User:Nikhil Malvankar/IW2018: Difference between revisions

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How to visualize, understand and share/present 3D protein molecular structures

by ~~Eric Martz~~, ~~2016~~

by Nikhil Malvankar, 2019

for

Adapted from Eric Martz

~~[https://www.micro.umass.edu/courses/catalog~~/~~microbio-497l-advanced-microbiology-lab-techniques Microbiology 497L: Advanced Microbiology Lab Techniques]~~

for

MB&B 420a/720a Macromolecular Structure Fall 2019

University ~~of Massachusetts, Amherst MA~~ USA

Yale University USA

~~ ~~

~~Get here via Moodle or with '''497L.MolviZ.Org'''~~

~~~~

</center>

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## FirstGlance in Jmol ([http://firstglance.jmol.org FirstGlance.Jmol.Org]), making it easy to see key structural features of a macromolecule.

# Take snapshots of your molecule, and paste them into Powerpoint slides, along with your answers.

# Email your .pptx file to ~~'''emartz@microbio.umass.edu'''~~ for grading.-->

# Email your .pptx file to TAs for grading.-->

==I. Getting Started ~~in the [https://www.it.umass.edu/computer-classrooms/it-computer-classroom-fine-arts-center-444 FAC444]~~==

==I. Getting Started==

~~~~

#Use '''FIREFOX''' or Safari.(DO NOT USE Chrome because molecule rotation will be slow/jerky. Internet Explorer and Edge are even worse with this software.)

#Use '''FIREFOX''' or Safari.

