to your computer by right-clicking on it and choosing an option like “Save as...” or “Save to desktop”. Save the image (1ema.gif) to your desktop.
*We now need to upload the image to Proteopedia. Back in your  Proteopedia ‘Sandbox’ page, click on the ‘upload file’ link in the  left-hand toolbox.
*At the ‘upload file’ page, next to ‘Source filename:’ click on the ‘Choose file’ button. Using the interface that pops up, browse to and select the 2D image we saved (1ema.gif).
*On the ‘upload file’ page, make sure to change the ‘Destination filename’ from ‘1ema.gif’ to something unique like ‘1ema_Workshop_579.gif’ where ‘Workshop’ is the name of your workshop, and ‘579’ is your ‘Sandbox’ number.
*Under ‘Summary’ type a short summary of what we see in the picture 1ema.gif. Click on the ‘Upload file’ button. Your file will be uploaded and you will be taken to its new page in Proteopedia. Copy the image’s name, so you have it for later.
*Go back to your ‘Sandbox’ page and click on ‘edit this page’. Click on the text-editing area just before text “Green fluorescent protein . . .” and hit Enter to add one blank line. Click so that your cursor is in the white space you just created.
*Now click on the button that looks like a picture. This will insert a wiki-text for a 2D image.
*After you clicked on the button that looks like a picture, some wiki-text should have popped up that says ‘[ [Image:Example.jpg] ]’. (Again - spaces are added so you can see the text and not its result). Note that this format of double square brackets is the same format as for internal links that we created earlier to ‘1ema’ ([[1ema]]).
*Change the word ‘Example.jpg’ to the name of your image (remember, you copied the name of your image before, now it comes in handy, you may paste it.)
*The final result should look something like this ‘[ [Image:1ema_Workshop_579.jpg] ]’

'''Save''' the page.

== Next ==

In the next page we will learn how to insert a quiz.

[[User:Shai Biran/Practice Proteopedia tutorial shai8|Previous page (9)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai10|Next Page (11)]]

User:Shai Biran/Practice Proteopedia tutorial shai9

2015-06-02T07:58:58Z

Shai Biran: New page: ==Adding 2D Images== Adding 2D images is very easy. All you need to do is to press the Upload file link in the toolbox on the left side of the screen Image:Upload_file.png Then cho...

File:Icon.png

2015-06-02T07:43:04Z

Shai Biran:

File:Upload file.png

2015-06-02T07:38:07Z

Shai Biran:

User:Shai Biran/Practice Proteopedia tutorial shai8

2015-06-02T07:27:45Z

Shai Biran:

==Adding References==

Let’s cite a reference in our page. Look at the reference at the bottom of our original example page: [[User:Shai Biran/GFP test page]].
We could add the reference by typing it out -- that’s the long way.
A much easier way is to refer to the paper by its PubMed ID: Click on ‘edit this page’ for your ‘Sandbox’ page. At the end of the 2nd paragraph, after the words ‘the glycine residues’, add the text ‘< ref >PMID:8703075</ ref >’ , but with no spaces (spaces are here so you can see this text and not its resulting reference sign).
‘< ref >’ is called the opening reference tag, and ‘< /ref >’ is the closing tag. Together they enclose the text ‘PMID:’ which stands for PubMed ID, and then the actual PubMed ID of the reference you want to cite.
You’ve added the citation, but you still need to specify where the bibliography will appear -- the list of all cited references in the page. This was automatically added when you created your page, i.e. the line ‘<references/>’ after the last paragraph.

Save the page.

your page should look like this:

↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓

[[Image:With_references.png]]

↑↑↑↑↑↑↑↑↑↑↑↑↑↑↑↑↑↑↑↑↑↑↑↑

In the next page we will learn about adding 2D images

[[User:Shai Biran/Practice Proteopedia tutorial shai7|Previous page (8)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai9|Next Page (10)]]

User:Shai Biran/Practice Proteopedia tutorial shai8

2015-06-02T07:19:48Z

Shai Biran: New page: ==Adding References== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> Let’s cite a reference in our page. Look at the reference at t...

==Adding References==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>

Let’s cite a reference in our page. Look at the reference at the bottom of our original example page: [[User:Shai Biran/GFP test page]].
We could add the reference by typing it out -- that’s the long way.
A much easier way is to refer to the paper by its PubMed ID: Click on ‘edit this page’ for your ‘Sandbox’ page. At the end of the 2nd paragraph, after the words ‘the glycine residues’, add the text ‘<ref>PMID:8703075</ref>’.
‘<ref>’ is called the opening reference tag, and ‘</ref>’ is the closing tag. Together they enclose the text ‘PMID:’ which stands for PubMed ID, and then the actual PubMed ID of the reference you want to cite.
You’ve added the citation, but you still need to specify where the bibliography will appear -- the list of all cited references in the page. This was automatically added when you created your page, i.e. the line ‘<references/>’ after the last paragraph.

Save the page.

your page should look like this:
↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓↓

[[Image:With_references.png]]
</StructureSection>
== References ==
<references/>

File:With references.png

2015-06-02T07:19:02Z

Shai Biran:

User:Shai Biran/Practice Proteopedia tutorial shai7

2015-06-02T07:10:38Z

Shai Biran:

== Adding a GREEN SCENE LINK 2 ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

<StructureSection load='1ema' size='300' frame='true' side='right' caption='GFP ([[1ema]])' scene=''>

Our scene is done, so let’s save it and put it into the page.
Click on the “save scene” tab in the Scene Authoring Tools. Give your scene a name and a description by entering text in the “Name” and “Description” text-areas (here it is named GFP tutorial).
Let’s make our scene spin when it loads. In the drop down menu next to the text “when this scene loads, I want it to” choose the option “spin”.
Click on the “save scene” button.

