{"id":1532,"date":"2021-04-08T12:49:50","date_gmt":"2021-04-08T03:49:50","guid":{"rendered":"https:\/\/mitsudo.net\/?p=1532"},"modified":"2021-06-21T09:17:13","modified_gmt":"2021-06-21T00:17:13","slug":"building-a-crystal-structure-analysis-environment-on-a-mac","status":"publish","type":"post","link":"https:\/\/mitsudo.net\/en\/building-a-crystal-structure-analysis-environment-on-a-mac\/","title":{"rendered":"Building a Crystal Structure Analysis Environment on a Mac"},"content":{"rendered":"

Crystal Structure Analysis on Mac<\/h2>\n

X-ray crystallography<\/strong> is one of the most direct methods to know the structure of molecules. Nowadays, data analysis of crystal structure can be done free of charge (for non-commercial use) on an individual’s PC. Among the various analysis software available, Olex2<\/strong> is one of the most popular software now. Olex2<\/strong> is freeware and has a beautiful screen, and thankfully there is also a Mac version<\/span>. Here is shown how to install Olex2<\/strong> for Mac.<\/p>\n

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ORTEP diagram displayed by Olex2<\/figcaption><\/figure>\n

How Olex2 works<\/h3>\n

Olex2<\/strong> is used in combination with SHELX<\/strong> and PLATON<\/strong>.<\/span>\u00a0 The analysis is performed on Olex2<\/strong>, and the actual crystal structure analysis is done by SHELX<\/strong>. PLATON<\/strong> help us to do miscellaneous things.<\/p>\n

Requirements<\/h3>\n

To install Olex2<\/strong>, Homebrew<\/strong>, Xquartz<\/strong>, iTerm2<\/strong> (or normal terminal), and zsh<\/strong> (or bash) are required. If you use Catalina or later, zsh<\/strong> is the default shell.<\/p>\n\r\n\t\t\t

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Related Article<\/div>\r\n\t\t\t\t
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Mac with Homebrew for Organic Chemists (for Intel Mac)<\/a><\/div>\r\n\t\t\t\t\t

Homebrew (A Package Manager for Mac)\r\nFor organic chemists, Homebrew is a very useful software, although it is not as es[\u2026]<\/p>\r\n\t\t\t\t<\/div>\r\n\t\t\t\t

\"\"<\/a><\/div>\r\n\t\t\t<\/div>\n

Installation of SHELX<\/h2>\n

You can download SHELX<\/strong> from The SHELX homepage<\/a>. After you register, you will receive a password for the download.<\/p>\n

\"\"<\/p>\n

From the download page, download a set of files with the .bz2<\/strong> extension in the mac folder<\/span>. If you are doing small molecule analysis, be sure to download shelxt.bz2<\/strong>, shelxl.bz2<\/strong>, and ciftab.bz2<\/strong>. Download them to a folder (for example, in temp<\/strong> folder) in your download folder (~\/Downloads<\/strong>).<\/p>\n

Next, open iTerm2<\/strong>, move to the temp<\/strong> folder, and extract the bz2<\/strong> files.<\/p>\n

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$ cd ~\/Downloads\/temp  #move to the temp folder\r\n$ bunzip2 *.bz2  #extract all the bz2 files\r\n<\/code><\/pre>\n<\/div>\n
Next, grant all users execute permissions to the extracted programs.<\/p>\n
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\r\n$ chmod ugo+x shelxt  #Grant execute permissions for all users\r\n$ chmod ugo+x shelxl\r\n$ chmod ugo+x ciftab\r\n$ chmod ugo+x <other extracted files><\/code><\/pre>\n<\/div>\n
Move all these unzipped files to \/usr\/local\/bin<\/strong>.<\/span><\/p>\n
Restart iTerm2<\/strong> and use the which<\/strong> command to confirm that the path is valid. If the output looks like the following, you have succeeded.<\/p>\n
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$ which shelxl #enter this command\r\n\/usr\/local\/bin\/shexl<\/code><\/pre>\n<\/div>\n
Installation of PLATON<\/h2>\n
Requirements<\/h3>\n
To install PLATON<\/strong>, gfortran<\/strong> is required. Check whether the gfortran<\/strong> command is available or not on iTerm2<\/strong>.
\n<\/strong><\/p>\n
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$ which gfortran  #enter this command\r\n\/usr\/local\/bin\/gfortran  #if installed, you see this answer\r\ngfortran not found  #if not installed, you see this answer\r\n\r\n<\/code><\/pre>\n<\/div>\n
If you see \/usr\/local\/bin\/gfortran<\/strong>, gfortran has been installed.<\/span><\/p>\n
If the message “gfortran not found<\/strong>” is displayed, gfortran<\/strong> is not installed<\/span>, so install it from Homebrew<\/strong>. gfortran<\/strong> is built into gcc<\/strong>, so install gcc<\/strong>.<\/p>\n
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$ brew install gcc  #If gfortran is not available, install gcc.<\/code><\/pre>\n<\/div>\n
Installation of PLATON<\/h3>\n
PLATON<\/strong> is installed according to the manual<\/a> (pdf) on the platon website<\/a>. (Some changes have been made.)<\/p>\n
Download platon.tar.gz<\/strong> from the platon download site<\/a> to your download folder (~\/Downloads). Unzip it and compile it.<\/p>\n
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$ cd ~\/Downloads  #move to the download folder\r\n$ tar zxvf platon.tar.gz  #extract the files\r\n$ cd platon  #move to the platon folder \r\n$ gunzip *.gz  #extract all the files\r\n$ gfortran -o platon platon.f xdrvr.c -L\/opt\/X11\/lib -lX11 -I\/opt\/X11\/include #compile the file \"platon\"<\/code><\/pre>\n<\/div>\n
The compilation by gfortran<\/strong> will take a while.<\/p>\n