Adding Structural Supports
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This Jmol Training Guide was created with funding from NIH Grant #1 R25 RR022749-01 and NSF-DUE #1323414 using the Jmol e-Poster Creator from the MSOE Center for BioMolecular Modeling

version 1.0
Adding Hydrogen Bonds, Disulfide Bonds, and Struts in Jmol

Unless otherwise indicated, this section of the Training Guide uses the protein Top 7 based on PDB file 1qys.pdb. Please see Getting Started with Jmol for information on how to download and open PDB files.

Hydrogen Bonds

Hydrogen bonds (referred to as "hbonds" in Jmol) are essential to the stability of secondary structures in a protein. They form between the backbone oxygen of one amino acid and the backbone nitrogen in a second amino acid.

Adding Hydrogen Bonds

To add hydrogen bonds to secondary structures within your model, use the calculate hbonds command. We typically do not add hydrogen bonds to alpha helices, since they do not add stability to the model and actually clutter the view of the structure. Adding hydrogen bonds to beta sheets provides additional support for the final model and is recommended. Use the following commands:

select sheet

calculate hbonds

Click the button below to see hydrogen bonds calculated in the beta sheets of Top 7.

Calculate hbonds

After you have entered this command, you will notice that dotted lines have appeared. These are the hydrogen bonds.

Giving Hydrogen Bonds Thickness

Hydrogen bonds, like wireframe, backbone, and spacefill, can be thickened by placing a number after the hbonds command. The standard size for building a physical model is 1.0 Ångström.

hbonds 1.0

Hbonds 1.0


Making Hydrogen Bonds Solid

The default display for hydrogen bonds is a dashed line. You will need to change this into a solid cylinder for building a physical protein model using 3D printing. You can do this using the command:

set hbonds solid

Set hbonds solid

Attaching Hydrogen Bonds to the Backbone

Notice that the hydrogen bonds are now thicker and solid, but that they appear to be floating in air. This appearance results from the fact that hydrogen bonds form between the backbone atoms of the amino acid (the nitrogen and the oxygen atoms), but since we have displayed only the alpha carbon atoms in Backbone Format, it appears as if the hydrogen bonds are floating in space. Therefore, we must set the hydrogen bonds to the backbone using the command:

set hbonds backbone

Set hbonds backbone

Summary of Commands to Add Hydrogen Bonds

select sheet

calculate hbonds

hbonds 1.0

set hbonds solid

set hbonds backbone

Note: Jmol recognizes both terms hbonds and hbond.

Removing All Hydrogen Bonds

To turn off all of the hydrogen bonds in the selected area, use the hbonds off command.

select sheet

hbonds off

Locating Triangle Bonds

When Jmol calculates hydrogen bonds, it occasionally inserts a hydrogen bond between two amino acids on the same strand, with a single amino acid between the two. If the first amino acid is residue number N then the second amino acid is residue number N+2. Because the backbone and hydrogen bond form a triangle, we refer to these rogue hydrogen bonds as "triangle bonds". These need to be identified and removed from your structure.

Note: Before searching for triangle bonds, save your model design! These instructions will make it easy to spot triangle bonds, but you will not want to lose all your work.

After you have displayed hydrogen bonds in your model and saved your work, enter the following command:

restrict sheet

The restrict command turns of the display of any portions of the molecule that are not identified in the command. Using restrict sheet turns off everything but the sheets. Even though you don't see the rest of the molecule, it is still present in the pdb file.

To see a triangle bond in acetylcholinesterase, based on 1eve.pdb, click the button below. Note that in the script that is executed, we have colored the triangle bond blue (see Coloring Bonds below), and we have added rotation to focus on the triangle bond. (See Advanced Scripting for details on the show orientation and moveto commands.)

Acetylcholinesterase - Triangle Bond

Once you have identified a triangle bond, click on the two amino acids to identify the residue numbers. Residue numbers should be two amino acids apart (N and N + 2). See below for instructions on removing a single hydrogen bond.

Adding or Removing Individual Hydrogen Bonds

At times you may want to add or remove a single hydrogen bond. First, you need to know the two amino acid residue numbers that the hydrogen bond connects. To do this, click on the two residues in the Display Window (see Getting Started for more information on identifying residue numbers). Once you know the two residue numbers, you must select only these two amino acids. Finally, use the hbonds 1.0 command to add a hydrogen bbond or the hbonds off command to remove the hydrogen bond between the two selected amino acids.

To add a hydrogen bond between two amino acids 73 and 167:

select 73 or 167

hbonds 1.0

To remove a hydrogen bond between amino acids 321 and 323:

select 321 or 323

hbonds off

Disulfide Bonds

Some molecules will have disulfide bonds (referred to as "ssbonds" in Jmol) present within the structure. These bonds form between two cysteine amino acids that lie close to each other in 3D space. Disulfide bonds are added using the command ssbonds on.

