Answer the following questions. SAVE YOUR ANSWERS TO THESE QUESTIONS IN A FILE NAMED zf_model_eval.txt. Save at least one Ramachandran plot in a InsightII folder named Ramachandran_Plot.psv (other objects may also be saved in this file). See the WWW/Alignment/Homology Assignment page for details.
The Homology module is currently licensed only on splatter. Therefore, unless you are working on splatter, it is necessary to run the program remotely on splatter, then display on your local monitor.
To run remotely on splatter,
xhost splatter
telnet splatter (then login)
insightII (to start the program)
This tutorial is MUCH FASTER if you use splatter. If splatter is not in use, choose this woorkstation!
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When you select a N_Std_Dev value in this menu, and select a default color and highlight color, you tell the program to color with the highlite color all CA-N-C-CA atoms that deviate more than N_Std_Dev deviations away from the average; all other angles that are within N_Std_Dev of the average are colored with the default color. This highlites "bad" parts of you model so that you can visualize & fix them. The program uses a N_Std_Dev value of 3 as the default. According to statistical theory, 95% of all measurements should be within 3 standard deviations of the average. (Statistitians say that measurements within 3 standard deviations have met the "95% confidence limit".) When you try this part of the tutorial with a conformer from the PDB, you'll find that nearly all measurements are within 3 standard deviations of their averages (yet it's interesting that some measurements---dihedral angles for end residues for example---are not within 3 standard deviations!). |
| Color | Secondary Structure |
|---|---|
| green | alpha-helix |
| red | beta-sheet |
| purple | reverse turn |
| white | random coil (GorII only) |
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Evaluating Secondary Structure Prediction Graphs
The absolute value of the propensity for a region of residues to form a
particular secondary structure is not useful. Instead, a significantly greater propensity for the most
likely type of secondary structure relative to the other less likely
secondary structures is important.
Secondary structure prediction methods are known to be only moderately accurate. To improve your confidence in a secondar structure prediction, PERFORM A MOLECULAR MODELING EXPERIMENT: try more than one prediction algorithm (e.g., Chou-Fasman and GorII) and compare their results. The contents of your znf_cf.htbl and znf_gorII.htbl files list the numbers used in these graphs and provide further details. |
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Evaluating Buried Polar Atoms
The information provided by InsightII to evaluate buried polar atoms is numerical, and not visual.
Therefore, evaluating buried polar atoms is not straightforward. Also, for this tutorial, almost
all residues are exposed to solvent, because the zinc finger structure is relatively small (only 34 residues).
The name_area.tab file lists surface areas for each residue. This table can be used
to identify polar residues that have relatively low surface areas, and therefore may be buried.
To filter
for particular residues, type
The name_polarity.tab file lists surface areas for each atom. This table can be used
to identify polar atoms that have relatively low surface areas, and therefore may be buried. To filter
for particular atoms, type |