iMolecules 3D Reference Guide

Reference Guide
iMolecules 3D Reference Guide
Contents
Introduction ...................................................................................................................................................................2
Basic steps .....................................................................................................................................................................3
The iMolecules 3D Author Tool Schematic ....................................................................................................................4
Register in iMolecules 3D ..............................................................................................................................................5
Create a manuscript ......................................................................................................................................................8
Sharing the tasks in iMolecules 3D ................................................................................................................................9
Create a figure .............................................................................................................................................................10
Add files to a figure ........................................................................................................................... 13
How to prepare the Initialization and Reset script files (.spt files) ................................................... 16
Enhancing the molecule’s visual appearance.................................................................................... 17
Preparing the state file externally ..................................................................................................... 18
Adding images ................................................................................................................................... 23
Adding figures ................................................................................................................................... 24
Two or more figures ....................................................................................................................................................25
Review your Figure text ...............................................................................................................................................27
Static image for article publication ..............................................................................................................................28
Figures Ready for Review ............................................................................................................................................29
Revisions during peer-review [optional] .....................................................................................................................30
Author Proofing after typesetting ...............................................................................................................................31
Online Publication .......................................................................................................................................................32
Linking to your published paper ..................................................................................................................................32
Linking to your published figures ................................................................................................................................32
Getting help ....................................................................................................................................... 33
Forgotten password .......................................................................................................................... 33
Collaboration – help uploading files and creating figures ................................................................. 33
Previewing your figures ..................................................................................................................... 35
Generating URLs for links to figures .................................................................................................. 35
Indicating figures are Ready for Peer Review ................................................................................... 35
Assign co-author................................................................................................................................ 36
Saving a figure as a template ............................................................................................................ 36
Sorting figures ................................................................................................................................... 39
Sorting images ................................................................................................................................... 42
Animated v non-animated figures..................................................................................................... 44
Non-animated figures ................................................................................................................... 45
Animated figures ........................................................................................................................... 46
Deleting images and figures .............................................................................................................. 47
Deleting images ............................................................................................................................ 47
Promoting/Demoting figures (from Intermediate to Expert authoring mode and back) ................. 49
Using multi-part Figures .................................................................................................................... 51
Author Workflow............................................................................................................................... 51
Correcting Published Figures ............................................................................................................. 52
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Introduction
The Wiley iMolecules 3D tool is used to create interactive figures based on Jmol to enhance
the presentation of macromolecular structures in Protein Science articles. It enables authors
to create interactive figures for manuscripts prior to submission and if accepted, figures are
displayed in your article online. Registration is required. Your e-mail address will be your
username.
Reviewers selecting the link(s) in your manuscript will see the interactive graphic figures
hosted on the site (registration not required). This document contains instructions on how
and where to add links to your figures in your manuscript document. You may wish to
consult the journal’s Author Guidelines for more information on preparation of your
manuscript. A link to the Author Guidelines is found in the For Authors menu on each page
of the iMolecules 3D author tool.
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Basic steps
1) Register in iMolecules 3D.
2) Set up an iMolecules 3D manuscript project or directory (basically this is a
complement to the manuscript of the article to be submitted to the editorial office
for consideration to be published in the journal; in iMolecules 3D, it is a collection of
all the files for all figures for only one manuscript).
3) Create your interactive figures – where a figure basically consists of the molecule
data part and a control file. The molecule data is usually a .pdb file (other formats
could be used as well – see the Jmol page...) containing the structural information
(3D coordinates, 2D sequence information etc), while the control file holds the
information how the molecule data is to be presented/rendered.
4)
5)
6)
7)
8)
9)
10)
Review figures and captions.
Create a high-resolution Static image for each interactive figure in your paper.
Embed links to your interactive figures into your manuscript document.
Submit your manuscript to the Editorial Office.
Revise, if requested.
Author proofing, when accepted (along with the manuscript).
Online Publication
These steps are outlined in detail in the document below.
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The iMolecules 3D Author Tool Schematic
The author creates one folder or directory (and perhaps, eventually more than one)
iMolecules 3D ‘manuscript’ – so the highest level is that of the manuscript. For each
manuscript several figures could be created – where each figure could contain several
images.
The images in each figure are usually combined by context, e.g. showing the same protein in
different presentations – which means the molecule data file would be the same, while
there are different control files allowing different aspects of the structure to be highlighted.
In this case it is possible to specify the molecule data file on the ‘figure’ level (if there is no
other molecule data file specified in an image, the image ‘inherits’ the molecule data file
definition from the figure). The advantage is that a molecule data file (which can be huge)
could easily be reused in different images.
The architecture also allows enough flexibility to define different molecule data files, so that
each image (within a figure) could show a different structure (e.g. closely related structures
or just motifs...)