#Go to our syllabus.

~~~~

(DO NOT USE Chrome because molecule rotation will be slow/jerky. Internet Explorer and Edge are even worse with this software.)

#Go to our syllabus~~: [http://497L.molviz.org 497L.MolviZ.Org]~~.

#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.

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3. Learn how ''FirstGlance in Jmol'' makes it easy to see structure-function relationships in the protein you chose.

4. Write a report including snapshots of your protein that illustrate your answers to the questions below. (Your report will be in the form of ~~[http://slides.google.com Google~~ Slides] emailed to ~~emartz@microbio.umass.edu~~. You will not present your report in class.)

4. Write a report including snapshots of your protein that illustrate your answers to the questions below. (Your report will be in the form of Slides emailed to TAs. You will not present your report in class.)

==III. Protein Structure and Structural Bioinformatics==

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==VI. Report Slides==

Answer the questions below in slides, using [http://slides.google.com '''Google Slides'''].

Answer the questions below in slides, using [http://slides.google.com '''Google Slides'''] or powerpoint.

*Name your report '''YourLastName-~~497L~~''', for example ~~Sandler~~-~~497L~~. ''If the name of your report does not begin with your family name, you will lose 2 points.'' When completed, email a link to your report to '''~~emartz@microbio.umass.edu~~''' for grading.

*Name your report '''YourLastName-IW2018''', for example Malvankar-IW2018. ''If the name of your report does not begin with your family name, you will lose 2 points.'' When completed, email a link to your report to '''TAs''' for grading.

::(While viewing your report slides, click the blue Share button at the upper right, then Get shareable link, and paste the link into the email.)

::(While viewing your report Google slides, click the blue Share button at the upper right, then Get shareable link, and paste the link into the email.)

:You will ''not'' be asked to present your report in class.

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*Each Section below may be answered in a single slide, or multiple slides. For example, suppose you want to show two snapshots for ''Section 3'', and make separate comments. You may choose to use two slides, labeled ''Section 3A'' and ''Section 3B''.

*For full credit, your slides must include at least 2 animations.

*Additional work beyond the minimum required may earn extra credit.

*Due date: ~~midnight Thursday March 3~~.

*Due date: 22 October 2018 .

This is not a test. It is to help you learn by doing. Ask for help!

[https://~~docs~~.google.com/~~presentation~~/d/~~1wW1fJfRBfQGXjoS989O5Wz2JuBXVU8LPMlhCq~~-~~dadnA~~/~~edit~~?usp=sharing Example of a Completed Report] (You may import these slides into a new presentation of your own, and use them as a templates, putting in your own content.)

[https://drive.google.com/file/d/1EswWlN_X6qwwrkP7d16mLOR0d4-1fVAN/view?usp=sharing Example of a Completed Report] (You may import these slides into a new presentation of your own, and use them as a templates, putting in your own content.)

===Section 1: Identity===

*The label ''Section 1'' at the top (and so forth for every slide).

*Your name.

*Your major; grad students, give the name of your ~~grad program~~ (Micro, ~~MCB~~, etc.) and whose lab you work in.

*Your major; grad students, give the name of your track (Micro, BQBS, MCGD, etc.) and whose lab you work in.

*Your [[PDB identification code]].

*The name of your molecule.

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===Section 3: Evolutionary Conservation===

See [[Introduction to Evolutionary Conservation]].   (Example 4d7b: [http://consurf.tau.ac.il~~/results/1454623073/output_with_form.php ConSurf~~], [http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/atlas/pdb/4d7b_consurf1454623073_pipe.pdb Result])

See [[Introduction to Evolutionary Conservation]].   (Example 4d7b: [http://consurf.tau.ac.il Consurf], [http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/atlas/pdb/4d7b_consurf1454623073_pipe.pdb Result])

Does your molecule have a highly conserved region? If so, what is its function? If there is no highly conserved region, is there a highly variable region? Show two snapshots illustrating a highly conserved region, and a contrasting region.

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===Section 7: Cation-Pi Interactions===

Use [http://capture.caltech.edu/ CaPTURE] program to identify energetically significant cation-pi interactions within proteins

Show a snapshot of an energetically significant [[Cation-pi_interactions|cation-pi interaction]]. Include a distance monitor in your snapshot. Also paste in the report from CaPTURE confirming its energetic significance. The cation-pi interaction tool, and instructions for measuring distances, are in the ''Tools Tab''.

===Section 8: Biological Unit===

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Show side-by-side two snapshots comparing the asymmetric unit with the biological unit. The ''Cartoon'' representation in FirstGlance is best for these snapshots. Make sure to label which is which.

===Section 9~~: Animation from Polyview-3D===~~

===Section 9 - Contacts/Non-covalent Bonds===

~~Minimal steps to make an animation:~~

~~<!--~~

~~#Use the Firefox browser. (Initial orientation, Set by Jmol does not work in Safari.)-->~~

~~#Go to [http://polyview.cchmc.org/polyview3d.html Polyview-3D].~~

~~#Enter your PDB code in the PDB ID slot near the top. (If the slot is not visible, open the section ''Source of Structural Data''.)~~

~~#Change "Type of request" from "Single slide" to "Animation". It is under the ''Image Settings'' section near the bottom.~~

~~#Click any "Preview" link.~~

#Optional: If you want to modify the orientation or zoom of the molecule, click on ''View by Jmol / Set orientation'' under ''Quick links'' at the upper left of the page. Use the mouse to rotate and zoom in Jmol. Then click the ''Set and close'' button.

#Optional: If you want to change the colors, hide portions of the molecule, emphasize certain residues, etc. feel free to try out these options in the form, using ''Preview'' to check your results.

~~#In the "Animation Settings" section at the bottom of the page, set Delay to 10/100.~~

~~#Change "Angle step" to 5 degrees.~~

~~#Check "Rocking".~~

~~#Change "angle range" for rocking to 30 degrees.~~

~~#Click "Submit".~~

The above steps are the minimum for an animation that avoids putting a heavy load on the server. Feel free to try other options, but while the class is in session, please don't make a large (>300 pixel) animation, or increase the angle range, or decrease the angle step size. Otherwise, the server may get overloaded and take a very long time to produce results. Optional: After class is over, feel free to submit more demanding jobs. If you highlight specific residues, please explain why.

~~<!--In Powerpoint, animations move only when the slides are projected (full-screen).~~

'''Method 1:''' When your Polyview-3D job is done, you will see the animation in the web browser. Simply drag the animation directly from the Polyview-3D web page and drop it into a slide. If the result does not animate when you project the slide, try the following method.

~~'''Method 2:''': -->~~

~~After your animation is completed and appears in the PolyView-3D web page:~~

~~#Right-click (Mac: control-click, or trackpad 2-finger click) on the animation in the Polyview-3D web page, and select Save Image As ...~~

~~#Save the image to the Desktop.~~

~~#Drag the image file (filename ending in .gif) from the Desktop and drop it into a slide.~~

~~#In Google Slides, the animation should move immediately.~~

~~~~

[https://docs.google.com/presentation/d/1PAzssvqDRBKFIl9DWvWpXXxM--gtIIdT0p8fMCXfE10/edit?usp=sharing Examples of Slides with Polyview-3D Animations] (These slides are only to show you what is possible. These are not in your assignment.)

