Calculate structure: Difference between revisions

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* All two-residue T segments indicate β-turns. The turns are often part of an helix, as many as three of the four residues can have the color of the helix. Isolated β-turns have two to three residues colored blue in the structure, rarely four.  
* All two-residue T segments indicate β-turns. The turns are often part of an helix, as many as three of the four residues can have the color of the helix. Isolated β-turns have two to three residues colored blue in the structure, rarely four.  
* T segments that have more than two residues indicate two contiguous or nested β-turns, β-turn nested in a 4- or 5-turn, isolated or nested 4 or 5-turns.  
* T segments that have more than two residues indicate two contiguous or nested β-turns, β-turn nested in a 4- or 5-turn, isolated or nested 4 or 5-turns.  
* After ''calculate structure'' and ''calculate hbonds structure'' has been run the following methods can be used to identify the different types of turns. Blue coloration and the hbond bond between ''i'' and ''i'' + 3 can be used to identify overlapping and isolated β-turns. The 4- or 5-turns which are nested in some way are easily identified by residue ''i'' being involved in at least two hbonds. β-turns VIa1, VIa2, and VIb can be identified by locating a trace that has the appearance of a β-turns and is not colored blue and checking for a cis-Pro at ''i + 2''. (Hover the cursor over the trace to display the name and number of the residues.) Also, the values for phi and psi angles at ''i + 1'' and ''i + 2'' can be [[Psi and Phi Angles|determined]] and compared to the values expected for classes VIa1, VIa2, and VIb.<ref name=beta />
* After ''calculate structure'' and ''calculate hbonds structure'' has been run the following methods can be used to identify the different types of turns. Blue coloration and the hbond bond between ''i'' and ''i'' + 3 can be used to identify overlapping and isolated β-turns. The 4- or 5-turns which are nested in some way are easily identified by residue ''i'' being involved in at least two hbonds. β-turn classes VIa1, VIa2, and VIb (Do not contain hydrogen bonds.) can be identified by locating a trace that has the appearance of a β-turns and is not colored blue and checking for a cis-Pro at ''i + 2''. (Hover the cursor over the trace to display the name and number of the residues.) Also, the values for phi and psi angles at ''i + 1'' and ''i + 2'' can be [[Psi and Phi Angles|determined]] and compared to the values expected for classes VIa1, VIa2, and VIb.<ref name=beta />


=== Illustrations ===
=== Illustrations ===
The user is urged to use the above directions to open Jmol version 12 and to run the ''calculate structure'' and the accompanying commands  so that the resulting display can be compared with the summary below. Without displaying the images generated by ''calculate structure'' and ''calculate hbonds structure'' the activities and comparisons described below can not be performed. Unless a green link is designed to change the color and structural representation, these two display parameters do not change after they have been set by ''calculate structure'', but all hbonds are deleted by clicking a green link so ''calculate hbonds structure'' has to be run from the console after every green link click in order to display hbonds.
Since hbonds are deleted by clicking a subsequent green link, ''calculate hbonds structure'' has to be run from the Jmol console, as described above, after every green link click in order to display hbonds. The display of hbonds can be helpful in identifying turns.


'''Myohemerytherin'''  (<scene name='Calculate_structure/Erythrin/2'>Restore initial scene</scene>)  
'''Myohemerytherin'''  (<scene name='Calculate_structure/Erythrin/2'>Restore initial scene</scene>)  
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