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Register in iMolecules 3D
http://imolecules3d.wiley.com/
Registration is a two-step process:
1. REGISTER, and provide your e-mail address. The system will send you a temporary
password.
2. LOG IN with your temporary password. You may change it to something more
memorable after login. Passwords are case sensitive.
Need Help? Contact [email protected] and provide the e-mail address where you
registered.
Welcome screen:
The sample image links to a published interactive figure. You may also read the paper
published online; note how interactive graphics are linked from the paper at the end of each
figure caption.
Note: any person familiar with Jmol may register as an author to create interactive graphics
to illustrate a scientific paper, such as a graduate student or post doc. It is not a requirement
that one of the named authors on a paper become the lead author using the tool. In this
case, the Electronic Editor may query the relationship of the lead author to the authors of
the paper for clarification.
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Use ‘Log in’ if you already registered and have a username and password for your
iMolecules 3D account. If not, use ‘Register Now’ to set up an account:
Fill in the fields in the ‘Self Registration’ dialog screen and when done click Proceed with
Registration to submit your registration data to the tool. You’ll be prompted with a
confirmation as shown in the following figure:
Note: Your password for iMolecules 3D will not be provided on the confirmation screen, but
be sent to the e-mail address you provided in the step above. Passwords are case sensitive.
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Once you have received your password go back to the Welcome page and use ‘Log in’ in the
left menu to get to the log-in screen:
After successful log in you will see the following screen (assuming that this is the first time
you log in and no manuscript has been set up before):
Note: You may change the password to something more
memorable by selecting your name, displayed in teal blue, in
the logged in area. Remember, passwords are case sensitive.
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Create a manuscript
This step creates the folder or directory for the interactive figures in your manuscript. It also
captures article-level details that pertain to all figures in your manuscript (such as title and
authors). These details are displayed on the interactive graphic linked from your published
article.
1. Select New Manuscript in left column under ‘ACTIONS’
2. Type the title of your manuscript in the field ‘Manuscript full title’ as it will appear
on your published article (this will be used on-screen at your published figure) – you
may edit this later.
a. Type the authors in the order they should appear in the attribution (this will
be used on-screen at your published figure) – you may edit these later.
Please follow the journal style. See the Author Guidelines for details (link in
left menu).
b. Other fields are optional at this point
i. Once submitted to the Editorial Office, the Description field may be
used to record the manuscript number.
ii. Once your article is accepted and published online, the Wiley
Production Editor will add Abstract’s URL and the article DOI. The
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Abstract URL will be used to link the figure to the published abstract
in Wiley Online Library.
c. Save the record.
Please see the next section ‘Create a figure’ for how to set up interactive figures for your
new manuscript.
Sharing the tasks in iMolecules 3D
NOTE: Please do not share your log-in details. If you have
co-authors or colleagues who will be assisting you in
uploading Jmol files or using this tool to prepare the
interactive figures, you may nominate them for
independent access.
Once you have created the ‘Manuscript’, select the Collaboration tab and provide your
co-authors’ e-mail addresses. When they register with the same e-mail addresses you
provided, they are automatically permitted to work on files relating to your manuscript.
Only the lead author can indicate Collaborations and specify that the manuscript is
ready for peer review; co-authors are not permitted these actions. For more
information, please see the instructions in Collaboration in the reference section of this
document.
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Create a figure
To the left of the manuscript name under “Actions”, click on the teal blue icon
select that manuscript.
a. You’ll see the General Properties
b. Click on Figures tab
i. Before adding any figures, you’ll see it says “no records found.’
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c. To add a Figure, from Left menu, select New Figure.
d. Select a template – click on
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button to see the loaded templates.
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NOTE: See the Reference section below on how to save a figure as a template.
Saving the figure as a template allows you to use the template to create
subsequent figures using the same settings.
e. Select one of the Default Intermediate Figure Templates.
f. Type the Figure short title and full title and enter the figure number.
g. Click OK.
You may continue to add new figure titles for all the figures, or go on to upload the files for
one figure next and then come back here and add additional titles and their files later.
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NOTE: The Figure titles should match those in your
manuscript. You may edit these later if required prior to
publication.
Add files to a figure
Now prepare to add the files for a figure: to the left of the Figure name under “Actions”,
click on the teal blue icon
to select that figure.
You’ll see the General Properties of the figure selected in the previous step:
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Go to the ‘Default Image Settings’ tab – this will allow you to specify the molecule data and
control files:
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Click on
the ‘upload’ icon in the line ‘Molecule Data File:’ to upload your structure data
(e.g. a .pdb file). Do the same for the Initialization and Reset Script files. You could prepare
these offline by downloading Jmol and running it on your own computer, or online after
uploading a molecule data file into the tool and clicking on ‘Preview’ which will load a Jmol
applet in a new browser window.
