Molecules (Miskatonic Studio) Mac OS

  • Operating system: Windows 8.1 or higher; OSX High Sierra or higher A PC or Mac lower than this minimum threshold will struggle to run some of the required software and web applications. Most PCs or Macs from the past 3-5 years should be able to meet this minimum hardware threshold, and be able to run the core software required.
  • There are several advanced features on Discovery Studio Visualizer including the ability to show ligand binding sites in proteins and create a surface around the ligand.- Functionality for building small molecules, and protein and nucleic acid structures. Molecular builder/editor for Windows, Linux, and Mac OS X.-Free, Open Source: Easy to.

Indigo 1.1.10¶

Arial font is used on Linux systems to render molecules. Previously this font was used only on Windows and Mac OS X, and rendered images on Windows and Linux were different. “deco-ignore-errors” option was added. Now there are no exceptions like ‘no embeddings obtained’ during the RGroup Decomposition if the flag set true.

19 April 2013

This release has two major additions:

  1. We started to support Mono and provide a .NET version that runs onLinux and Mac OS X. This was done with help of developers from RoyalSociety of Chemistry (http://www.rsc.org) who also helped us tolocalize and fix several stability issues in our .NET version.

  2. Indigo now understand aromatic rings with external double bonds suchas O=C1C=CC=CC=C1. To enable this mode you have to set“aromaticity-model” option to “generic” (while default version is“basic”).

Molecules (miskatonic Studio) Mac Os 11

All changes:

Molecules (miskatonic Studio) Mac Os X

Mac

Molecules (miskatonic Studio) Mac Os Download

  • Mono support: now we provide .NET modules for Windows, Linux, Mac OSX, and a universal bundle that works on all the specified platforms.Thanks to Dimitry Ivanov for various suggestions:https://groups.google.com/d/msg/indigo-dev/ObLkSecXrOw/g2RGOojqjosJ

  • Indigo Renderer automatically selects output format based on the fileextension. It is not necessary to specify “render-output-format”option if you are rendering into a file.

  • Original hydrogens are not folded during molecule transformations.Thanks to Ken for the bug report:https://groups.google.com/d/msg/indigo-bugs/359gCN9OrMg/fKoMt5kS9XcJ

  • Either cis/trans bond marked is preserved during molfile loading even if substitutes are collinear.
    Again thanks to Ken for the suggestion: https://groups.google.com/d/msg/indigo-bugs/oszcYWrwctI/3t2XuonNAaYJ

  • Indigo Renderer now has additional options for partial image sizespecification. These options are: “render-image-width”,“render-image-height”, “render-image-max-width”,“render-image-max-height”

  • Fixed an issue in the SMILES loader module that set invalid number of implicit hydrogens:

  • Generic aromaticity model that can be enabled by “aromaticity-model”option. Thanks to Daniel for pushing us to implement thisfunctionality.

  • Another aromaticity option for find any kekulize configuration ifIndigo cannot dearomatize a structure. For example Indigo cannotdearomatize the structure c1ccc2c(ccc2)cc1, because there are nobonds configuration such that the structure is aromatic. But you cantry to find approximate kekulize configuration if you specify option“dearomatize-verification” to “false”.

  • Indigo now uses dearomatization module to find number of hydrogens inaromatic rings in the IndigoObject.canonicalSmiles() method. Ifhydrogens configuration is ambiguous then Indigo throws an exceptionabout this.

  • Additional “unique-dearomatization” option. If this option is set to true Indigo will throw an exception of dearomatization configuration is ambiguous (that means that canonical SMILES cannot be generated):
  • IndigoInchi.loadMolecule can now load molecules from InChI Aux infromation.
    Thanks to Nico: http://tech.knime.org/forum/indigo/inchi-conversion-into-2d-structure#comment-28514

  • Indigo Renderer doesn’t have a dependency on the new GLIBC any more.This dependency prevented loading of Indigo Renderer on CentOS 5.9and less.

  • Minor changes in Java and C# bindings: expandAbbreviations method hasbeen add, typo in countDataSGroups has been fixed

  • Thanks to Daniel for the feature request:

  • Fingerprints computation now works 30% faster.

  • All stereocenter exceptions now includes also atom index:
Install‎ > ‎

Python Molecular Viewer (PMV) Installation

autoPACK: INSTALLATION for the Python Molecular Viewer (PMV)

autoPACK for PMV is a very early alpha version released only for MAC as of March 14, 2013. Please check back frequently for updates.

Overview
This installation uses a preview nightly build of PMV and requires the installation of two additional modules to the package.

PMV is a powerful molecular viewer that has a number of customizable features and comes with many pluggable commands ranging from displaying molecular surfaces to advanced volume rendering.

Pre-requisites

  1. Windows, Mac, or Linux
  2. Respect the license that you will agree to during installation.

Install the latest version of MGL Tools that includes PMV

  1. Install the latest build of MGL Tools (which includes PMV) from here
  2. or directly for Mac OS here http://mgltools.scripps.edu/downloads/tars/releases/nightly/latest/REL/mgltools_i86Darwin9_latest.dmg
  3. or directly for Windows here http://mgltools.scripps.edu/downloads/tars/releases/nightly/latest/REL/mgltools_win32_latest_Setup.exe


Install autoPACK and patch MGLTools on Windows

Download the following installer and follow the instruction. Restart PMV.

uPy-PMV installer for Windows

Install autoPACK and patch MGLTools on MAC OS

  1. Download the following zipped file for Mac OS
  2. Unzip the file
  3. Place the contents of the unzipped file as follow into your MGL folder location.

    4. Move upy, ePMV, and AutoFill contents of MGLToolsPkgs goes to /Library/MGLTools/latest/MGLToolsPckgs/


    Move the contents of MGLToolsPckgs/DejaVu to /Library/MGLTools/latest/MGLToolsPckgs/


    Move the contents of site-package-2.7 to /Library/MGLTools/latest/lib/python2.7/site-packages



Open PMV and start autoPACK

  1. Start PMV by...
    1. Mac: Application/MGLTools-Latest/PMV-latest...
    2. In order to activate autoPack plugin open the python shell and paste this line :
    3. self.browseCommands('autoPackpmvCommands', package='AutoFill.plugin', commands=['autoPACK'],topCommand=0)

  2. Start autoPACK by....
    1. Click on Compute -> autoPACK

Load the HIV model v 1.4

After Selecting the recipe HIV and the version 1.4 click 'Construct' and wait while the plugin build the scene. You know it is done when the viewer Gui appears.
In the viewport you should see something similar as the imge below after recentering the scene (click on the cross or type 'r','c','n')
PMV is molecular viewer as well as a 3D framework. Thus it provide two distinct outliner, one for the molecules loaded (here none), and one for the geometries. The outliner will let you hide/show and change the material. To access click on
To access the 3D outliner click on
After playing around, and activating the SSAO (type 'o' while the mouse is over the 3D viewport). At first you will not see any change, we need to change the near and far clipping plane.