<scene name='70/703443/Tutorial_gfp/3'>GFP tutorial</scene>

As soon as we saved our scene, some wikitext appeared in the text-area titled “Wikitext” that was previously empty.
The new text in the “Wikitext” text-area instructs you to copy a line in the text-area & paste it in the text of the Proteopedia page where you would like the green scene link to appear. The line looks similar to this:

--scene name='61/612803/GFP tutorial/1'>TextToBeDisplayed</scene--
Highlight that line in the “Wikitext” text-area and copy it.
Scroll up the page, past the Scene Authoring Tools to the text-editing area of the Proteopedia page.
Find the word “chromophore” in the text-editing area. Highlight it and replace it by pasting the text you previously copied.

The text that you just pasted from the “Wikitext” section of the Scene Authoring Tools creates a green scene link wherever you place it in the Proteopedia page.
The word “TextToBeDisplayed” will be the part that shows up as the text of the green link on the page.
Change “TextToBeDisplayed” to say “chromophore. It should look something like: 

--scene name='Sandbox_780/GFP tutorial/1'>chromophore</scene--
Scroll down to the bold text “Scene Authoring Tools [hide]” next to the colored molecule, and click on “hide” to hide the Scene Authoring Tools.
Scroll down and click on “Save page” to save the Proteopedia page you edited.
Try clicking on the new green scene link you have created.

Now to give your page a nice touch, change the heading from - Your Heading Here (maybe something like 'Structure') , to whichever heading you want.

</StructureSection>

== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai6|Previous page (7)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai8|Next Page (9)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai7

2015-06-02T07:05:55Z

Shai Biran:

== Adding a GREEN SCENE LINK 2 ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

<StructureSection load='1ema' size='300' frame='true' side='right' caption='GFP ([[1ema]])' scene=''>

Our scene is done, so let’s save it and put it into the page.
Click on the “save scene” tab in the Scene Authoring Tools. Give your scene a name and a description by entering text in the “Name” and “Description” text-areas (here it is named GFP tutorial).
Let’s make our scene spin when it loads. In the drop down menu next to the text “when this scene loads, I want it to” choose the option “spin”.
Click on the “save scene” button.

<scene name='70/703443/Tutorial_gfp/3'>GFP tutorial</scene>

As soon as we saved our scene, some wikitext appeared in the text-area titled “Wikitext” that was previously empty.
The new text in the “Wikitext” text-area instructs you to copy a line in the text-area & paste it in the text of the Proteopedia page where you would like the green scene link to appear. The line looks similar to this: scene name='61/612803/GFP tutorial/1'>TextToBeDisplayed</scene>
Highlight that line in the “Wikitext” text-area and copy it.
Scroll up the page, past the Scene Authoring Tools to the text-editing area of the Proteopedia page.
Find the word “chromophore” in the text-editing area. Highlight it and replace it by pasting the text you previously copied.

The text that you just pasted from the “Wikitext” section of the Scene Authoring Tools creates a green scene link wherever you place it in the Proteopedia page.
The word “TextToBeDisplayed” will be the part that shows up as the text of the green link on the page.
Change “TextToBeDisplayed” to say “chromophore. It should look something like:  --scene name='Sandbox_780/GFP tutorial/1'>chromophore</scene--
Scroll down to the bold text “Scene Authoring Tools [hide]” next to the colored molecule, and click on “hide” to hide the Scene Authoring Tools.
Scroll down and click on “Save page” to save the Proteopedia page you edited.
Try clicking on the new green scene link you have created.

Now to give your page a nice touch, change the heading from - Your Heading Here (maybe something like 'Structure') , to whichever heading you want.

</StructureSection>

== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai6|Previous page (7)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai8|Next Page (9)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai7

2015-06-02T06:50:04Z

Shai Biran:

== Adding a GREEN SCENE LINK 2 ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

<StructureSection load='1ema' size='300' frame='true' side='right' caption='GFP ([[1ema]])' scene=''>

Our scene is done, so let’s save it and put it into the page.
Click on the “save scene” tab in the Scene Authoring Tools. Give your scene a name and a description by entering text in the “Name” and “Description” text-areas (here it is named GFP tutorial).
Let’s make our scene spin when it loads. In the drop down menu next to the text “when this scene loads, I want it to” choose the option “spin”.
Click on the “save scene” button.

<scene name='70/703443/Tutorial_gfp/3'>GFP tutorial</scene>

As soon as we saved our scene, some wikitext appeared in the text-area titled “Wikitext” that was previously empty.
The new text in the “Wikitext” text-area instructs you to copy a line in the text-area & paste it in the text of the Proteopedia page where you would like the green scene link to appear. The line looks similar to this: <scene name='61/612803/GFP tutorial/1'>TextToBeDisplayed</scene>>
Highlight that line in the “Wikitext” text-area and copy it.
Scroll up the page, past the Scene Authoring Tools to the text-editing area of the Proteopedia page.
Find the word “chromophore” in the text-editing area. Highlight it and replace it by pasting the text you previously copied.

The text that you just pasted from the “Wikitext” section of the Scene Authoring Tools creates a green scene link wherever you place it in the Proteopedia page.
The word “TextToBeDisplayed” will be the part that shows up as the text of the green link on the page.
Change “TextToBeDisplayed” to say “chromophore. It should look something like: <scene name='Sandbox_780/GFP tutorial/1'>chromophore</scene>
Scroll down to the bold text “Scene Authoring Tools [hide]” next to the colored molecule, and click on “hide” to hide the Scene Authoring Tools.
Scroll down and click on “Save page” to save the Proteopedia page you edited.
Try clicking on the new green scene link you have created.

Now to give your page a nice touch, change the heading from - Your Heading Here (maybe something like 'Structure') , to whichever heading you want.

</StructureSection>

== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai6|Previous page (7)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai8|Next Page (9)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai7

2015-06-02T06:49:28Z

Shai Biran:

== Adding a GREEN SCENE LINK 2 ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

<StructureSection load='1ema' size='300' frame='true' side='right' caption='GFP ([[1ema]])' scene=''>

Our scene is done, so let’s save it and put it into the page.
Click on the “save scene” tab in the Scene Authoring Tools. Give your scene a name and a description by entering text in the “Name” and “Description” text-areas (here it is named GFP tutorial).
Let’s make our scene spin when it loads. In the drop down menu next to the text “when this scene loads, I want it to” choose the option “spin”.
Click on the “save scene” button.

