Calculate structure: Difference between revisions

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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''.

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'''Calculate structure''' is based on Defined Secondary Structure of Protein (DSSP), a program written in Pascal.<ref name=DSSP>W. Kabsch & C. Sanders, ''Biopolymers'', '''22''', 2577-2636, 1983.</ref> The secondary structure recognition algorithms are based mainly on hydrogen-bonding patterns along with geometric structures , such as bends. There are two different hydrogen-bonding patterns which are recognized. The one determines the value of n in the expression i + n (i is a residue that forms a hydrogen bond with a residue n residues removed from residue i.) where n = 3, 4 or 5. These values define three types of turns. The other recognized pattern is hydrogen bonds which are between residues which are not close together in sequence. This pattern of hydrogen bonds define bridges.

'''Calculate structure''' is based on Defined Secondary Structure of Protein (DSSP), a program written in Pascal.<ref name=DSSP>W. Kabsch & C. Sanders, ''Biopolymers'', '''22''', 2577-2636, 1983.</ref> The secondary structure recognition algorithms are based mainly on hydrogen-bonding patterns along with geometric structures , such as bends. There are two different hydrogen-bonding patterns which are recognized. The one determines the value of n in the expression ''i'' + n (''i'' is a residue that forms a hydrogen bond with a residue n residues removed from residue ''i''.) where n = 3, 4 or 5. These values define three types of turns. The other recognized pattern is hydrogen bonds which are between residues which are not close together in sequence. This pattern of hydrogen bonds define bridges.

==Your Heading Here (maybe something like 'Structure')==<StructureSection load='1dq8' size='500' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[1dq8]])' scene=''>Anything in this section will appear adjacent to the 3D structure and will be scrollable.

Calculate structure: Difference between revisions

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 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''.
 </blockquote>
-'''Calculate structure''' is based on Defined Secondary Structure of Protein (DSSP), a program written in Pascal.<ref name=DSSP>W. Kabsch & C. Sanders, ''Biopolymers'', '''22''', 2577-2636, 1983.</ref> The secondary structure recognition algorithms are based mainly on hydrogen-bonding patterns along with geometric structures , such as bends. There are two different hydrogen-bonding patterns which are recognized. The one determines the value of n in the expression i + n (i is a residue that forms a hydrogen bond with a residue n residues removed from residue i.) where n = 3, 4 or 5. These values define three types of turns. The other recognized pattern is hydrogen bonds which are between residues which are not close together in sequence. This pattern of hydrogen bonds define bridges.
+'''Calculate structure''' is based on Defined Secondary Structure of Protein (DSSP), a program written in Pascal.<ref name=DSSP>W. Kabsch & C. Sanders, ''Biopolymers'', '''22''', 2577-2636, 1983.</ref> The secondary structure recognition algorithms are based mainly on hydrogen-bonding patterns along with geometric structures , such as bends. There are two different hydrogen-bonding patterns which are recognized. The one determines the value of n in the expression ''i'' + n (''i'' is a residue that forms a hydrogen bond with a residue n residues removed from residue ''i''.) where n = 3, 4 or 5. These values define three types of turns. The other recognized pattern is hydrogen bonds which are between residues which are not close together in sequence. This pattern of hydrogen bonds define bridges.
 ==Your Heading Here (maybe something like 'Structure')==<StructureSection load='1dq8' size='500' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[1dq8]])' scene=''>Anything in this section will appear adjacent to the 3D structure and will be scrollable.