# Platon on macOS Sierra

A while ago, I wrote a post on installing Platon on a Mac. I have just reinstalled Platon on my MacBook Pro, running macOS Sierra, and it works just fine. Check out my earlier post for a more in-depth run down of how to install Platon, but, in brief, the process is this:

2. Install gfortran, which is included in gcc. (Again, using Homebrew this is ‘brew install gcc’).
4. In the terminal, go to the folder containing the two previously mentioned files (probably ~/Downloads).
5. Then, type ‘gfortran -o platon platon.f xdrvr.c -I/opt/X11/include -L/opt/X11/lib -lX11’. Hopefully, this should do its thing and produce an executable file named ‘Platon’.
6. Move the file somewhere useful, such as /opt.

*Foresman, James B., and Æleen Frisch. Exploring chemistry with electronic structure methods: a guide to using Gaussian. Gaussian, 1993.

**  chmod u+x

# Pymol for computational chemistry.

A picture is worth a thousand words.

So goes the saying, and it is true.

The pymol wiki has lots of ideas for styling atoms. Below are instructions for styling atoms, as in the image shown below, which I think produces an image that is particularly clear (and pretty) and suited to publication in journal articles.


hide everything
show sticks
show spheres
set sphere_scale, .18
set sphere_scale, .13, elem H
set bg_rgb=[1, 1, 1]
set stick_quality, 50
set sphere_quality, 4
color gray85, elem C
color red, elem O
color slate, elem N
color gray98, elem H
set stick_color, black
set ray_trace_mode, 1
set ray_texture, 2
set antialias, 3
set ambient, 0.5
set spec_count, 5
set shininess, 50
set specular, 1
set reflect, .1
set dash_gap, 0
set dash_color, black
set dash_gap, .15
set dash_length, .05
set dash_round_ends, 0
ray



This can be copied directly into the pymol command line, followed by enter. If you have non-bonded atoms such as a central metal with attached ligands, for which pymol sometimes does not detect, you can use the measurement tool and then remove the labels and change dash_radius to a very small number; alternatively, use the bond command.

Another nice effect is to change the display types of certain atoms. For example, I have highlighted the  coordination of the oxygen atoms in the crown ether molecules by hiding the spheres:

 hide spheres, elem C

Also, shown below is a GIF animation an animation of an optimization of the crown ether complex.

/

# Platon on Mac OS X Yosemite (10.10)

UPDATE (16 March, 2017): This also works on macOS Sierra (10.12.3).
UPDATE: This also works on Mac OS X El Capitan (10.11.5).

One of the most popular pages here (well, there is little else) is the page about Platon for Mac OS X.

I mainly use a computer running Ubuntu for crystallography at work so I haven’t had to compile Platon, the essential crystallographic program, for my Mac. I have seen that some people have had problems compiling the program (remember you do need Xquartz, and a compiler for Fortran and C). I compiled platon, but I also had some difficulty doing so, although I have compiled previous versions without a problem. So, if you have a problem compiling using the standard instructions on the platon website, try this, and you should be able to compile it, without sudo, using:

gfortran -o platon platon.f xdrvr.c -I/opt/X11/include -L/opt/X11/lib -lX11

If you don’t use -I/opt/X11/include then it won’t find the X11 libraries that are above /opt/X11/lib.

Afterwards, copy it into somewhere like sudo cp platon /opt/platon2015 (check that it has run privileges (i.e., ls -g) and, if not, run chmod u+x platon). You can then add the folder that contains the executable to your path and add an alias if in you profile script (.bashrc/.bash_profile etc.) e.g., alias platon="/opt/platon2015/platon“.

You can then run it with, for example, on a shelx res file:

platon file.res

References: A.L.Spek, Acta Cryst. 2009, D65, 148-155.