~~----~~

~~===Section 10~~ - Contacts/Non-covalent Bonds===

Example: [http://firstglance.jmol.org/fg.htm?mol=4d7b 4d7b].

#Click ''Contacts'' in the ''Tools Tab'' in FirstGlance.

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Describe the moiety you selected as a target. Include a snapshot showing '''exactly one hydrogen bond'''. Be sure to identify the two entities (amino acids, nucleotides, ligand) by name, chain, and sequence number. I need enough detail to be able to reproduce what you are reporting.

===Section 11 - How Structure Supports Function===

===Section 10 - How Structure Supports Function===

Write a brief description ''in your own words'' (avoid plagiarism!) of how the structure of this protein supports its function. Doing some online research will strengthen your description.

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

Section 11 in the [https://~~docs~~.google.com/~~presentation~~/d/~~1wW1fJfRBfQGXjoS989O5Wz2JuBXVU8LPMlhCq~~-~~dadnA~~/~~edit~~?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 27: / Line 27: @@
 <center>
 <span style="font-size:160%">How to visualize, understand and share/present 3D protein molecular structures</span><br>
-<span style="font-size:130%">by Eric Martz, 2016
+<span style="font-size:130%">by Nikhil Malvankar, 2019
 <!--<font color="magenta"> DRAFT UNDER REVISION</font>-->
 </span><br>
-<span style="font-size:115%">for
+Adapted from Eric Martz <br>
-[https://www.micro.umass.edu/courses/catalog/microbio-497l-advanced-microbiology-lab-techniques Microbiology 497L: Advanced Microbiology Lab Techniques]</span>
+<span style="font-size:130%">for
+MB&B 420a/720a Macromolecular Structure Fall 2019</span>
 <br>
-University of Massachusetts, Amherst MA USA
+Yale University USA
-<br>
-<span style="font-size:130%">Get here via Moodle or with <font color="red">'''497L.MolviZ.Org'''</font>
-</span>
 </center>
@@ Line 48: / Line 46: @@
 ## FirstGlance in Jmol ([http://firstglance.jmol.org FirstGlance.Jmol.Org]), making it easy to see key structural features of a macromolecule.
 # Take snapshots of your molecule, and paste them into Powerpoint slides, along with your answers.
-# Email your .pptx file to '''emartz@microbio.umass.edu''' for grading.-->
+# Email your .pptx file to TAs for grading.-->
-==I. Getting Started in the [https://www.it.umass.edu/computer-classrooms/it-computer-classroom-fine-arts-center-444 FAC444]==
+==I. Getting Started==
-<!--#Log in using your Biology Dept. account. If you brought your own '''laptop''', you are welcome to use it. (iPads will be too slow.)-->
+#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.)
-#Use <font color="red">'''FIREFOX''' or Safari</font>.
+#Go to our syllabus.
-<!--: click Spotlight ([[Image:Spotlight-icon.png]] upper right corner of screen), enter "firefox" and click on the top hit. -->
-(DO NOT USE Chrome because molecule rotation will be slow/jerky. Internet Explorer and Edge are even worse with this software.)
-#Go to our syllabus: [http://497L.molviz.org 497L.MolviZ.Org].
 #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.
@@ Line 67: / Line 62: @@
 . Learn how ''FirstGlance in Jmol'' makes it easy to see structure-function relationships in the protein you chose.
+<!--4. Write a report including snapshots of your protein that illustrate your answers to the questions below. (Your report will be in the form of [http://slides.google.com Google Slides] emailed to emartz@microbio.umass.edu. You will not present your report in class.)-->
-. Write a report including snapshots of your protein that illustrate your answers to the questions below. (Your report will be in the form of [http://slides.google.com Google Slides] emailed to emartz@microbio.umass.edu. You will not present your report in class.)
+. Write a report including snapshots of your protein that illustrate your answers to the questions below. (Your report will be in the form of Slides emailed to TAs. You will not present your report in class.)
 ==III. Protein Structure and Structural Bioinformatics==
@@ Line 182: / Line 178: @@
 ==VI. Report Slides==
-Answer the questions below in slides, using [http://slides.google.com '''Google Slides'''].