Not every PDB file has disulfide bonds. Since Top 7 does not have a disulfide bond, we will use human insulin (2hiu.pdb) to display disulfide bonds.

ssbonds on

ssbonds on

Note: Jmol recognizes both terms ssbonds and ssbond.

Adjusting Thickness of Disulfide Bonds

As we saw with the hydrogen bonds, simply typing ssbonds by itself will only produce thin lines. To give these bonds dimension, we must add a thickness (number) to the ssbonds. The standard thickness for building a physical model is 1.0 Ångström.

ssbonds 1.0

ssbonds 1.0

Setting Disulfide Bonds to the Backbone

Notice that this command gives the disulfide bonds a thicker dimension, but as we saw with hydrogen bonds, the bonds are "floating" in space. This is because the disulfide bond is actually between the sulfur groups of the cysteine sidechains, and not the alpha carbons. To make the disulfide bond connect between the backbone units, we need to set the bonds to the backbone. Note that the disulfide bond is yellow (the CPK color for sulfur).

set ssbonds backbone

set ssbonds backbone

Note: You may wish to display the sidechains of the cysteines involved in the disulfide bond. If that is the case, then you will not need to set ssbonds to the backbone.

Adding or Removing Individual Disulfide Bonds

At times you may want to add or remove a single disulfide bond. You first need to know the two amino acid residue numbers that the bond connects. To do this, click on the two residues in the Display Window (see Getting Started for more information on identifying residue numbers). Once you know the two residue numbers, you must select only these two amino acids. Finally, use the ssbonds 1.0 command to add a disulfide bond or the ssbonds off command to remove the bond between the two selected amino acids.

To add a disulfide bond between amino acids 29 and 93:

select 29 or 93

ssbonds 1.0

To remove a disulfide bond between amino acids 44 and 168:

select 44 or 168

ssbonds off

Struts

When a model is built on a 3D printer, additional support struts are added within the model to provide stability and durability. To add struts, select your entire model, and use the calculate struts command.

select all

calculate struts

calculate struts

Because you've already added hydrogen bonds to your beta sheets, you don't also need to add struts to the beta sheets. Use the next set of commands to remove the struts within the beta sheets, while keeping the struts between the beta sheets.

select sheets

connect strut delete

removing struts between beta sheets

Note: Jmol recognizes both terms struts and strut.

Giving Struts Thickness

Struts, like hydrogen bonds and disulfide bonds, can be set to different thicknesses by adding a number after the strut command. The standard thickness for building a physical model is 1.0 Ångström.

strut 1.0

strut 1.0

Summary of Commands to Add Struts

select all

calculate struts

struts 1.0

select sheets

connect strut delete

Adding or Removing Individual Struts

At times you may want to remove a single strut (for example, if it goes through a sidechain you have represented). You first need to know the atom numbers of the two atoms the strut connects. To do this, click on the two atoms in the Display Window (see Getting Started for more information on identifying atom numbers). Once you know the two atom numbers, you must select only those two atoms using the select atomno= command. Finally, use the struts 1.0 command to add a strut or the strut off command to remove the bond between the two selected atoms.

To add a strut between atom numbers 172 and 863:

select atomno=172 or atomno=863

connect strut

strut 1.0

To remove a strut between atom numbers 227 and 1120:

select atomno=227 or atomno=1120

connect strut delete

Note: The calculate strut command may not always provide enough structural support. Additional struts may be necessary. In addition, struts will need to be added manually to attach any ligands (substrate, inhibitor, cofactors) to the protein, or to indicate any specific bonds.

Coloring Bonds and Struts

Default Bond Colors

When bonds or struts initially appear, they will be the default Jmol colors (a translucent white for struts and the colors of the atoms that they connect for hydrogen and disulfide bonds).

  • If the two atoms the bond is connecting are the same color, then the hydrogen or disulfide bond will be the same color throughout the entire length of the bond.
  • If the two atoms are different colors, then the hydrogen or disulfide bond will be half one color and half the other color.

Changing the Color of All Bonds

To color all of a certain type of bond or strut, select all and then use the color command followed by the type of bond or strut you want to color and then the color you would like to color them.

For example, to color all of the hydrogen bonds red:

select all

color hbond red

color hbond red

To color all of the struts blue:

select all

color strut blue

color strut blue

Note: We recommend that you choose a light color for your struts, such as white or light gray. Struts are support structures and should not be the emphasis of your model. A vibrant or dark color will draw the user's eye to the struts, and that should not be the focus of your model. Similarly, if you don't want the focus of your model to be on the hydrogen or disulfide bonds, these should be soft colors.

Changing the Color of a Single Bond

At times, you may wish to emphasize a specific bond that is important to the function of your protein. Follow the same steps for removing an individual bond or strut. Identify the two atom numbers that the bond or strut connects. Then, select only those two atoms. Finally, use the color command to apply the new color.

For example, to turn the hydrogen bond between atom numbers 333 and 65 green:

select atomno=333 or atomno=65

color hbond green

color hbond green


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