Jmol/Superposition: Difference between revisions

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compare {2.1} {1.1} ATOMS {~actnagal} {~actgal} ROTATE TRANSLATE

</nowiki>

The first two parameters "{2.1}{1.1}" define which atoms will be affected by the superposition. Here, we choose all of the atoms in the two structures. Next, the atom selections after the "ATOMS" keyword define which equivalent pairs of atoms. Here, we are using the atoms selections previously defined, but you can also use atom selections on the fly. Within these selections, atoms will be paired up in order (first atom in first selection pairs with first atom in second selection, ..., N-th atom in first selection pairs with N-th atom in second selection). If this is not the ~~pair~~ you want, you can split up the selection and add more selection statements, i.e. something like "{selection A of structure 1}{selection A of structure 2}{selection B of structure 1}{selection B of structure 2}...".

The first two parameters "{2.1}{1.1}" define which atoms will be affected by the superposition. Here, we choose all of the atoms in the two structures. Next, the atom selections after the "ATOMS" keyword define which equivalent pairs of atoms. Here, we are using the atoms selections previously defined, but you can also use atom selections on the fly. Within these selections, atoms will be paired up in order (first atom in first selection pairs with first atom in second selection, ..., N-th atom in first selection pairs with N-th atom in second selection). If this is not the pairing you want, you can split up the selection and add more selection statements, i.e. something like "{selection A of structure 1}{selection A of structure 2}{selection B of structure 1}{selection B of structure 2}...".

Finally, the "ROTATE TRANSLATE" keywords do the actual superposition, i.e. ~~changes~~ the coordinates of the first structure (in our case all coordinates because we specified this with the first parameter "2.1"). This change of parameters is permanent, so for all following commands displaying structures, the coordinates will be superimposed.

Finally, the "ROTATE TRANSLATE" keywords do the actual superposition, i.e. change the coordinates of the first structure (in our case all coordinates of the single model in the second structure because we specified this with the first parameter "2.1"). This change of parameters is permanent, so for all following commands displaying structures, the coordinates will be superimposed.

==Displaying the superposed structures==

Jmol/Superposition: Difference between revisions

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 compare {2.1} {1.1} ATOMS {~actnagal} {~actgal} ROTATE TRANSLATE
 </nowiki>
-The first two parameters "{2.1}{1.1}" define which atoms will be affected by the superposition. Here, we choose all of the atoms in the two structures. Next, the atom selections after the "ATOMS" keyword define which equivalent pairs of atoms. Here, we are using the atoms selections previously defined, but you can also use atom selections on the fly. Within these selections, atoms will be paired up in order (first atom in first selection pairs with first atom in second selection, ..., N-th atom in first selection pairs with N-th atom in second selection). If this is not the pair you want, you can split up the selection and add more selection statements, i.e. something like "{selection A of structure 1}{selection A of structure 2}{selection B of structure 1}{selection B of structure 2}...".
+The first two parameters "{2.1}{1.1}" define which atoms will be affected by the superposition. Here, we choose all of the atoms in the two structures. Next, the atom selections after the "ATOMS" keyword define which equivalent pairs of atoms. Here, we are using the atoms selections previously defined, but you can also use atom selections on the fly. Within these selections, atoms will be paired up in order (first atom in first selection pairs with first atom in second selection, ..., N-th atom in first selection pairs with N-th atom in second selection). If this is not the pairing you want, you can split up the selection and add more selection statements, i.e. something like "{selection A of structure 1}{selection A of structure 2}{selection B of structure 1}{selection B of structure 2}...".
-Finally, the "ROTATE TRANSLATE" keywords do the actual superposition, i.e. changes the coordinates of the first structure (in our case all coordinates because we specified this with the first parameter "2.1"). This change of parameters is permanent, so for all following commands displaying structures, the coordinates will be superimposed.
+Finally, the "ROTATE TRANSLATE" keywords do the actual superposition, i.e. change the coordinates of the first structure (in our case all coordinates of the single model in the second structure because we specified this with the first parameter "2.1"). This change of parameters is permanent, so for all following commands displaying structures, the coordinates will be superimposed.
 ==Displaying the superposed structures==