Jmol/Superposition: Difference between revisions
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==Introduction== | ==Introduction== | ||
Superpositions (or overlays) are a way to compare two structures by moving them on top of one another so the "equivalent atoms" are close to one another. Because the two structures are different, not all equivalent atoms can match at the same time. Instead, you minimize the root-mean-square of the distances to achieve a compromise. If you want to see superpositions in the context of a proteopedia page (and look at the underlying jmol scripts), take a look at [[Garman lab: Interconversion of lysosomal enzyme specificities]] and [[Schubert lab: bacterial InIC disrupts human Tuba complexes]]. | This page is a tutorial on how to superimpose two structures in jmol and show them in proteopedia. Superpositions (or overlays) are a way to compare two structures by moving them on top of one another so the "equivalent atoms" are close to one another. Because the two structures are different, not all equivalent atoms can match at the same time. Instead, you minimize the root-mean-square of the distances to achieve a compromise. If you want to see superpositions in the context of a proteopedia page (and look at the underlying jmol scripts), take a look at [[Garman lab: Interconversion of lysosomal enzyme specificities]] and [[Schubert lab: bacterial InIC disrupts human Tuba complexes]]. | ||
==Loading two structures== | ==Loading two structures== | ||
Before you can superimpose two structures in jmol, they have to be loaded at the same time. The "load files" command accomplishes that. In the following, the related structures with the PDB IDs 3HG5 and 3H54 are loaded: | |||
<nowiki> | |||
load files "=3HG5" "=3H54" | |||
</nowiki> | |||
Once they are loaded, you refer to them as "1.1" and "2.1". The number before the decimal point refers to the two structures, while the "1" after the decimal point refers to the first model in the respective coordinate set. (If you want to superimpose different parts of a single structure, for example the two subunits in a dimer, you just load one structure, and access the subunits via the chain identifier - examples will follow). | |||
==Equivalent atoms== | |||
You have to choose which sets of atoms should be superimposed, i.e. the distances of which pairs of atoms should be minimized. In this example, we choose the alpha carbons of the respective active sites, but other choices are possible. In jmol, you need two atom selection expressions, one for each structure. Because you want pairs of equivalent atoms, the number of atoms selected in the first structure should be equal to the number of atoms selected in the second set. In our example, we first define two atom selections, and then use these later. | |||
<nowiki> | |||
# define active site C-alpha atoms | |||
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *.CA:A | |||
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *.CA:A | |||
</nowiki> | |||
==Compare command== | |||
The jmol command to superimpose structures is called "compare", and it has a lot of parameters. Here is an example: | |||
<nowiki> | |||
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}...". | |||
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. | |||
<nowiki> | |||
load files "=3HG5" "=3H54" | |||
restrict none # display is cleared | |||
# define active site residues and superimpose structures | |||
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A | |||
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A | |||
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~actnagal and *.CA}{~actgal and *.CA} ROTATE TRANSLATE | |||
select protein and 1.1; cartoon; color palegreen; center selected | |||
select 801-802; wireframe 100; color cpk | |||
select protein and 2.1; cartoon; color cornflowerblue; | |||
select 1000,2000; wireframe 100; color cpk | |||
select group within(3.0, (BMA, NAG, MAN)) and (sidechain or *.CA) | |||
select selected or (BMA, NAG, MAN); wireframe 50 | |||
model 1 # or model 2 | |||
</nowiki> | |||
==Demonstrations== | ==Demonstrations== | ||
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> | <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> | ||