Teaching Points (and troubleshooting) for PyMol 2 lab

Make sure they save their files often (preferably naming session files with different names every once in a while)

They have some pre-lab exercises. They should write brief methods for these in the lab notebook, but not the report. However, they will need to save images of each pre-lab exercise for the Appendix (that will go on the end o f their report)

The rotamers percentage that is shown in PyMol is a representation on how frequently that conformation shows up in the PDB out of all of the other possibilities.

Volume= 4/3pi (r^3)                                  ~  3.26631E-20            cm^3


MW     20,000 daltons

1 dalton =        1gram/(6.02×10^23)

3.32E-20          grams for one molecule of DHFR     20,000/ 6.02×10^23

3.32E-17          mg

3.32E-14          ug

3.32E-11          ng

Calculated Density of protein = mass/volume = grams/cm^3

(use grams above and cm^3 above)

1.02     g/cm^3

Density of water

1                    g/cm^3

For DHFRcats – there are two parts – the Ionic interactions and then the Hydrogen bonds within a Beta-sheet (these are two separate locations on the protein)

To label the DHFRcats, they can use:

label (DHFRcats & n;ca), resi  + resn

There should be 5 ionic contacts between phosphate oxygens and positively charged amino acids (DHFRcats)

The beta-sheet is the one from the pre-lab exercises


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