Then adjust the presentation of your structures within the tool, and if satisfied with it, save
the ‘state’ to an .spt file which you could then upload a Initialization Script File.
NB: The uploaded file is automatically compressed and stored as a .zip file.
Figure: Showing that a molecule data file has been uploaded.
Note: If you have prepared the files offline using Jmol, double-check the version you
use; files created with a different version than the one used in this tool may not
include all the functionality. The version of Jmol in iMolecules 3D is shown in the
Help page accessible from the
icon. As a check, always use the Preview feature
in the tool once you have uploaded your file.
Expert Mode
If you are proficient at Javascript, you may wish to create your own scripts/files. If so, the
Promote mode link changes the authoring mode to Expert for that figure. The Electronic
Editor can provide help and advice. See the Reference Section below for more details.
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How to prepare the Initialization and Reset script files (.spt files)
Using the tool’s built-in Jmol applet
Once you have uploaded your molecule data file, click the Preview action. This opens a new
window showing the default settings for the Selection and Rendering options. Since no
commands are yet applied to the molecule data, you will not see your structure.
To make sure that it really is loaded, either use the buttons in the ‘Rendering Options’ box
or move your mouse into the empty display area and click with the right mouse button (or if
you have a single-button mouse, holding the Control key pressed while clicking into the
display area). This will bring up a menu from which you will set different presentation and
coloring styles.
If you want to start learning more about Jmol see
the Jmol documentation for details at
http://jmol.sourceforge.net/docs/ . A good starting
point on how to use the Jmol applet’s menu is given
at:
http://higheredbcs.wiley.com/legacy/college/boyer
/0471661791/structure/jmol_intro/jmol.htm
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Enhancing the molecule’s visual appearance
In addition to specifying the visual appearance of the structure using the Jmol menu, (e.g. if
you find that this doesn’t give you all the flexibility you need), it is also possible to enter the
rendering commands in a text console. The Jmol console can be opened from the Jmol
menu using the Console item.
A small window, the Jmol Console, will appear at the upper left corner of your screen. A
cursor will be blinking in the lower part of the window. This is where you can enter
commands; a description of available commands for creating basic and advanced scripts is
given at: http://chemapps.stolaf.edu/jmol/docs/ .
Once your desired structure is shown, the current rendering can be written to a file (a socalled ‘state’ file). This state file should be given the extension .spt and uploaded as
initialization (and reset) script file for an image. To facilitate the saving of the current state
to a .spt file, use the Show Jmol State button below the Jmol applet.
You will see a text box in the bottom part of the webpage. Select all the text shown in the
box – either by holding the appropriate mouse button pressed while moving over all lines,
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or by clicking into the box and then using Ctrl-A. Copy (Ctrl-C) the marked text and put it
into a text file.
Save this text file preferably with a meaningful name (one you can easily identify) and with
the extension .spt. Upload this file as Initialization and Reset script file for the corresponding
image in your figure manuscript.
Preparing the state file externally
If you have a Jmol application installed on your computer, you can also use that for
preparing the init and reset (.spt) files. Please note that if you are using a newer version of
Jmol than is available for visualizing structure in Protein Science not all features might be
available in the online version. The version of Jmol in iMolecules 3D is shown in the Help
page accessible from the
icon.
Also, if you are preparing the Initialization and Reset script (.spt) files offline, i.e. using your
own local installation of Jmol, please note that Jmol will write ‘state’ file which contains a
file path to the structure data file (usually a .pdb file) which is that of your local file system.
When the .spt file with that file path is uploaded, the Jmol in the tool will not be able to
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point that file path. Therefore, it should be (a) removed before the .spt file is uploaded, or (b)
removed after upload.
The following figure shows the main window of the external, stand-alone Jmol application:
To create the ‘state’ file using an external Jmol application:
1. Open the console window using File/Output Console…
2. Enter the command ‘show state’
3. Press the Return key.
If you already entered commands in the console window, you should clear the console using
the Clear Input and Clear Output buttons before issuing the ‘show state’ command.
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Copy the complete content of the ‘show state’ command (e.g. by clicking into the console
window and press Ctrl-a, then Ctrl-c to copy the text into memory, open a text editor and
paste from memory (e.g. using Ctrl-v) to a text file. Within the text editor remove the line
which has a file specification referring to your molecule data file on your local hard disk (in
the next figure below this line is highlighted in light blue). When done, save the text file,
preferably with the extension .spt – e.g. figure-1_init.spt).
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To create a reset script file from the init script file, just open the init script in a text editor
and go to the last line. This line should read:
_setState;
Change this line to:
_resetState;
Save the file with a different name, e.g. figure-1_reset.spt .
Go (back) to the Default Image Settings screen for your figure and click on the icon on the
right side in the line where it says ‘Initialization Script File.’ This brings up a new window
allowing the selection of a file from your local hard disk. Select the initialization script file
you created before, and when done repeat these actions analogously for the reset script file.