+Answer the questions below in slides, using [http://slides.google.com '''Google Slides'''] or powerpoint.
-*Name your report '''YourLastName-497L''', for example <font color='red'><b>Sandler-497L</b></font>. ''If the name of your report does not begin with your family name, you will lose 2 points.'' When completed, email a link to your report to '''emartz@microbio.umass.edu''' for grading.
+*Name your report '''YourLastName-IW2018''', for example <font color='red'><b>Malvankar-IW2018</b></font>. ''If the name of your report does not begin with your family name, you will lose 2 points.'' When completed, email a link to your report to '''TAs''' for grading.
-::(While viewing your report slides, click the blue <i>Share</i> button at the upper right, then <i>Get shareable link</i>, and paste the link into the email.)
+::(While viewing your report Google slides, click the blue <i>Share</i> button at the upper right, then <i>Get shareable link</i>, and paste the link into the email.)
 :You will ''not'' be asked to present your report in class.
@@ Line 191: / Line 187: @@
 *Each Section below may be answered in a single slide, or multiple slides. For example, suppose you want to show two snapshots for ''Section 3'', and make separate comments. You may choose to use two slides, labeled ''Section 3A'' and ''Section 3B''.
+*For full credit, your slides must include at least 2 animations.
 *Additional work beyond the minimum required may earn extra credit.
-*<font color="red">Due date: midnight Thursday March 3.</font>
+*<font color="red">Due date: 22 October 2018 .</font>
 <font color='e000e0'>This is not a test. It is to help you learn by doing. Ask for help!</font>
 <br><!--http://bioinformatics.org/molvis/ppt/martz-565-2014rev2.ppt-->
-<span style="font-size:140%;background:#c0ffc0;">[https://docs.google.com/presentation/d/1wW1fJfRBfQGXjoS989O5Wz2JuBXVU8LPMlhCq-dadnA/edit?usp=sharing Example of a Completed Report]</span> (You may import these slides into a new presentation of your own, and use them as a templates, putting in your own content.)
+<span style="font-size:140%;background:#c0ffc0;">[https://drive.google.com/file/d/1EswWlN_X6qwwrkP7d16mLOR0d4-1fVAN/view?usp=sharing Example of a Completed Report]</span> (You may import these slides into a new presentation of your own, and use them as a templates, putting in your own content.)
 ===Section 1: Identity===
 *The label ''Section 1'' at the top (and so forth for every slide).
 *Your name.
-*Your major; grad students, give the name of your grad program (Micro, MCB, etc.) and whose lab you work in.
+*Your major; grad students, give the name of your track (Micro, BQBS, MCGD, etc.) and whose lab you work in.
 *Your [[PDB identification code]].
 *The name of your molecule.
@@ Line 226: / Line 224: @@
 ===Section 3: Evolutionary Conservation===
-See [[Introduction to Evolutionary Conservation]]. &nbsp; (Example 4d7b: [http://consurf.tau.ac.il/results/1454623073/output_with_form.php ConSurf], [http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/atlas/pdb/4d7b_consurf1454623073_pipe.pdb Result])
+See [[Introduction to Evolutionary Conservation]]. &nbsp; (Example 4d7b: [http://consurf.tau.ac.il Consurf], [http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/atlas/pdb/4d7b_consurf1454623073_pipe.pdb Result])
 Does your molecule have a highly conserved region? If so, what is its function? If there is no highly conserved region, is there a highly variable region? Show <font color='e000e0'><b>two snapshots</b></font> illustrating a highly conserved region, and a contrasting region.
@@ Line 245: / Line 243: @@
 ===Section 7: Cation-Pi Interactions===
+Use [http://capture.caltech.edu/ CaPTURE] program to identify energetically significant cation-pi interactions within proteins
 Show a <font color='e000e0'><b>snapshot</b></font> of an energetically significant [[Cation-pi_interactions|cation-pi interaction]]. Include a distance monitor in your snapshot. Also paste in the report from CaPTURE confirming its energetic significance. <font color='gray'>The cation-pi interaction tool, and instructions for measuring distances, are in the ''Tools Tab''.</font>
 ===Section 8: Biological Unit===
@@ Line 255: / Line 257: @@
