Calculate structure
From Proteopedia
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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>) | ||
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| + | 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 command the residues involved in the α-helices and the 3<sub>10</sub>-helices can easily be identified. The turns need some additional explanation. | ||
| - | SUMMARY: | + | SUMMARY:(Key for the structural components is '''H''': α-helix; '''B''': β-bridge; '''E''': β-strand; '''G''': 3<sub>10</sub>-helix; '''I''': π-helix; '''T''': 3-, 4-, 5-turn; '''S''': bend.)<br> |
G : A:12_A:14<br> | G : A:12_A:14<br> | ||
H : A:19_A:37<br> | H : A:19_A:37<br> | ||
Revision as of 18:13, 1 July 2011
An important part of protein structure is the secondary structure which is made up of helices, sheets and turns and Jmol as described in Secondary structure is capable of determining and displaying these three types of structures. The Calculate structure[1] command which re-calculates the secondary structure does a more complete job of identifying and displaying the secodnary structures, is available in Jmol ver. 12, but is not available in Jmol 11.8 which is used in Proteopedia as of June 2011.
Any one page of Proteopedia can be run in the signed ver. 12 by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and reloading the page. The user must give permission for the signed version of Jmol to open, and when it does it has a red frank, whereas in the unsigned version it is grey. Click on the Jmol frank, in the main menu which opens click on Console, in the bottom box enter the commands: select protein; calculate structure; cartoon; color structure and then click Run.
Basis of Secondary Structure Determination
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References
- ↑ A detailed description is at [1].
- ↑ 2.0 2.1 W. Kabsch & C. Sanders, Biopolymers, 22, 2577-2636, 1983.