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When the files are uploaded, you’ll see the filenames in the respective rows – and some
additional icons which allow you (from left to right) to:
view some information
upload a new script file (replacing the current one)
download the current script file to your hard disk
edit the content of the uploaded file on-line (without the need to
make changes off-line with a text editor and re-upload)
remove (delete) the current script file from the system.
The settings made on the Default Image Settings screen (as shown in the example above)
become the default values for all images which you set up for a figure. Individual settings for
each image can be made by changing the corresponding parameters on each of the
individual images pages. To do so, click the Images link (indicated by the mouse pointer in
the figure above) and select the image for which changes should be made from the list of
images displayed.
Note that in this example, only one image has been created so far. If your figure will consist
of only one image, we recommend making all settings on the Default Image Settings page. If
you add a second or subsequent images to your figure, all subsequent images will inherit the
settings made on the Default Image Settings screen. This way you don’t have to repeat some
of the steps and can reuse molecular data files already uploaded (useful especially if the
structure data files are huge), selection and rendering options already customized etc.
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Adding images
Select the figure for which you want to add a new image. Click the link New Image in the
Actions menu:
A new screen appears where you can enter the new image’s title, the image letter and the
image caption. It also allows you to define whether the image should be a non-animated or
an animated one (see the Reference section for an explanation of the difference). Nonanimated is the default setting.
There is no need to specify ‘Molecule Data File’ etc. if you specified these on the Default
Image Settings page for the figure before. The settings can also be made later on the
image’s General Properties screen (on the screen shown above you would need to have the
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molecule data and/or initialization/reset scripts uploaded in advance since files residing on
your local hard disk cannot be accessed from this screen).
Adding figures
Using the Figures tab, view the Figures list of your manuscript and click New Figure in the
Actions box in the upper left:
You can create additional figures using the same steps as described above. For details on
more advanced features see the Reference section at the end of this document. It describes:
 Adding a figure from a template
 Sorting Figures
 Sorting Images
 Animated v non-animated figures
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



Deleting images and figures
Deleting images
Delete a complete figure (containing one or more images)
Promoting/Demoting figures (from Intermediate to Expert authoring mode and back)
Two or more figures
The iMolecules 3D author tool accommodates one, two, or more figures for your manuscript.
When you create two or more figures, the shortened title for each figure appears along tabs
above the molecule viewer window. This is designed to make it easier for your readers to
jump easily to the next figure without having to return to your published paper. The tool
fields require you to provide a shortened title for the tab and automatically adds “Fig x’ to
the tab when you have added a Figure number. Please confirm you have added the correct
figure number so the tool can display them correctly in the tabs. See the examples below.
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This manuscript shows three Figures.
Select the
icon to edit the attributes of the Figure
The Figure short title appears as a tab in the Viewer when two or more figures are created.
A tab is not created when there is only one figure, but the figure number is used in the
display next to the full figure title and main caption to the right of the molecule window.
See the example above.
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Review your Figure text
Check that all text that is to appear in the molecule viewer is added to the tool exactly as it
should appear in the viewer (the Preview Figures feature shows the viewer in a separate
browser tab). It is important that the following fields of information match your published
article.
1.
2.
3.
4.
5.
6.
7.
Manuscript title
Author names
Figure Number (1, 2, 3 etc)
Figure title and main caption
Image letter (A, B, C, etc.)
Image title (If applicable)
Image caption (if applicable)
Please refer to the journal’s Author Guidelines for the style and format of these “metadata”,
especially for author names.
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Static image for article publication
It is customary to display a static Figure or set of images comprising a figure in the body of
the article itself, with a link to the interactive figure. This tool provides a mechanism to
generate a high-quality image suitable for publication. Please be sure that you provide a
static image when you submit the manuscript to the editorial office. The image or images
will be published in the body of the article, just as with a conventional image. A link to your
interactive figure will appear after each caption (using the links you embed; see the next
section of this document).
1. Select Preview Figures from the left menu.
2. Manipulate the image until you see the view you wish to use for the sample static
image in your article.
3. Scroll down until the Create Image button is visible on the left side of the window
under your figure.
4.
5.
6.
7.
8.
9.
10.
11.
12.
Select Create Image.
Adjust the molecule to the desired angle and size.
Right-click on the image and from the menu select: Console.
Type in the lower panel: write frames {*} 2000 2000
"imageName.png" (where imageName is your selected filename. 2000 is default.
You can use 2500 or other resolution.)
Press: Enter (carriage return key)
On the right hand PNG Compression slider, choose Quality: 9.
Click Save button.
Wait several seconds until console is updated.
Browse to find the image in your My Documents folder (XP).
