User Guide - Frequently Asked Questions and Troubleshooting

Table of Contents

• FAQ
  • General
    • Source code availability
    • SweetUnityMol vs UnityMol?
    • How to save the current state
    • How to make a screenshot without the UserInterface?
    • I want to have a white background!
    • I want to use a Texture on Hyperballs!
    • I want to use a Texture on the Surface representation!
    • Which platforms are supported in UnityMol?
  • Sugar representations
    • I don’t have the surface representation for sugar!
    • I have a sugar molecule, but the SugarRibbons don’t work!
    • The RingBlending or SugarRibbons coloration is gray!
    • I want to use the Sugar Coloration mode!
    • I want to represent a glycoprotein in SurfaceMode and the Sugar molecule in SugarRibbons!
    • I want to represent a glycoprotein in Hyperballs for amino acids and SugarRibbons for sugar!
• Troubleshooting
  • General
    • UnityMol does not launch
    • I have a black screen, or parts of the screen stay black
  • Platform-specific
    • Issues with shaders under windows
    • Some bonds in my molecule are missing!
  • Virtual reality-related (Oculus, Vive, ..)
    • Oculus Rift installation issues
• Known bugs and inconveniences

post-0.9.5

Todo:

Add relevant discussions from email exchanges (SF mailing list, gmail mailing list, ..)

FAQ

General

Source code availability

Q: I found recent binary builds of UnityMol on the sourceforge website, but the corresponding source code does not seem available there. I could only find Unity3D project sources for older versions of UnityMol.

A: Currently, the everyday development of UnityMol is not on a public repository. We release source code with every major UnityMol version, typically when the related paper gets accepted. If you need source code access in between these releases, please contact us to find an appropriate solution.

SweetUnityMol vs UnityMol?

SweetUnityMol was the working name of an extension to UnityMol that has particular functionalities for the representation of sugars and derived molecules. SweetUnityMol is now fully integrated within the current UnityMol version

How to save the current state

Unfortunately this very useful functionality is not (yet) implemented in UnityMol. Stay tuned, it's on our todo list.

How to make a screenshot without the UserInterface?

There are two options. The first one should work for all versions of UnityMol. Press the backspace key (typically locate above the Return key) to hide the graphical user interface (GUI). Then press the P key to generate a screenshot. Typically screenshots are saved in the Screenshots subdirectory of the directory from which UnityMol was started.

In newer versions of UnityMol, you have actually an option to generate screenshots with a transparent background (in the Advanced menu). When you use this option, the GUI elements are not present in the screenshot, even though you see them on the screen.

I want to have a white background!

Go to the Advanced menu and choose White as Background.

I want to use a Texture on Hyperballs!

Atom Appareance > Renderer > click on a sphere image (you can apply your texture only on a selection with Residues, Chain, Extended atoms selection).

I want to use a Texture on the Surface representation!

Surface > Generate (if you didn’t do it already)

Surface > Texture > Click on a sphere image.

Which platforms are supported in UnityMol?

Todo:

Add a table listing supported platforms (priority, status, observations)

Sugar representations

I don’t have the surface representation for sugar!

This is because by default, the surface representation for sugar molecules is disabled. Like that, you can easily represent a glycoprotein in surface mode and locate the sugar molecules. To be able to see the actual sugar surface, click on the Sugar toggle button present on the Surface Menu (last element of this menu).

I have a sugar molecule, but the SugarRibbons don’t work!

There might be several causes for this issue:

1. The 3 letter code for your sugar molecules in your PDB file is not recognized (check for instance the Color code for monosaccharides in the quickstart guide appendix).
   • Change the 3 letter sugar name in your PDB file into a recognized code.
   • In the Tune Menu, uncheck Sugar Only? and click on Enable SugarRibbons again (maybe twice to uncheck, then check again).
2. You have a connectivity issue. This happens for rings of 4 or 7 or more atoms, or 2 rings for 1 sugar.
   • Currently no solution here. It’s still a beta version and we have to fix that

Todo:

Fix 4, 7 or 7+ sugar ring connectivity and also double rings

The RingBlending or SugarRibbons coloration is gray!

The 3 letter code for your sugar molecules in your PDB file is not recognized (check for instance the Color code for monosaccharides in the quickstart guide appendix).

I want to use the Sugar Coloration mode!

Atom Appareance > Panels > Sugar

I want to represent a glycoprotein in SurfaceMode and the Sugar molecule in SugarRibbons!

Surface menu > Generate

Sugar Menu > Enable SugarRibbons.

I want to represent a glycoprotein in Hyperballs for amino acids and SugarRibbons for sugar!

You have to play with the Sugar/Non Sugar checkbox in the Sugar Menu. You may have to click twice on theses checkboxes (issues with the UserInterface. Will be fixed in a future version).

For example with 3FUS from a new session of SweetUnityMol: In the input PDB ID : 3FUS > Fetch PDB

Sugar > Enable SugarRibbons

Sugar > Non Sugar (twice)

Troubleshooting

General

UnityMol does not launch

Has been observed under linux. Seems to be related to installed libraries, notably OpenGL etc. No further diagnostic yet.

I have a black screen, or parts of the screen stay black

Try to not use the full screen mode (check Windowed in the UnityMol Configuration menu (this menu is the menu where you choose your resolution and click on the Play! button).

We discovered this issue with some of the new versions of Unity3D on some platforms. We did not yet precisely locate where this problem comes from.

Platform-specific

Issues with shaders under windows

(This should no longer apply to current/recent UnityMol windows builds!) There was some shader bug on windows (with DirectX). If you wanted to execute a compiled UnityMol version on windows, you had to force the open-gl use by doing the following steps.

In your working folder (with UnityMol.exe and UnityMol_Data folders):

• create a batch file (like run.bat)
• right click > modify
• write UnityMol.exe -force-opengl (with the program name being UnityMol.exe)
• Launch UnityMol by running run.bat (if your batch name is this one)

Some bonds in my molecule are missing!

Our shader needs OpenGl. Use the file Run_SweetUmol_32.bat or Run_SweetUmol_32.bat depending on your version of the software (the line has to be something like umol-winXX-20141002.exe –force- opengl.

Virtual reality-related (Oculus, Vive, ..)

Oculus Rift installation issues

Sometimes Oculus installation is problematic. Some of the issues we ran also into are described at https://www.reddit.com/r/oculus/comments/4caiwr/failed_install/. One was the error message Problems with installation: OVRLibrarian.exe exited with code 7 (failure). In many cases, to diagnose further, you can do the following:

• check the file OculusSetup.log
• test installation by running the installer from drive C:
• check that TEMP% is on C:, too
• uninstall McAfee (or other network protection agents).. this solved it in my case!

Known bugs and inconveniences

Will be added soon.