<scene name='70/703443/Tutorial_gfp/3'>GFP tutorial</scene>

As soon as we saved our scene, some wikitext appeared in the text-area titled “Wikitext” that was previously empty.
The new text in the “Wikitext” text-area instructs you to copy a line in the text-area & paste it in the text of the Proteopedia page where you would like the green scene link to appear. The line looks similar to this: <scene name='61/612803/GFP tutorial/1'>TextToBeDisplayed</scene>>
Highlight that line in the “Wikitext” text-area and copy it.
Scroll up the page, past the Scene Authoring Tools to the text-editing area of the Proteopedia page.
Find the word “chromophore” in the text-editing area. Highlight it and replace it by pasting the text you previously copied.

The text that you just pasted from the “Wikitext” section of the Scene Authoring Tools creates a green scene link wherever you place it in the Proteopedia page.
The word “TextToBeDisplayed” will be the part that shows up as the text of the green link on the page.
Change “TextToBeDisplayed” to say “chromophore. It should look something like: <scene name='Sandbox_780/GFP tutorial/1'>chromophore</scene>
Scroll down to the bold text “Scene Authoring Tools [hide]” next to the colored molecule, and click on “hide” to hide the Scene Authoring Tools.
Scroll down and click on “Save page” to save the Proteopedia page you edited.
Try clicking on the new green scene link you have created.

Now to give your page a nice touch, change the heading from - Your Heading Here (maybe something like 'Structure') , to whichever heading you want.

== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai6|Previous page (7)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai8|Next Page (9)]]

== References ==
<references/>

User:Shai Biran/GFP test page

2015-06-02T06:42:42Z

Shai Biran:

== Your Heading Here (maybe something like 'Structure') ==
<StructureSection load='1ema' size='300' frame='true' side='right' caption='GFP ([[1ema]])' scene=''>
[[Image:1ema.gif|thumb|left|450px|Green fluorescent protein (1ema)]]

Green fluorescent protein (GFP), originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.

Exploring the Structure
GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.<ref>PMID:8703075</ref>

</StructureSection>

==References==
<references/>

==Quiz==
<quiz display=sample>
{How many alpha helics are in this structure?}
- One
- None
+ Eleven
- Twelve
</quiz>

User:Shai Biran/Practice Proteopedia tutorial shai7

2015-06-02T06:37:44Z

Shai Biran:

== Adding a GREEN SCENE LINK 2 ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

<StructureSection load='1ema' size='300' frame='true' side='right' caption='GFP ([[1ema]])' scene=''>

Our scene is done, so let’s save it and put it into the page.
Click on the “save scene” tab in the Scene Authoring Tools. Give your scene a name and a description by entering text in the “Name” and “Description” text-areas (here it is named GFP tutorial).
Let’s make our scene spin when it loads. In the drop down menu next to the text “when this scene loads, I want it to” choose the option “spin”.
Click on the “save scene” button.

<scene name='70/703443/Tutorial_gfp/3'>GFP tutorial</scene>

As soon as we saved our scene, some wikitext appeared in the text-area titled “Wikitext” that was previously empty.
The new text in the “Wikitext” text-area instructs you to copy a line in the text-area & paste it in the text of the Proteopedia page where you would like the green scene link to appear. The line looks similar to this: <scene name='61/612803/GFP tutorial/1'>TextToBeDisplayed</scene>>
Highlight that line in the “Wikitext” text-area and copy it.
Scroll up the page, past the Scene Authoring Tools to the text-editing area of the Proteopedia page.
Find the word “chromophore” in the text-editing area. Highlight it and replace it by pasting the text you previously copied.

The text that you just pasted from the “Wikitext” section of the Scene Authoring Tools creates a green scene link wherever you place it in the Proteopedia page.
The word “TextToBeDisplayed” will be the part that shows up as the text of the green link on the page.
Change “TextToBeDisplayed” to say “chromophore. It should look something like: <scene name='Sandbox_780/GFP tutorial/1'>chromophore</scene>
Scroll down to the bold text “Scene Authoring Tools [hide]” next to the colored molecule, and click on “hide” to hide the Scene Authoring Tools.
Scroll down and click on “Save page” to save the Proteopedia page you edited.
Try clicking on the new green scene link you have created.

[[User:Shai Biran/Practice Proteopedia tutorial shai6|Previous page (7)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai8|Next Page (9)]]

== References ==
<references/>

User:Shai Biran/ SAT

2015-06-02T06:34:37Z

Shai Biran:

== Example page for Green fluorescent protein ("GFP") ==
<StructureSection load='1ema' size='300' frame='true' side='right' caption='GFP ([[1ema]])' scene=''>
[[Image:1ema.gif|thumb|left|450px|Green fluorescent protein (1ema)]]

Green fluorescent protein (GFP), originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.

Exploring the Structure
GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.<ref>PMID:8703075</ref>

</StructureSection>

==References==
<references/>

==Quiz==
<quiz display=sample>
{How many alpha helics are in this structure?}
- One
- None
+ Eleven
- Twelve
</quiz>

User:Shai Biran/Practice Proteopedia tutorial shai7

2015-06-01T13:43:47Z

Shai Biran:

User:Shai Biran/Practice Proteopedia tutorial shai7

2015-06-01T13:42:10Z

Shai Biran:

== Adding a GREEN SCENE LINK 2 ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

<StructureSection load='1ema' size='300' frame='true' side='right' caption='GFP ([[1ema]])' scene=''>

<scene name='70/703443/Tutorial_gfp/3'>GFP tutorial</scene>

[[User:Shai Biran/Practice Proteopedia tutorial shai6|Previous page (7)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai8|Next Page (9)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai7

2015-06-01T13:40:45Z

Shai Biran:

== Adding a GREEN SCENE LINK 2 ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

