Mac
[Year 2024] How to Install AutoDock Vina on ARM Mac
AutoDock Vina is an open-source program used for molecular docking and works on Linux, Mac, and Windows. It is designed to be user-friendly, requiring only the molecular structures of the ligand and protein, along with the binding site specification. Recently I had trouble installing AutoDock Vina v1.2.5 in a Conda environment on my M1 Mac. The instruction "AutoDock Vina installation in a Conda environment" in the official document led to a failure. After a struggle, I figured out a solution. Environment Right Commands That's it. Be sure to use conda only. No pip. Python version has to be between 3.5 and 3.8 if you are going to use Meeko, too.
Can't Create Bootable USB Sonoma 14.1 Installer
How to clean-install macOS Sonoma is explained here. However, there is an issue with the Sonoma 14.1 installer, and it gives an error message when asked to create a bootable USB stick. So, it seems that you need to download Sonoma 14.0 first, create a bootable USB stick from it, do a clean install, and update the OS to the latest version.
How to Successfully install PyCaret on M1 Mac
Conda-forge provides an older version of PyCaret than PIP (2.3.10 vs. 3.0.2 as of June 1, 2023). You can install the latest version of PyCaret on M1 Mac by entering the following commands.
You Need to Replace Miniforge Version of Miniconda to Get Latest one
My Mac's Miniconda was old (version 4.11.0). There seemed to be a much newer version 22.11.1 available, but when I typed 'conda update -n base conda' in the terminal as instructed, the update didn't take effect (see the output below). It also looked like various issues had accumulated. Upon recollection, I installed Miniconda with Miniforge when the official Conda version for Apple Silicon was still unavailable. Conda is an open-source package management and environment management system for installing multiple versions of software packages and their dependencies and switching easily between them. It is commonly used for data science, scientific computing, and machine learning. Miniconda is a minimal distribution of Conda. […]
FM-7 Emulator on Mac
I installed on my Mac an emulator of Fujitsu FM-7 Series, Japanese popular PCs in the 1980's. Here are the steps. Environment Installation Installation of cmake Installation of the emulator Starting up the emulator CUI Type "python <path>/77AVEMU/scripts/runav.py" on your terminal. GUI Type "python <path>/77AVEMU/scripts/runGUI.py" on your terminal as in Step 7.
Steps to install EMBL-EBI EMBOSS on Apple Silicon Mac
EMBL-EBI EMBOSS is a set of bioinformatics tools, such as the pairwise sequence alignment software Needle, that run on Mac, Linux, and Windows. But neither Anaconda or Homebrew provides the package for Apple Silicon (ARM64). Furthermore, Safari doesn't allow users to access EMBOSS' or any other FTP site due to security concerns. Also, the command line ftp is long gone from Mac OS. The remaining option for M1 and M2 Mac users is Finder. Get it, not a web browser, to open the URL ftp://emboss.open-bio.org/pub/EMBOSS/ and download the latest source package (version 6.6.0 as of November 4, 2022). Once you have downloaded and uncompressed the tar.gz file, open Terminal.app and […]
Variables exported from Mac's Photos.app to XMP
There is an option to "Export IPTXC as XMP" when you export photos from Mac's Photos.app by selecting File＞Export＞Export Unmodified Original... Variables in XMP is useful for arranging photos. but what are they? I have tinkered with variables on Photos and by using exiftool to map them onto those in XMP files. Here is the correspondence table. Information edited on Photos is prioritized over EXIF metadata. XMP Photos.app EXIF dc:title Title Title photoshop:DateCreated Date and time Date/Time Original exif:GPSTimeStamp - Date/Time Original dc:description Caption Image Description rdf:li Keyword, People ? exif:GPSLongitudeexif:GPSLongitudeRefexif:GPSLatitudeexif:GPSLatitudeRef Location GPS information