iMolecules 3D Help


Help Page iMolecules 3D


If assistance is required with registration or log-in procedures, please contact

Use the Quick Start or Reference Guide for more information on how to use iMolecules 3D. If technical assistance is required with preparation of figures, please contact the Electronic Editor of Protein Science, Doug Juers, at

About iMolecules 3D

The Wiley iMolecules 3D tool is used to create interactive figures based on Jmol to enhance the presentation of macromolecular structures in journal articles. It enables authors to create interactive figures for manuscripts prior to submission and if accepted, figures are displayed in the article online. Registration is required.

Reviewers selecting the link(s) in the manuscript will see the interactive graphic figures hosted on the site (registration is not required).

iMolecules 3D is a joint development project of The Protein Society and John Wiley & Sons. The author tool is Copyright 2009-2011 The Protein Society & Wiley Periodicals, Inc. The current version of the tool is 0.3.10

About Jmol

Jmol: an open-source Java viewer for chemical structures in 3D.


iMolecules3D Frequently Asked Questions

Are interactive images part of the manuscript review process? 

No. Currently (June 2014) the manuscript and the interactive images are reviewed separately. If you prefer the interactive images to be included in the review of the manuscript, the interactive images should be prepared before manuscript submission as described in the iMolecules3D reference guide (pp. 51-52).


How do interactive images get incorporated into the paper?

After you choose “Ready to review” the Protein Science editorial staff will paste URLs into the manuscript. At the proof stage you will have the opportunity to relocate the URLs to a different location in the paper if desired.


I am unfamiliar with Jmol, where can I get more information?

 A good starting point on how to use the JMol applet’s menu is at:

For general Jmol information:


What are the Selection, Rendering and Coloring options in iMolecules all about ?

The Rendering & Coloring options alter the appearance of the currently selected atoms. You can set up various selections with Selection Options. Note that the Selection Options are not display toggles, but affect which atoms are acted on by the Rendering and Coloring options.


How can I create a morph to use in iMolecules?

 One approach is to use rigimol in Pymol to create a multimodel pdb file. The multimodel pdb file can then be read into iMolecules. Below is an example Pymol script used to create a three-state morph.

! Example Three State Morph Script for Pymol
load /Users/juersdh/Documents/Prosci/morphs/a.pdb,amol
load /Users/juersdh/Documents/Prosci/morphs/b.pdb,bmol
load /Users/juersdh/Documents/Prosci/morphs/c.pdb,cmol
create astate,amol & (! resname wat & ! name na & ! name mg ) 
create bstate,bmol & (! resname wat & ! name na & ! name mg )
create cstate,cmol & (! resname wat & ! name na & ! name mg )
from epymol import rigimol
for x in range(51): cmd.create("morph","astate",1,x)
for x in range(51,101): cmd.create("morph","bstate",1,x)
for x in range(101,151): cmd.create("morph","cstate",1,x)
smooth morph,1,50,1,150
! To output as multimodel pdb file: Save -> Molecule -> One file and all states

How can I get different pdb files into different images of the same figure?

·         Create a new figure and click on the icon for it.

·         Click on Images.

·         Click on the icon for Default image and then remove the default image.

·         Click New Image. Enter the image title etc., but not the Molecule or Script data & Save.

·         Click on the icon for your newly created image and upload the pdb file for that image.

·         Create another image in the same way to upload a different pdb file.