The image generated by the tool using this process satisfies the publisher’s requirements
for resolution and file type.
As with conventional figures, you should submit these static images representing your
interactive figures as separate files during the manuscript-submission process.
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Figures Ready for Review
NOTE: Only the Lead author may change the status to ‘Ready to
Review’ in preparation for peer-review. The co-authors are not
permitted this action.
When you have uploaded all the files for your figures, and completed the preparation so
that the figures are done to your satisfaction, the next step is to copy the URL for each
figure into your manuscript (then you will upload the manuscript and any static figures and
tables using the online manuscript submission system for the journal, ScholarOne
Manuscripts, unrelated to this tool and hosted elsewhere.)
1. View the General Properties for the figure.
2. Select Ready to Review from the ACTIONS menu – this makes the figure noneditable and generates the specific URL for the Figure.
See the screen example below.
3. Copy each URL and paste it at the end of your figure caption in your manuscript
document. Static figures are uploaded as separate files at the time of manuscript
submission. For links to your interactive figures, paste the URL at the end of the
figure caption in the body of the manuscript itself.
a. Click the Select URL link. This highlights the URL to the right.
b. Right Click the highlighted URL and select Copy.
c. Paste into your manuscript.
4. Repeat for each Figure.
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5. Your manuscript is now ready to submit to the journal’s editorial office using
ScholarOne Manuscripts. A link is provided here for your convenience:
http://mc.manuscriptcentral.com/proteinscience
The reviewers appointed by the editorial office will link to your interactive graphic(s) from
the PDF and will see them in a view identical to that in the Preview mode. Registration or
log in is not required (reviewers cannot access the tool, they may only view the interactive
Figures). Note the label “Figure under Review.”
Revisions during peer-review [optional]
During the peer-review process, the journal’s Editor may require you to make changes to
your figures to improve them.
1. You will receive an e-mail notifying you that the tool has been unlocked and your
figures are available for editing. The Editor will have changed the status of your
manuscript in iMolecules 3D to enable you to make changes. In most cases, a note
from the editor about what changes are recommended will precede the tool
unlocking message.
2. Log into iMolecules 3D.
3. Open your manuscript project directory.
4. Make any and all changes to your figures. If you have renumbered any, you must
change the numbering for the Figure captions so that in the Preview mode you see
the revised numbering; see the reference section at the end of this document for
details on changing the Sort Order of your figures. Figure numbers and image letters
must match your manuscript, of course.
5. Notify the editor that the changes have been made by selecting the Ready to
Review button in the left menu.
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Author Proofing after typesetting
VERY IMPORTANT NOTE: Changes may not be made to published
articles of record, and this restriction also pertains to interactive
figures. Any corrections after publication (EarlyView or paginated-inissue version) must be done via an erratum, just as with static figures
or tables. Therefore, please ensure that your figures are correct and
complete before publication. You will not be able to change them
after publication of your article.
It is important that the following fields of information match your published article:
1. Manuscript title
2. Author names
3. Figure number (1, 2, 3 etc)
4. Figure titles and main captions
5. Image letter (A, B, C, etc.)
6. Image title (if applicable)
7. Image caption (if applicable)
It is the lead author’s responsibility to ensure that they match, so check these during the
proofing stage. The links in the PDF proof will take you to the molecule viewer. If there are
any errors, use the Request to Edit link in the left menu to ask that the figures be unlocked
so you can correct them. Be sure to indicate you have finished the corrections by clicking on
the Ready to Review link.
1. From the PDF author proof, click on the link to each interactive figure at the end of
each figure caption.
2. Proof the image, title, authors, and figure titles and captions, image titles and
captions. If for some reason the links do not take you to each correct figure, please
alert the Production Editor, using the same e-mail address as for other author
corrections.
3. If no changes are required. You do not need to use the iMolecules 3D tool.
a. Inform the journal’s Electronic Editor and the Production Editor via e-mail
[[email protected]; [email protected]] that your graphics have been
proofed and that you will not be making any changes.
b. Include your name and the title of your article.
4. If you must make changes to your figures
a. Log into the iMolecules 3D tool.
b. Select your manuscript.
c. In the left column, select the Request to Edit link. This requests that the files
be unlocked so you can make changes. The system will send an e-mail to the
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editorial office and your figures will be unlocked for editing. You’ll receive
an automatic e-mail when the figures are unlocked and ready to edit.
d. Make your changes.
e. Click Ready to Review in the left column. This notifies the editorial office
(and the Production Editor) that you have made corrections. Once they have
reviewed the changes, the journal’s Electronic Editor will use the tool to
promote your figures to Published status. Once the article itself has been
published online the Production Editor will then add the Abstract URL and
the article’s DOI.