<StructureSection load='1ema' size='300' frame='true' side='right' caption='GFP ([[1ema]])' scene=''>

<scene name='70/703443/Tutorial_gfp/1'>GFP tutorial</scene>

[[User:Shai Biran/Practice Proteopedia tutorial shai6|Previous page (7)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai8|Next Page (9)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai7

2015-06-01T13:37:44Z

Shai Biran:

== Adding a GREEN SCENE LINK 2 ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

<scene name='70/703443/Tutorial_gfp/1'>GFP tutorial</scene>

[[User:Shai Biran/Practice Proteopedia tutorial shai6|Previous page (7)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai8|Next Page (9)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai6

2015-06-01T13:36:52Z

Shai Biran:

== Adding a GREEN SCENE LINK ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

[[Image:Limit_to_residue_number.png]]

With the chain segment selected, it’s time to change its color to match the image in the Molecule of the Month.
Click on the “colors” tab of the Scene Authoring Tools. Click on a lime color in the color palette to change the color of the selected chain segment. Turn off selection halos to better view the change in color.

[[Image:Colors.png]]

Now let’s make the background black.
In the section titled “color”, mark the button next to “background”. Now any color you select from the color palette will affect the background instead of the selection.
Click on the color black in the color palette.

[[Image:Black_Bckgrnd.png]]

All that’s left is to show the chromophore and color it in the CPK scheme.
Click on the “selections” tab. In the input box under “limit to residue types:” type “CRO”. (In the PDB file, the chromophore is listed as a residue with type “CRO”)
Click on the “replace selection” button. Turn on selection halos.

[[Image:Selecting_CRO.png]]

Click on the “representations” tab.
In the section titled “set selection representation” mark the checkbox next to stick/wireframe. Click on the “set representation” button.
Click on the “colors” tab. In the section titled “color” click on the button titled “CPK (by element)”.
Turn off selection halos to better view the new color.

[[Image:CRO_in_CPK.png]]

Notice that connection between the chromophore & the chain is missing, but is seen in the original picture: [[User:Shai Biran/GFP test page]]. Let’s '''visualize''' those missing bonds in the chain.

Click on the “selections” tab; in the ‘build your selection’ box, under ‘groups’ select ‘backbone/mainchain’; In the input box under “limit to residue numbers:” type “64,68”. (These are the numbers of the residues directly preceding and following the chromophore.) Click on the “add to selection” button. Click on the “representations” tab. In the section titled “set selection representation” mark the checkbox next to stick/wireframe. Click on the “set representation” button. Click on the “colors” tab. In the section titled “color” click on the button titled “CPK (by element)”.
Turn off selection halos to better view the new color.

== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai5|Previous page (6)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai7|Next Page (8)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai6

2015-06-01T13:27:32Z

Shai Biran:

== Adding a GREEN SCENE LINK ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

[[Image:Limit_to_residue_number.png]]

With the chain segment selected, it’s time to change its color to match the image in the Molecule of the Month.
Click on the “colors” tab of the Scene Authoring Tools. Click on a lime color in the color palette to change the color of the selected chain segment. Turn off selection halos to better view the change in color.

[[Image:Colors.png]]

Now let’s make the background black.
In the section titled “color”, mark the button next to “background”. Now any color you select from the color palette will affect the background instead of the selection.
Click on the color black in the color palette.

[[Image:Black_Bckgrnd.png]]

All that’s left is to show the chromophore and color it in the CPK scheme.
Click on the “selections” tab. In the input box under “limit to residue types:” type “CRO”. (In the PDB file, the chromophore is listed as a residue with type “CRO”)
Click on the “replace selection” button. Turn on selection halos.

[[Image:Selecting_CRO.png]]

Click on the “representations” tab.
In the section titled “set selection representation” mark the checkbox next to stick/wireframe. Click on the “set representation” button.
Click on the “colors” tab. In the section titled “color” click on the button titled “CPK (by element)”.
Turn off selection halos to better view the new color.

[[Image:CRO_in_CPK.png]]

Notice that connection between the chromophore & the chain is missing, but is seen in the original picture: [[User:Shai Biran/GFP test page]]. Let’s '''visualize''' those missing bonds in the chain.
Click on the “selections” tab; in the ‘build your selection’ box, under ‘groups’ select ‘backbone/mainchain’; In the input box under “limit to residue numbers:” type “64,68”. (These are the numbers of the residues directly preceding and following the chromophore.)
Click on the “add to selection” button.
Click on the “representations” tab.
In the section titled “set selection representation” mark the checkbox next to stick/wireframe. Click on the “set representation” button.
Click on the “colors” tab.
In the section titled “color” click on the button titled “CPK (by element)”.
Turn off selection halos to better view the new color.

== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai5|Previous page (6)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai7|Next Page (8)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai6

2015-06-01T13:25:17Z

Shai Biran:

File:CRO in CPK.png

2015-06-01T13:24:36Z

Shai Biran:

File:Selecting CRO.png

2015-06-01T13:17:48Z

Shai Biran:

User:Shai Biran/Practice Proteopedia tutorial shai6

2015-06-01T13:17:31Z

Shai Biran:

User:Shai Biran/Practice Proteopedia tutorial shai6

2015-06-01T13:13:58Z

Shai Biran:

File:Black Bckgrnd.png

2015-06-01T13:12:57Z

Shai Biran:

User:Shai Biran/Practice Proteopedia tutorial shai6

2015-06-01T13:11:20Z

Shai Biran:

File:Colors.png

2015-06-01T13:10:29Z

Shai Biran: uploaded a new version of "Image:Colors.png"

User:Shai Biran/Practice Proteopedia tutorial shai6

2015-06-01T12:58:21Z

Shai Biran:

== Adding a GREEN SCENE LINK ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

[[Image:Limit_to_residue_number.png]]

== Next ==

File:Limit to residue number.png

2015-06-01T12:57:23Z

Shai Biran:

User:Shai Biran/Practice Proteopedia tutorial shai5

2015-06-01T12:51:35Z

Shai Biran:

