User:Nikhil Malvankar/MB&B 420a-720a 2019: Difference between revisions

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==I. Getting Started==

#~~Use <font color="red">'''FIREFOX''' or Safari</font>.(DO NOT USE Chrome because molecule rotation will be slow/jerky. Internet Explorer and Edge are even worse with this software.)~~

#Go to '''[http://atlas.molviz.org Atlas.MolviZ.Org]'''.

~~#Go to our syllabus.~~

~~#Now you can see this document in your browser.~~ Go to '''[http://atlas.molviz.org Atlas.MolviZ.Org]'''.

#In the Atlas, choose any molecule deemed ''Straightforward'' and click on the link to '''FirstGlance'''. After a minute or so to load, you should see a rotating molecule.

#If you have any difficulty or the molecule does not appear, ask for help!

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The main tool we will use is '''FirstGlance in Jmol''': [http://firstglance.jmol.org FirstGlance.Jmol.Org]. (To google it later, use the single word (no space) '''firstglance'''.)

* Use '''Firefox''' (or Safari). The molecule will rotate slowly with jerky jumps in other browsers. Internet Explorer and Edge are especially bad for Jmol.

*Enter your 4-character PDB code at FirstGlance, and you should see the molecule you have chosen.

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*In the ''Views'' tab, there are 10 links at the top that show you different aspects of the molecule. Try them all, as well as any of the other tools in FirstGlance that interest you.

~~<ul><ul>~~

FirstGlance does NOT use '''[[Java]]''' unless you tell it to. Using Java will make larger proteins load faster, rotate more smoothly, and change views quicker. Use '''Firefox or Internet Explorer''' (or Safari) for Java. Chrome and Edge do not support Java. In your Java-compatible browser, display a molecule in FirstGlance, and then click on the ''Preferences'' tab in FirstGlance. See [[Installing and enabling Java]].

~~</ul></ul>~~

Here are two Views in FirstGlance that will be used in your report:

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Your description should be at least 75 words. More work, if well done, will earn more credit.

Section 10 in the [https://drive.google.com/file/d/~~1EswWlN_X6qwwrkP7d16mLOR0d4~~-~~1fVAN~~/view?usp=sharing Sample Report] is longer than the minimum required, but illustrates the sort of thing that could be done if you can spend the time.

Section 10 in the [https://drive.google.com/file/d/1NyNhIJTVhmdNwry6Q3nxucig9x6e5-jx/view?usp=sharing Sample Report] is longer than the minimum required, but illustrates the sort of thing that could be done if you can spend the time.

==VII. See Also==

@@ Line 49: / Line 49: @@
 ==I. Getting Started==
-#Use <font color="red">'''FIREFOX''' or Safari</font>.(DO NOT USE Chrome because molecule rotation will be slow/jerky. Internet Explorer and Edge are even worse with this software.)
+#Go to '''[http://atlas.molviz.org Atlas.MolviZ.Org]'''.
-#Go to our syllabus.
-#Now you can see this document in your browser. Go to '''[http://atlas.molviz.org Atlas.MolviZ.Org]'''.
 #In the Atlas, choose any molecule deemed ''Straightforward'' and click on the link to '''FirstGlance'''. After a minute or so to load, you should see a rotating molecule.
 #If you have any difficulty or the molecule does not appear, ask for help!
@@ Line 152: / Line 150: @@
 The main tool we will use is '''FirstGlance in Jmol''': [http://firstglance.jmol.org FirstGlance.Jmol.Org]. (To google it later, use the single word (no space) '''firstglance'''.)
-* Use '''Firefox''' (or Safari). The molecule will rotate slowly with jerky jumps in other browsers. Internet Explorer and Edge are especially bad for Jmol.
 *Enter your 4-character PDB code at FirstGlance, and you should see the molecule you have chosen.
@@ Line 160: / Line 156: @@
 *In the ''Views'' tab, there are 10 links at the top that show you different aspects of the molecule. Try them all, as well as any of the other tools in FirstGlance that interest you.
-<ul><ul>
-FirstGlance does NOT use '''[[Java]]''' unless you tell it to. Using Java will make larger proteins load faster, rotate more smoothly, and change views quicker.  Use '''Firefox or Internet Explorer''' (or Safari) for Java. Chrome and Edge do not support Java. In your Java-compatible browser, display a molecule in FirstGlance, and then click on the ''Preferences'' tab in FirstGlance. See [[Installing and enabling Java]].
-</ul></ul>
 Here are two Views in  FirstGlance that will be used in your report:
@@ Line 280: / Line 274: @@
 Your description should be at least 75 words. More work, if well done, will earn more credit.
-Section 10 in the [https://drive.google.com/file/d/1EswWlN_X6qwwrkP7d16mLOR0d4-1fVAN/view?usp=sharing Sample Report] is longer than the minimum required, but illustrates the sort of thing that could be done if you can spend the time.
+Section 10 in the [https://drive.google.com/file/d/1NyNhIJTVhmdNwry6Q3nxucig9x6e5-jx/view?usp=sharing Sample Report] is longer than the minimum required, but illustrates the sort of thing that could be done if you can spend the time.
 ==VII. See Also==