 Show side-by-side <font color='e000e0'><b>two snapshots</b></font> comparing the asymmetric unit with the biological unit. The ''Cartoon'' representation in FirstGlance is best for these snapshots. Make sure to label which is which.
-===Section 9: Animation from Polyview-3D===
+===Section 9 - Contacts/Non-covalent Bonds===
-Minimal steps to make an animation:
-<!--
-#Use the Firefox browser. (Initial orientation, Set by Jmol does not work in Safari.)-->
-#Go to [http://polyview.cchmc.org/polyview3d.html Polyview-3D].
-#Enter your PDB code in the PDB ID slot near the top. (If the slot is not visible, open the section ''Source of Structural Data''.)
-#Change "Type of request" from "Single slide" to "Animation". It is under the ''Image Settings'' section near the bottom.
-#Click any "Preview" link.<font color='gray'>
-#Optional: If you want to modify the orientation or zoom of the molecule, click on ''View by Jmol / Set orientation'' under ''Quick links'' at the upper left of the page. Use the mouse to rotate and zoom in Jmol. Then click the ''Set and close'' button.
-#Optional: If you want to change the colors, hide portions of the molecule, emphasize certain residues, etc. feel free to try out these options in the form, using ''Preview'' to check your results.</font>
-#In the "Animation Settings" section at the bottom of the page, set Delay to 10/100.
-#Change "Angle step" to 5 degrees.
-#Check "Rocking".
-#Change "angle range" for rocking to 30 degrees.
-#Click "Submit".
-The above steps are the minimum for an animation that avoids putting a heavy load on the server. Feel free to try other options, but while the class is in session, please don't make a large (>300 pixel) animation, or increase the angle range, or decrease the angle step size. Otherwise, the server may get overloaded and take a very long time to produce results. <font color="gray">Optional: After class is over, feel free to submit more demanding jobs. If you highlight specific residues, please explain why. </font>
-<!--In Powerpoint, animations move only when the slides are projected (full-screen).
-'''Method 1:''' When your Polyview-3D job is done, you will see the animation in the web browser. Simply drag the animation directly from the Polyview-3D web page and drop it into a  slide. If the result does not animate when you project the slide, try the following method.
-'''Method 2:''': -->
-After your animation is completed and appears in the PolyView-3D web page:
-#Right-click (Mac: control-click, or trackpad 2-finger click) on the animation in the Polyview-3D web page, and select Save Image As ...
-#Save the image to the Desktop.
-#Drag the image file (filename ending in .gif) from the Desktop and drop it into a slide.
-#In Google Slides, the animation should move immediately.
-<!--http://bioinformatics.org/firstglance/fgij/ppt/polyview-3d-examples.ppt-->
-<span style="font-size:140%;background:#c0ffc0;">[https://docs.google.com/presentation/d/1PAzssvqDRBKFIl9DWvWpXXxM--gtIIdT0p8fMCXfE10/edit?usp=sharing Examples of Slides with Polyview-3D Animations]</span> (These slides are only to show you what is possible. These are not in your assignment.)
-----
-===Section 10 - Contacts/Non-covalent Bonds===
 Example: [http://firstglance.jmol.org/fg.htm?mol=4d7b 4d7b].
 #Click ''Contacts'' in the ''Tools Tab'' in FirstGlance.
@@ Line 307: / Line 273: @@
 Describe the moiety you selected as a target. Include a <font color='e000e0'><b>snapshot</b></font> showing '''exactly one hydrogen bond'''. Be sure to identify the two entities (amino acids, nucleotides, ligand) by name, chain, and sequence number.  I need enough detail to be able to reproduce what you are reporting.
-===Section 11 - How Structure Supports Function===
+===Section 10 - How Structure Supports Function===
 Write a brief description ''in your own words'' (avoid plagiarism!) of how the structure of this protein supports its function. Doing some online research will strengthen your description.
@@ Line 314: / Line 280: @@
 Your description should be at least 75 words. More work, if well done, will earn more credit.
-Section 11 in the [https://docs.google.com/presentation/d/1wW1fJfRBfQGXjoS989O5Wz2JuBXVU8LPMlhCq-dadnA/edit?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==