== Adding a GREEN SCENE LINK ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>
*First, let's clean things a bit. Change the heading in your page (where it says 'your heading here'). Feel free to choose any new heading you want.
Delete the two rows starting with 'This is a default text...'
*Now let's change the displayed 3D structure into the structure of GFP. In the row starting with StructureSection load change 1stp to GFP's pdb code. Hint - if you're not sure which pdb code to use, look at the GFP test page. Change the caption as well from caption='Caption for this structure’ to caption='GFP (PDB entry [[1ema]])'.
use the 'show preview' button to check what changed in your page.
----
Now that we have our 3D model on the page, let’s create a green scene link that shows 1ema as it looks in the the left part of the 2D image on the GFP Sample page where we got our text. (go back to that page to see what the picture looks like [[User:Shai Biran/GFP test page]])
To create a green scene link, we will need to use the 'Proteopedia Scene Authoring Tools'.
*After clicking '''edit this page''', scroll down to the bold text that says “Scene authoring tools [show]” next to a colorful molecule. Click on “show” to expand the Scene Authoring Tools.
[[Image:SAT.png]]
*Click on the tab “load molecule” in the Scene Authoring Tools.
*Load the PDB file 1ema by entering the PDB code “1ema” in the input box next to the words “By PDB code:” and then pressing the adjacent button marked “load”
*Now we have 1ema loaded into the Scene Authoring Tools’ Jmol applet. The idea behind the Scene Authoring Tools (SAT) is to create the exact scene that you would like to have load when your green link is clicked. This is generally done by first loading a PDB file into the SAT’s applet, then using the “selections”, “representations”, “colors”, and “labels” tabs to manipulate the 3D model into the desired state, finally saving the green scene link using the “save scene” tab.
*Our structure is currently displayed in cartoon representation. The first step in recreating the picture in the Molecule of the Month is to display the molecule in backbone representation.
*Click on the “selections” tab.
[[Image:Selections.png]]
*In the “all or nothing and halos” section, click on the “select all” button.
[[Image:GFP_Halos_off.png]]
*Nothing changed because “selection halos” were not on. Turn them on by marking the checkbox next to the word “selection halos”.
[[Image:GFP_Halos_On.png]]

Selection halos serve to show you what is currently selected. They will not be displayed when the green scene link you eventually create is clicked.

Now that we have everything selected, click on the “representations” tab of the SAT.
[[Image:Representations.png]]

Mark the checkbox next to “backbone” in the section titled “set selection representation”.
Click on the “set representation” button.
Notice the representation of the 3D model has changed from cartoon to backbone. To help see this better, turn off the selection halos by unmarking the checkbox next to “selection halos”.

[[Image:Backbones.png]]

Now we want to select the segment of the protein that runs through the barrel and color it green.
To make a selection, click on the “selections” tab.
We will select the segment that runs through the barrel by its residue numbers. To do this we need to know the first and the last residue numbers that make up this segment.
Notice that when you hover with your mouse over an atom in the Jmol applet, information about that atom is displayed, including the residue that atom is part of, and the residue number. Use this “hover” feature to find the residue numbers for the beginning and the end of the segment we are interested in.

[[Image:Hover_over_atom.png]]

Enter the starting and ending residue numbers, separated by a hyphen, into the input box under the text “limit to residue numbers:”.
Before making our new selection, let’s turn on selection halos so we see the change in the selection take place. Mark the checkbox next to “selection halos”. Notice that everything is selected.
Now go ahead and make the new selection by clicking “replace selection”. This will replace the old selection (everything) with our new selection (limited to a stretch of residues).
== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai4|Previous page (5)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai6|Next Page (7)]]

== References ==
<references/>

User:Shai Biran/ SAT

2015-06-01T12:47:28Z

Shai Biran: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Shai Biran/ SAT'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai6

2015-06-01T12:43:28Z

Shai Biran:

== Adding a GREEN SCENE LINK ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

Now we want to select the segment of the protein that runs through the barrel and color it green.
To make a selection, click on the “selections” tab.
We will select the segment that runs through the barrel by its residue numbers. To do this we need to know the first and the last residue numbers that make up this segment.
Notice that when you hover with your mouse over an atom in the Jmol applet, information about that atom is displayed, including the residue that atom is part of, and the residue number. Use this “hover” feature to find the residue numbers for the beginning and the end of the segment we are interested in.

[[Image:Hover_over_atom.png]]

Enter the starting and ending residue numbers, separated by a hyphen, into the input box under the text “limit to residue numbers:”.
Before making our new selection, let’s turn on selection halos so we see the change in the selection take place. Mark the checkbox next to “selection halos”. Notice that everything is selected.
Now go ahead and make the new selection by clicking “replace selection”. This will replace the old selection (everything) with our new selection (limited to a stretch of residues).
== Next ==

User:Shai Biran/Practice Proteopedia tutorial shai6

2015-06-01T12:36:48Z

Shai Biran: New page: == Adding a GREEN SCENE LINK == <scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

== Adding a GREEN SCENE LINK ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>

User:Shai Biran/Practice Proteopedia tutorial shai5

2015-06-01T12:34:07Z

Shai Biran:

== Adding a GREEN SCENE LINK ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>
*First, let's clean things a bit. Change the heading in your page (where it says 'your heading here'). Feel free to choose any new heading you want.
Delete the two rows starting with 'This is a default text...'
*Now let's change the displayed 3D structure into the structure of GFP. In the row starting with StructureSection load change 1stp to GFP's pdb code. Hint - if you're not sure which pdb code to use, look at the GFP test page. Change the caption as well from caption='Caption for this structure’ to caption='GFP (PDB entry [[1ema]])'.
use the 'show preview' button to check what changed in your page.
----
Now that we have our 3D model on the page, let’s create a green scene link that shows 1ema as it looks in the the left part of the 2D image on the GFP Sample page where we got our text. (go back to that page to see what the picture looks like [[User:Shai Biran/GFP test page]])
To create a green scene link, we will need to use the 'Proteopedia Scene Authoring Tools'.
*After clicking '''edit this page''', scroll down to the bold text that says “Scene authoring tools [show]” next to a colorful molecule. Click on “show” to expand the Scene Authoring Tools.
[[Image:SAT.png]]
*Click on the tab “load molecule” in the Scene Authoring Tools.
*Load the PDB file 1ema by entering the PDB code “1ema” in the input box next to the words “By PDB code:” and then pressing the adjacent button marked “load”
*Now we have 1ema loaded into the Scene Authoring Tools’ Jmol applet. The idea behind the Scene Authoring Tools (SAT) is to create the exact scene that you would like to have load when your green link is clicked. This is generally done by first loading a PDB file into the SAT’s applet, then using the “selections”, “representations”, “colors”, and “labels” tabs to manipulate the 3D model into the desired state, finally saving the green scene link using the “save scene” tab.
*Our structure is currently displayed in cartoon representation. The first step in recreating the picture in the Molecule of the Month is to display the molecule in backbone representation.
*Click on the “selections” tab.
[[Image:Selections.png]]
*In the “all or nothing and halos” section, click on the “select all” button.
[[Image:GFP_Halos_off.png]]
*Nothing changed because “selection halos” were not on. Turn them on by marking the checkbox next to the word “selection halos”.
[[Image:GFP_Halos_On.png]]

Selection halos serve to show you what is currently selected. They will not be displayed when the green scene link you eventually create is clicked.

Now that we have everything selected, click on the “representations” tab of the SAT.
[[Image:Representations.png]]
Mark the checkbox next to “backbone” in the section titled “set selection representation”.
Click on the “set representation” button.
Notice the representation of the 3D model has changed from cartoon to backbone. To help see this better, turn off the selection halos by unmarking the checkbox next to “selection halos”.

[[Image:Backbones.png]]

Now we want to select the segment of the protein that runs through the barrel and color it green.
To make a selection, click on the “selections” tab.
We will select the segment that runs through the barrel by its residue numbers. To do this we need to know the first and the last residue numbers that make up this segment.
Notice that when you hover with your mouse over an atom in the Jmol applet, information about that atom is displayed, including the residue that atom is part of, and the residue number. Use this “hover” feature to find the residue numbers for the beginning and the end of the segment we are interested in.

[[Image:Hover_over_atom.png]]

Enter the starting and ending residue numbers, separated by a hyphen, into the input box under the text “limit to residue numbers:”.
Before making our new selection, let’s turn on selection halos so we see the change in the selection take place. Mark the checkbox next to “selection halos”. Notice that everything is selected.
Now go ahead and make the new selection by clicking “replace selection”. This will replace the old selection (everything) with our new selection (limited to a stretch of residues).
== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai4|Previous page (5)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai6|Next Page (7)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai7

2015-06-01T11:45:30Z

Shai Biran: New page: == Adding a GREEN SCENE LINK 2 == <scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene> *First, let's clean things a bit. Change the heading in your page (where it says 'your head...

== Adding a GREEN SCENE LINK 2 ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>
*First, let's clean things a bit. Change the heading in your page (where it says 'your heading here'). Feel free to choose any new heading you want.
Delete the two rows starting with 'This is a default text...'
*Now let's change the displayed 3D structure into the structure of GFP. In the row starting with StructureSection load change 1stp to GFP's pdb code. Hint - if you're not sure which pdb code to use, look at the GFP test page. Change the caption as well from caption='Caption for this structure’ to caption='GFP (PDB entry [[1ema]])'.
use the 'show preview' button to check what changed in your page.
----

[[User:Shai Biran/Practice Proteopedia tutorial shai6|Previous page (7)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai8|Next Page (9)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai5

2015-02-25T15:54:23Z

Shai Biran:

== Adding a GREEN SCENE LINK ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>
*First, let's clean things a bit. Change the heading in your page (where it says 'your heading here'). Feel free to choose any new heading you want.
Delete the two rows starting with 'This is a default text...'
*Now let's change the displayed 3D structure into the structure of GFP. In the row starting with StructureSection load change 1stp to GFP's pdb code. Hint - if you're not sure which pdb code to use, look at the GFP test page. Change the caption as well from caption='Caption for this structure’ to caption='GFP (PDB entry [[1ema]])'.
use the 'show preview' button to check what changed in your page.
----
Now that we have our 3D model on the page, let’s create a green scene link that shows 1ema as it looks in the the left part of the 2D image on the GFP Sample page where we got our text. (go back to that page to see what the picture looks like [[User:Shai Biran/GFP test page]])
To create a green scene link, we will need to use the 'Proteopedia Scene Authoring Tools'.
*After clicking '''edit this page''', scroll down to the bold text that says “Scene authoring tools [show]” next to a colorful molecule. Click on “show” to expand the Scene Authoring Tools.
[[Image:SAT.png]]
*Click on the tab “load molecule” in the Scene Authoring Tools.
*Load the PDB file 1ema by entering the PDB code “1ema” in the input box next to the words “By PDB code:” and then pressing the adjacent button marked “load”
*Now we have 1ema loaded into the Scene Authoring Tools’ Jmol applet. The idea behind the Scene Authoring Tools (SAT) is to create the exact scene that you would like to have load when your green link is clicked. This is generally done by first loading a PDB file into the SAT’s applet, then using the “selections”, “representations”, “colors”, and “labels” tabs to manipulate the 3D model into the desired state, finally saving the green scene link using the “save scene” tab.
*Our structure is currently displayed in cartoon representation. The first step in recreating the picture in the Molecule of the Month is to display the molecule in backbone representation.
*Click on the “selections” tab.
[[Image:Selections.png]]
*In the “all or nothing and halos” section, click on the “select all” button.
[[Image:GFP_Halos_off.png]]
*Nothing changed because “selection halos” were not on. Turn them on by marking the checkbox next to the word “selection halos”.
[[Image:GFP_Halos_On.png]]

Selection halos serve to show you what is currently selected. They will not be displayed when the green scene link you eventually create is clicked.

