The PLIP Protein-Ligand Interaction Profiler has been updated.
According to the Changelog
- Support for DNA and RNA as ligands__
- Detection of metal complexes with proteins/ligands, including prediction of geometry__
- Extended result files with detailed information on binding site residues and unpaired atoms__
- Support for zipped and gzipped files__
- Rich verbose mode in command line with information on detected functional groups and interactions
- Automatic fixing of common errors in custom PDB files
- Refined binding site selection
- Better overall performance
- Initial test suite for metal coordination
- Classification of ligands
- Improves detection of aromatic rings and interactions involving aromatic rings
- Single nucleotides and ions not excluded anymore as ligands
- Generation of canonical smiles for complete (composite) ligands
- Generation of txt files is now optional
- Basic support for PDBQT files
- Correct handling of negative chain positions of ligands
- Improved check for valid PDB IDs
- Fixes several bug
The web service includes all the updates and integrates BioLip for flagging biologically relevant interactions. Since ligand molecules (e.g., Glycerol, Ethylene glycol) are often used as additives (i.e., false positives) for solving the protein structures, not all ligands present in the PDB database are biologically relevant.
Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Given that this seems to be an incremental upgrade I'm hoping most things will be unaffected. I’ll update the list regularly and feel free to send in information.
So far the only issues I've hit are those that involve Java, reading around it looks like this is widespread issue.
When I compiled a similar list for Yosemite it proved very popular with 13,000 page views, and I hope this page is similarly useful.
Aabel 3 seems to be working fine
Avogadro all OK
BBEdit all OK
ChemBioDraw I was in touch with their support and was told "No support for ChemBioDraw on El Capitan", however a couple of readers have said that it appears to work. No information yet on round trip editing.
No issues reported for Cresset tools Torch, Spark, Forge
DataWarrior requires Java installation
Findings 1.2.4 is compatible with El Capitan
iPython Notebook all working fine
KNIME all working OK
line 128: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/java: No such file or directory
I updated ChemAxon Beans to version 18.104.22.168 and this seems to fix the problem.
Papers 3 is compatible with El Capitan
PYMOL seems fine after initial testing
R all seems fine
Safari Extensions still seem to be working.
SeeSAR no issues so far
Stardrop not aware of any issues
Spartan 14 seems fine.
Vortex no problems so far
Wizard Pro all seems fine
Updating Homebrew packages
Part of the OS X 10.11/El Capitan changes is something called System Integrity Protection or "SIP". SIP prevents you from writing to many system directories such as /usr, /System & /bin, regardless of whether or not you are root. However /usr/local is open for developers to use, so Homebrew can still be used as expected. To fix your Homebrew installation if you see permission issues type
sudo chown $(whoami):admin /usr/local && sudo chown -R $(whoami):admin /usr/local
There is a more detailed explanation here
You will also need to install the latest version of the command line tools
Then you can type
brew update brew upgrade
I did the usual simple tests on the following packages and all worked fine after brew upgrade.
OpenBabel RDkit CDK Opsin Osra Inch Chemspot
Updated 5 October 2015
CLC Drug Discovery Workbench 2.5 has been released.
- Protein optimizer: New interactive tool invoked from the side panel in molecule projects. It allows for manual mutation and repair of amino acids, flipping of side chains, manual selection of side chain rotamers, and local adaption of protein structure to point mutations.
- Ligand optimizer: The ligand optimizer allows now for custom modification and creation of ring structures. 3D molecule viewer:
- Molecule surfaces can now be transparent, A clipping plane can cut into surfaces and secondary structures, Options for creating atom groups and visualizing hydrogen bonds have been improved
CLC Drug Discovery Workbench is your virtual lab bench. It gives you access to atomic level insights in protein-ligand interaction, and allows new ideas for improved binders to be quickly tested and visualized.
OS X El Capitan review: bringing even older Macs up to speed
The latest version of Apple’s laptop and desktop operating system OS X 10.11 El Capitan will genuinely speed up your computer, particularly if you’ve got an older Mac