Teaching+Points+for+Labs+Spring+12

Teaching Points For VDS Spring 2012 Labs
=Enzyme Assay Lab= **File Not Found**

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They can use multiple cuvettes to do their readings faster (i.e. have 9 or 10 of the same cuvettes instead of washing one multiple times)

Make them save their spectrophotometer file – NameEnzymeAssayDATE Make them save their spectrophotometer file – NameEnzymeAssayDATE Make them save their spectrophotometer file – NameEnzymeAssayDATE

MAKE sure they clean up afterwards before you sign them out.

=VS3 lab= **File Not Found**

= = =Protein Characterization Lab= **File Not Found**

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=Virtual Screening 2= **File Not Found**

= = =Protein Purification Lab= **File Not Found**

= = = = =Virtual Screening 1= **File Not Found**

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=PyMol3= **File Not Found**

= = =Buffer Titration= **File Not Found**



Henderson-Hasselbalch exercise answer sheet (password protected).

they need to have all 3 titrations on the same graph in the end - to do so, they will need to creat 3 calculated volume columns and give them each a different name (e.g. CV1, CV2, and CV3).
 * Tips & Hints**

=PyMol2= **File Not Found**



show them how to use UT Webspacehttps://webspace.utexas.edu/xythoswfs/. to save their Image (.png) and Session (.pse) files. The first time they use it the have to 'sign up' on the Sign Up page. Also there is an 'Advanced Upload' button that lets them have a drag and drop folder instead of uploading each file individually. (Much faster).
 * Tips & Hints**

=Beer's Law= **File Not Found**



warm up specs for about 10 minutes before use Henry spec reads very high on the Absorbance values - need to make sure they don't record their data if it is saturating the dector (>1.5 or 2 on the absorbance units)
 * Tips & Hints**

Students should empty their cuvettes between EACH reading (i.e. for n=3 replicates, they shoudl empty the cuvette 3 times). This takes longer but reinforces that just hitting the COLLECT button 3 times on the exact same sample does not constitute a true replicate. To speed things up - they can get 3 cuvettes at a time and fill with a given dilution (Dil1, Dil2, Dil3, etc.) -- then measure 3 in a row quickly.

They don't have to measure Dilution 1 - IF they know it is going to be above 1.5 Absorbance units.

=PyMOL1=

this one is locked with the Mentor password (ask another mentor if you can't remember it!)
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Lab Notebook should include Lab Safety - no liquids in lab to prevent electrocution Materials - computer, PyMol program, helix.pdb, Betasheet.pdb
 * Tips & Hints**

Figure captions - should include "carbons as green, oxygens as red, nitrogens as blue ....... etc. "


 * Timestamp for Word:** ALT + i together, release and hit T
 * Date Stamp for Excel:** CTRL + ;
 * Time Stamp for Excel:** CTRL + SHFT + :

Show them how to do CROP in Word - to resize images.

When measuring across the helix for the diameter, they won't be able to go directly across the width(it will be on an angle). They should be sure to address this in their comments and/or error analysis.

PyMol 3
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