Now that we have everything selected, click on the “representations” tab of the SAT.
[[Image:Representations.png]]
Mark the checkbox next to “backbone” in the section titled “set selection representation”.
Click on the “set representation” button.
Notice the representation of the 3D model has changed from cartoon to backbone. To help see this better, turn off the selection halos by unmarking the checkbox next to “selection halos”.

[[Image:Backbones.png]]

Now we want to select the segment of the protein that runs through the barrel and color it green.
To make a selection, click on the “selections” tab.
We will select the segment that runs through the barrel by its residue numbers. To do this we need to know the first and the last residue numbers that make up this segment.
Notice that when you hover with your mouse over an atom in the Jmol applet, information about that atom is displayed, including the residue that atom is part of, and the residue number. Use this “hover” feature to find the residue numbers for the beginning and the end of the segment we are interested in.

[[Image:Hover_over_atom.png]]

Enter the starting and ending residue numbers, separated by a hyphen, into the input box under the text “limit to residue numbers:”.
Before making our new selection, let’s turn on selection halos so we see the change in the selection take place. Mark the checkbox next to “selection halos”. Notice that everything is selected.
Now go ahead and make the new selection by clicking “replace selection”. This will replace the old selection (everything) with our new selection (limited to a stretch of residues).
== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai5|Previous page (6)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai7|Next Page (8)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai5

2015-02-25T15:39:30Z

Shai Biran:

== Adding a GREEN SCENE LINK ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>
*First, let's clean things a bit. Change the heading in your page (where it says 'your heading here'). Feel free to choose any new heading you want.
Delete the two rows starting with 'This is a default text...'
*Now let's change the displayed 3D structure into the structure of GFP. In the row starting with StructureSection load change 1stp to GFP's pdb code. Hint - if you're not sure which pdb code to use, look at the GFP test page. Change the caption as well from caption='Caption for this structure’ to caption='GFP (PDB entry [[1ema]])'.
use the 'show preview' button to check what changed in your page.
----
Now that we have our 3D model on the page, let’s create a green scene link that shows 1ema as it looks in the the left part of the 2D image on the GFP Sample page where we got our text. (go back to that page to see what the picture looks like [[User:Shai Biran/GFP test page]])
To create a green scene link, we will need to use the 'Proteopedia Scene Authoring Tools'.
*After clicking '''edit this page''', scroll down to the bold text that says “Scene authoring tools [show]” next to a colorful molecule. Click on “show” to expand the Scene Authoring Tools.
[[Image:SAT.png]]
*Click on the tab “load molecule” in the Scene Authoring Tools.
*Load the PDB file 1ema by entering the PDB code “1ema” in the input box next to the words “By PDB code:” and then pressing the adjacent button marked “load”
*Now we have 1ema loaded into the Scene Authoring Tools’ Jmol applet. The idea behind the Scene Authoring Tools (SAT) is to create the exact scene that you would like to have load when your green link is clicked. This is generally done by first loading a PDB file into the SAT’s applet, then using the “selections”, “representations”, “colors”, and “labels” tabs to manipulate the 3D model into the desired state, finally saving the green scene link using the “save scene” tab.
*Our structure is currently displayed in cartoon representation. The first step in recreating the picture in the Molecule of the Month is to display the molecule in backbone representation.
*Click on the “selections” tab.
[[Image:Selections.png]]
*In the “all or nothing and halos” section, click on the “select all” button.
[[Image:GFP_Halos_off.png]]
*Nothing changed because “selection halos” were not on. Turn them on by marking the checkbox next to the word “selection halos”.
[[Image:GFP_Halos_On.png]]

Selection halos serve to show you what is currently selected. They will not be displayed when the green scene link you eventually create is clicked.

Now that we have everything selected, click on the “representations” tab of the SAT.
[[Image:Representations.png]]
Mark the checkbox next to “backbone” in the section titled “set selection representation”.
Click on the “set representation” button.
Notice the representation of the 3D model has changed from cartoon to backbone. To help see this better, turn off the selection halos by unmarking the checkbox next to “selection halos”.

[[Image:Backbones.png]]

Now we want to select the segment of the protein that runs through the barrel and color it green.
To make a selection, click on the “selections” tab.
We will select the segment that runs through the barrel by its residue numbers. To do this we need to know the first and the last residue numbers that make up this segment.
Notice that when you hover with your mouse over an atom in the Jmol applet, information about that atom is displayed, including the residue that atom is part of, and the residue number. Use this “hover” feature to find the residue numbers for the beginning and the end of the segment we are interested in.

[[Image:Hover_over_atom.png]]

Enter the starting and ending residue numbers, separated by a hypen, into the input box under the text “limit to residue numbers:”.
== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai5|Previous page (6)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai7|Next Page (8)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai5

2015-02-25T15:39:09Z

Shai Biran:

== Adding a GREEN SCENE LINK ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>
*First, let's clean things a bit. Change the heading in your page (where it says 'your heading here'). Feel free to choose any new heading you want.
Delete the two rows starting with 'This is a default text...'
*Now let's change the displayed 3D structure into the structure of GFP. In the row starting with StructureSection load change 1stp to GFP's pdb code. Hint - if you're not sure which pdb code to use, look at the GFP test page. Change the caption as well from caption='Caption for this structure’ to caption='GFP (PDB entry [[1ema]])'.
use the 'show preview' button to check what changed in your page.
----
Now that we have our 3D model on the page, let’s create a green scene link that shows 1ema as it looks in the the left part of the 2D image on the GFP Sample page where we got our text. (go back to that page to see what the picture looks like [[User:Shai Biran/GFP test page]])
To create a green scene link, we will need to use the 'Proteopedia Scene Authoring Tools'.
*After clicking '''edit this page''', scroll down to the bold text that says “Scene authoring tools [show]” next to a colorful molecule. Click on “show” to expand the Scene Authoring Tools.
[[Image:SAT.png]]
*Click on the tab “load molecule” in the Scene Authoring Tools.
*Load the PDB file 1ema by entering the PDB code “1ema” in the input box next to the words “By PDB code:” and then pressing the adjacent button marked “load”
*Now we have 1ema loaded into the Scene Authoring Tools’ Jmol applet. The idea behind the Scene Authoring Tools (SAT) is to create the exact scene that you would like to have load when your green link is clicked. This is generally done by first loading a PDB file into the SAT’s applet, then using the “selections”, “representations”, “colors”, and “labels” tabs to manipulate the 3D model into the desired state, finally saving the green scene link using the “save scene” tab.
*Our structure is currently displayed in cartoon representation. The first step in recreating the picture in the Molecule of the Month is to display the molecule in backbone representation.
*Click on the “selections” tab.
[[Image:Selections.png]]
*In the “all or nothing and halos” section, click on the “select all” button.
[[Image:GFP_Halos_off.png]]
*Nothing changed because “selection halos” were not on. Turn them on by marking the checkbox next to the word “selection halos”.
[[Image:GFP_Halos_On.png]]

Selection halos serve to show you what is currently selected. They will not be displayed when the green scene link you eventually create is clicked.

Now that we have everything selected, click on the “representations” tab of the SAT.
[[Image:Representations.png]]
Mark the checkbox next to “backbone” in the section titled “set selection representation”.
Click on the “set representation” button.
Notice the representation of the 3D model has changed from cartoon to backbone. To help see this better, turn off the selection halos by unmarking the checkbox next to “selection halos”.

[[Image:Backbones.png]]

Now we want to select the segment of the protein that runs through the barrel and color it green.
To make a selection, click on the “selections” tab.
We will select the segment that runs through the barrel by its residue numbers. To do this we need to know the first and the last residue numbers that make up this segment.
Notice that when you hover with your mouse over an atom in the Jmol applet, information about that atom is displayed, including the residue that atom is part of, and the residue number. Use this “hover” feature to find the residue numbers for the beginning and the end of the segment we are interested in.

[[Image:Hover_over_atom.png]]
Enter the starting and ending residue numbers, separated by a hypen, into the input box under the text “limit to residue numbers:”.
== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai5|Previous page (6)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai7|Next Page (8)]]

== References ==
<references/>

User:Shai Biran/Practice Proteopedia tutorial shai5

2015-02-25T15:38:38Z

Shai Biran:

== Adding a GREEN SCENE LINK ==

<scene name='69/693565/Sticks-gfp/1'>Green Scene Link</scene>
*First, let's clean things a bit. Change the heading in your page (where it says 'your heading here'). Feel free to choose any new heading you want.
Delete the two rows starting with 'This is a default text...'
*Now let's change the displayed 3D structure into the structure of GFP. In the row starting with StructureSection load change 1stp to GFP's pdb code. Hint - if you're not sure which pdb code to use, look at the GFP test page. Change the caption as well from caption='Caption for this structure’ to caption='GFP (PDB entry [[1ema]])'.
use the 'show preview' button to check what changed in your page.
----
Now that we have our 3D model on the page, let’s create a green scene link that shows 1ema as it looks in the the left part of the 2D image on the GFP Sample page where we got our text. (go back to that page to see what the picture looks like [[User:Shai Biran/GFP test page]])
To create a green scene link, we will need to use the 'Proteopedia Scene Authoring Tools'.
*After clicking '''edit this page''', scroll down to the bold text that says “Scene authoring tools [show]” next to a colorful molecule. Click on “show” to expand the Scene Authoring Tools.
[[Image:SAT.png]]
*Click on the tab “load molecule” in the Scene Authoring Tools.
*Load the PDB file 1ema by entering the PDB code “1ema” in the input box next to the words “By PDB code:” and then pressing the adjacent button marked “load”
*Now we have 1ema loaded into the Scene Authoring Tools’ Jmol applet. The idea behind the Scene Authoring Tools (SAT) is to create the exact scene that you would like to have load when your green link is clicked. This is generally done by first loading a PDB file into the SAT’s applet, then using the “selections”, “representations”, “colors”, and “labels” tabs to manipulate the 3D model into the desired state, finally saving the green scene link using the “save scene” tab.
*Our structure is currently displayed in cartoon representation. The first step in recreating the picture in the Molecule of the Month is to display the molecule in backbone representation.
*Click on the “selections” tab.
[[Image:Selections.png]]
*In the “all or nothing and halos” section, click on the “select all” button.
[[Image:GFP_Halos_off.png]]
*Nothing changed because “selection halos” were not on. Turn them on by marking the checkbox next to the word “selection halos”.
[[Image:GFP_Halos_On.png]]

Selection halos serve to show you what is currently selected. They will not be displayed when the green scene link you eventually create is clicked.

Now that we have everything selected, click on the “representations” tab of the SAT.
[[Image:Representations.png]]
Mark the checkbox next to “backbone” in the section titled “set selection representation”.
Click on the “set representation” button.
Notice the representation of the 3D model has changed from cartoon to backbone. To help see this better, turn off the selection halos by unmarking the checkbox next to “selection halos”.

[[Image:Backbones.png]]

Now we want to select the segment of the protein that runs through the barrel and color it green.
To make a selection, click on the “selections” tab.
We will select the segment that runs through the barrel by its residue numbers. To do this we need to know the first and the last residue numbers that make up this segment.
Notice that when you hover with your mouse over an atom in the Jmol applet, information about that atom is displayed, including the residue that atom is part of, and the residue number. Use this “hover” feature to find the residue numbers for the beginning and the end of the segment we are interested in.
[[Image:Hover_over_atom.png]]

Enter the starting and ending residue numbers, separated by a hypen, into the input box under the text “limit to residue numbers:”.
== Next ==

[[User:Shai Biran/Practice Proteopedia tutorial shai5|Previous page (6)]]

[[User:Shai Biran/Practice Proteopedia tutorial shai7|Next Page (8)]]

== References ==
<references/>