Calculate structure: Difference between revisions
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After Jmol completes the ''calculate structure'' computation the results of the computation is printed in the upper box of the console. One part of that output is a summary of the different types of secondary structure with each type having a one letter identifier. It is possible for a residue or a segment of residues to be assigned more than one structural type, for this reason the key list given below is rank ordered in decreasing priority of assignment. With bend having the lowest priority in assignment a structure is identified as a bend only if it is not assigned any other structural type. Below is a copy of the summary for myohemerytherin (2mhr): (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) | After Jmol completes the ''calculate structure'' computation the results of the computation is printed in the upper box of the console. One part of that output is a summary of the different types of secondary structure with each type having a one letter identifier. It is possible for a residue or a segment of residues to be assigned more than one structural type, for this reason the key list given below is rank ordered in decreasing priority of assignment. With bend having the lowest priority in assignment a structure is identified as a bend only if it is not assigned any other structural type. Below is a copy of the summary for myohemerytherin (2mhr): (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) | ||
The user is urged to use the above directions to perform the calculate structure command so that the resulting display can be compared with the summary below. After running the commands the segments displayed as α-helices and 3<sub>10</sub>-helices can easily be associated with peptide segments in the summary. | The user is urged to use the above directions to open version 12 and to perform the ''calculate structure'' command so that the resulting display can be compared with the summary below. Without doing this the images described below can not be observed. After running the commands the segments displayed as α-helices and 3<sub>10</sub>-helices can easily be associated with peptide segments in the summary. | ||
The turns need some additional explanation. One might expect that the segments that have one residue are 3-turns, the segments with two residues are 4-turn and the segments with three residues are 5-turns. This is often the case, but in many cases it is more complex. The turn may overlap with a structure that has higher priority, so therefore these overlapping residues are not included in the summary. Another possibility would be that one turn is nested in a second one. Two determinations can be used to clarify the situation. Displaying the hbonds shows the residues between which the hbond occurs and therefore which type of n-turn is present. If it is a β-turn (4-turn) or γ-turn (3-turn), determining the values of the torsional angles determines its class. | The turns need some additional explanation. One might expect that the segments that have one residue are 3-turns, the segments with two residues are 4-turn and the segments with three residues are 5-turns. This is often the case, but in many cases it is more complex. The turn may overlap with a structure that has higher priority, so therefore these overlapping residues are not included in the summary. Another possibility would be that one turn is nested in a second one. Two determinations can be used to clarify the situation. Displaying the hbonds shows the residues between which the hbond occurs and therefore which type of n-turn is present. If it is a β-turn (4-turn) or γ-turn (3-turn), determining the values of the torsional angles determines its class. | ||