Online Publication
Once your article has been published online, the Production Editor at Wiley will add the URL
of the article abstract and the article’s DOI so they appear on the interactive graphic. There
may be a slight delay. Viewers of your graphic can use the link to return to your article.
If you find an error in your interactive graphic, you must submit an erratum and create the
new figure (see Reference Section below). It is not possible to change published graphics or
remove them (except in extreme cases where articles are retracted). Once you have created
the new graphic, the publisher will ensure it is linked from the article and from the incorrect
graphic.
Linking to your published paper
Once your paper has been published online, you may link to its abstract to promote use
among those colleagues who may be interested in the content and seeing how interactive
graphics can enhance an article.
To link to an article from the author's homepage, take the DOI (digital object identifier) and
append it to "http://dx.doi.org/" as per following example:
DOI 10.1002/pro.489, becomes http://dx.doi.org/10.1002/pro.489.
Linking to your published figures
If you wish to send links to the figures in an e-mail to colleagues, copy the URL from your
Figure 1. You may do this using the tool (use the Figure URL link in the left Actions menu) or
from your manuscript document; the same URL is operational from the reviewing stage to
final published figures. From Figure 1, your colleagues can link to any other figure (if you
have two or more).
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Reference section
Getting help
For help registering or logging in, please contact [email protected].
For technical assistance with the author tool, please contact the journal’s electronic editor,
Arthur Palmer at [email protected]. Please add “iMolecules 3D – author help” in the
subject line.
Forgotten password
Use the Forgot your password? feature on the Log in box to retrieve your password. The
link to Log in is in the left menu and in the top right. Remember, passwords are case
sensitive.
Collaboration – help uploading files and creating figures
Colleagues or co-authors on your manuscript who help you use the author tool to create
interactive figures or upload files should register separately. When you use the
Collaboration tab once you have created a ‘Manuscript’, you can provide your colleagues’ email addresses to authorize their access to your files.
1. At the Manuscript level, select the Collaboration tab.
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2. In the left menu, select Assign Co-Author.
3. In the box, add the details of your colleague or co-author you wish to permit access
to your files.
Once added, the iMolecules 3D system will send your co-author an e-mail alert. When they
register with the same address you provided, the system automatically connects them to
your manuscript.
Note: this feature works only on one manuscript, and for addresses that match. If the
colleague will help you on a second or subsequent manuscript, then you must invite
collaboration again. The e-mail addresses must match. If your colleague has not received an
alert, double-check the address, and ask your colleague to check his/her junk mail folder.
For help, please contact [email protected].
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If for some reason you wish to rescind editing privileges to a colleague, please contact [email protected] and include the full title of your manuscript.
Previewing your figures
At any point in preparing your figures you may use the Preview Figures link in the left menu
to examine the figures in your manuscript.
Generating URLs for links to figures
When you have completed creating and preparing your figures, you must provide a link in
your manuscript to each of the figures in your manuscript document for peer review. The
iMolecules 3D tool provides a mechanism for generating the URLs.
1. View your completed figure(s).
2. Select the link Ready to Review from the left menu. This locks the figures and
generates the URLs, one per figure.
3. Select the link Figure URL from the left menu.
4. For each figure, copy the URL and paste it into your manuscript prior to submission
to the Editorial office for peer-review. Place each URL at the end of the figure
caption in your manuscript.
The editor and reviewers will use these links to view your interactive figures (no login is
required).
Indicating figures are Ready for Peer Review
When you have completed creating and preparing your figures, you then need to add links
to the interactive figures in your manuscript document and submit it to the editorial office.
1. View your completed figure.
2. Select the link Ready to Review from the left menu. This locks the figures and
generates the URLs, one per figure.
3. Select the link Figure URL from the left menu.
4. For each figure, copy the URL and paste it into your manuscript prior to submission
to the Editorial office for peer-review. Place each URL at the end of the figure
caption in your manuscript.
5. At the online manuscript submission website, submit your manuscript in the usual
way.
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Assign co-author
See Collaboration.
Saving a figure as a template
You can add a new figure by saving all settings made for an already existing figure to a
template and read this in as basis for a new figure (basically ‘copying’ a figure). Go to the
Figures listing of your manuscript and select the figure you want to use as basis for a new
figure and click Save as Template in the Actions box in the upper left:
This brings up a dialog box where you can specify the name of the template:
Click OK when done. In the list of Figure Templates you will see the template you just
created (marked as ‘Private’) and the system-wide template files (marked as ‘Shared’):
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Go back to the Figure listing of your manuscript and select New Figure from the Action box
in the upper left. Enter the details for the new figure into the text fields:
Then click the button named Template to open a dialog box from which you could select a
figure template you created before (or one of two provided by default):
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Note that you could as well select the Figure Template first, and then enter the text into the
text fields. When all settings are made (i.e. text fields are filled in and a template is selected),
click OK:
You will see your new figure being added to the list of figures for your manuscript:
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Go to the figure details of the new image created from the template file to see that it indeed
is a copy of the figure from which the template was created:
Note that the new figure is already populated with molecule data and initialization and reset
script file names – and if you have modified Selection or Rendering options in the original
figure before saving it as a figure template, you would see these modifications in the new
figure as well.
