Jmol/Superposition
IntroductionIntroduction
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 structuresLoading 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:
load files "=3HG5" "=3H54"
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 atomsEquivalent 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.
# 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
Compare commandCompare command
The jmol command to superimpose structures is called "compare", and it has a lot of parameters. Here is an example:
compare {2.1} {1.1} ATOMS {~actnagal} {~actgal} ROTATE TRANSLATE
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.
Displaying the superposed structuresDisplaying the superposed structures
Once the structures are superimposed, you can show them using the usual selection and drawing commands. To avoid selecting atoms from the second structure by accident when you just want atoms from the first structure, the easiest is to add a "and 1.1" to your selections. Here is an example of two separate sets of commands to draw a cartoon of the first structure in green and the second in blue.
select protein and 1.1; cartoon; color palegreen; center selected select protein and 2.1; cartoon; color cornflowerblue;
TroubleshootingTroubleshooting
Jmol does not alert you if your sets of equivalent atoms used in a superposition contain different number of atoms. Let's say you made a mistake in your selection and the first atom set contains 50 atoms and the second contains 51. Jmol will just ignore the last atom in the second set. However, your mistake might have messed up the pairing of atoms you intended. The only feedback jmol gives is the so-called RMSD (the root-mean-square distance of equivalent atom pairs). You can also check if your superposition makes sense by displaying both structures, and checking if equivalent atoms are close to each other.
If something did go awry, an efficient way of troubleshooting is to list the selected atoms.
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
DemonstrationsDemonstrations
The opening scene is a result of the following script: 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 0
It is nice to offer the viewer to look at the structures separately, or animate to go back and forth. This makes it easier to see the structures. The four buttons below were created with the following script: <jmol> <jmolButton> <script>!exit; delay 1.2; model 1</script> <text>GAL</text> </jmolButton> </jmol> <jmol> <jmolButton> <script>!exit; delay 1.5; model 2</script> <text>NAGAL</text> </jmolButton> </jmol> <jmol> <jmolButton> <script>!exit; delay 1.5; model 0</script> <text>both</text> </jmolButton> </jmol> <jmol> <jmolButton> <script>animation mode loop; animation on</script> <text>animate</text> </jmolButton> </jmol>
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