Sorting figures
If you have more than one figure it may be necessary to change their order for a correct
display in the viewer. E.g. in the figure below (showing a cut-out from the (pre)viewer
display) the tab for Fig 3 should actually be at the right-most side of the tabs line:
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Although the figures seem to be correctly ordered in the figures list, they are actually not,
since the sort order depends on the ‘index’ numbers given in the right-most column:
To change the sort order of the figures click action Order Figures which brings up a new
window allowing you to
a. change the order with which the figures are given in the public viewer and
b. remove (‘park’) figures from being displayed in the viewer (without the
figure being deleted from the tool).
For a), select a figure for which the position in the list should be changed and move it –
using the ‘up’ and ‘down’ buttons – to the desired position in the list. In the example below,
the easiest way would be to select the first figure in the list and move it down to the end of
the list.
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When done click OK. In the figures list you can see the changed index values for the figures:
And, in the (pre)view window you can see that the figure tabs appear in the desired order:
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Regarding option b), go back to the list of figures and click Order Figures to get to the dialog
box again. Move a figure to be ‘parked’ – not being displayed in the (pre)viewer display – to
the left box by selecting the figure listed in the right box and click on the button where the
arrow points to the left.
When done click OK and open the preview window – where you’ll see that the ‘parked’
figure is not rendered in the display:
Sorting images
If you have more than one image in one of your figures it may be necessary to change the
order of the images for a correct display in the viewer. E.g. in the screenshot below
(showing a cut-out from the (pre)viewer display) the order of the two images is reversed
from the desired order:
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To change the sort order of the images in a figure, go to the images list and click action
Order Images:
This brings up a new window allowing you to:
a. change the order in which the images are listed in the public viewer and
b. remove (‘park’) images from being displayed in the viewer (without the images
being deleted from the tool).
For a), select an image for which the position in the list should be changed and move it –
using the ‘up’ and ‘down’ buttons – to the desired position in the list. In the example here
the second image has been selected and could now be moved to the top of the list by
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clicking the ‘up’ button. When all images are correctly sorted, click OK for getting back to
the image listing:
In the Preview display you can now see the changed sort order for the images:
Animated v non-animated figures
In the iMolecules tools are two different default layouts available for images: Animated and
non-animated. The main visible difference between the two images is that you will have
different menu bars in the different images, depending on if your image shows an animation
or just a ‘still’ image (which can still be interactively moved – ‘still’ here just means that the
control file doesn’t contain any commands for animations/moving the molecule around...).
‘Animated’ here usually means that you will use then with multi-model .pdb or multiframe .xyz files – for which an animated image would allow you to start and stop the
animation as well as to step through such an animation forwards and backwards.
Shown below are examples for non-animated and animated images – each followed by a
crop-out of its specific control bar layout.
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Non-animated figures
In the majority of all cases the non-animated image is the one which is used to render the
interactive graphics, thus this type of image will be shown/discussed first:
Control Bar below structure:
Spin X and Spin Y – starts rotating the molecule around the x and the y axis, respectively.
Rock X and Rock Y – starts rocking the molecule around the x and the y axis, respectively
(rocking = rotating 15° in one direction, then 15° in opposite direction).
Stop – stops rotating or rocking the molecule.
Center on selected atom – select an atom in the molecule displayed (clicking with left
mouse button on an atom), when button ‘Center on selected atom’ is clicked, this atom will
be placed in the center of the Jmol display area.
Reset – Re-instates the original centering and orientation of the displayed molecule. This
‘Reset’ button has no effect on the structure rendering (i.e. drawing styles like cartoon,
spacefill, wireframe etc and coloring styles will not change).
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Animated figures
Control Bar below structure:
Step back and Step forward – go through a series of frames one-by-one / one frame at a
time in the direction indicated
Play – starts playing through a series of frames in forward direction
Stop – stops the playing of frames
Resume – restarts playing a series of frames from the current position (e.g. where it was
stopped)
Center on selected atom – select an atom in the molecule displayed (clicking with left
mouse button on an atom), when button ‘Center on selected atom’ is clicked, this atom will
be placed in the center of the Jmol display area.
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Reset – Re-instates the original centering and orientation of the displayed molecule. This
‘Reset’ button has no effect on the structure rendering (i.e. drawing styles like cartoon,
spacefill, wireframe etc and coloring styles will not change).
Deleting images and figures
WARNING: Please note that there is no Undo function for
retrieving the figure or image once it is deleted. For this
reason you will be asked to confirm the removal of the
image or figure when you select the corresponding Remove
action.
Deleting images
Go to Figures, select the figure containing the image you want to delete. From the list of
images select the image to be deleted by clicking on the ‘View Details’ icon
of the image’s name.
to the left
When you are on the General Properties page of the image to be deleted, click the Remove
action in the upper left box:
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Delete a complete figure (containing one or more images)
Deleting a figure is very similar to deleting an image from within a figure: Go to the Figures
level and select the figure to be deleted by clicking on the View Details icon
of the Figure’s short title.
to the left
When you are on the General Properties page of the figure to be deleted, click the Remove
action in the upper left box:
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Promoting/Demoting figures (from Intermediate to Expert authoring
mode and back)
To use the Expert authoring mode for a figure, select the Promote Mode link in the Actions
menu.
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Note that in Expert mode you still have access to the General Properties screen for a figure,
while the Default Image Settings and Images tabs are now replaced by a tab titled ‘Files’:
Clicking the Files tab gives you a listing of available files:
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From the Files screen – or when going back to the ‘General Properties’ tab – you could
change back into ‘Intermediate’ authoring mode by clicking the Demote Mode action in the
‘Figure Authoring Mode’ box:
Using multi-part Figures
It’s not uncommon to display a number of images as components of one Figure. The
iMolecules 3D tool enables this for interactive figures, too. Each figure may be made of
several images. The images in each figure are usually combined by context, e.g. showing the
same protein in different presentations – which means the molecule data file would be the
same, while there are different control files allowing different aspects of the structure to be
highlighted. In this case it is possible to specify the molecule data file on the ‘figure’ level (if
there is no other molecule data file specified in an image, the image ‘inherits’ the molecule
data file definition from the figure). The advantage is that a molecule data file (which can be
huge) could easily be reused in different images.
It is not possible to have multi-part images, only multi-part figures.
Author Workflow
The iMolecules 3D author tool contains elements of the author’s workflow in drafting,
submitting and proofing a manuscript for publication. The tool provides access to create and
edit figures at certain points in the process, and also locks the figures from editing when the
manuscript is under peer-review, and (if accepted) when published online.
1. The tool starts in the ready state, and you may set up a folder for the figures for a
manuscript, create figures, add files, etc.
2. When you have completed creating the figures to your satisfaction, you use the
Ready to Review link to signify you’re done. This locks the figures from editing and
generates one URL per figure for you to insert into your manuscript document.
3. Using the peer-review system (a separate website from the author tool), you submit
your manuscript (now containing links to your interactive figures). As usual, a PDF of
your manuscript is sent to the reviewers selected by the editor; the reviewers use
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4.
5.
6.
7.
8.
9.
the links in the PDF to view your figures. Reviewers do not need access to the tool,
and therefore do not need a login.
Optional: the editor may ask you to make changes to your figures prior to
acceptance. The editor will unlock the figures, and you will receive an alert from the
iMolecules 3D tool that figures are unlocked ready for editing. Make your changes.
When you are done, use the Ready to Review link again. This sends an e-mail to the
editor to say that you have completed the changes.
If your manuscript is accepted for publication, the editorial office uses the
iMolecules 3D tool designates your manuscript (figures and files) to the Postacceptance state, which then ensures that the journal’s production editor is notified
that the manuscript has interactive figures.
When you are prompted by the Typesetter to proof your paper prior to publication,
you simply use the links in the PDF to view your interactive figures. If the figures
require no changes, you do not need to use the iMolecules 3D tool. If you need to
make changes to one or more figures, log into the tool, and use the Request to
Unlock link. This sends the request to the Editorial office, and they unlock the
figures. The tool sends you an e-mail letting you know when the figures are
unlocked ready for editing (copying the Production Editor). Make your corrections.
Use the Ready to Review link again. This action locks the figures again and alerts
both the Editor and the Production Editor that you are done.
The Electronic Editor reviews your figures, approves them and moves them to a
Published state. No changes can be made to Published figures.
Shortly after online publication of your article, the Production Editor will add the
article DOI to the tool and the URL of the abstract on Wiley Online Library so
viewers of the interactive graphic can link to the published paper.
To promote your paper you may create links to your published paper and directly to
figures on your personal, department, or institutional website.
Correcting Published Figures
After publication, if you discover an error in a figure, you will need to alert the Editorial
office. They will help you to submit an erratum. It is not possible to correct published
graphics, as the version of record must remain unchanged. The publishing convention is to
publish an erratum, linked to and from the new replacement graphic and the existing
graphic, just as with errata for text, static graphics or tables.
To create a replacement graphic, you will use the tool again, create a new ‘manuscript’
folder, create a new figure, and upload your files. The production editor will ensure that
your published article links to the new figure.
Document FINAL May n2012 nw
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