alexholehouse/vmd_on_hdpi_displays.md

## vmd_on_hdpi_displays.md

      
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              vmd_on_hdpi_displays.md
            
          
    Guide on running VMD on high DPI screens

Running VMD on HDPI (high DPI - i.e. high resolution) screens in Linux remains a challenge due in part to the underlying FLTK library.
After exploring this for a while I came across the current solution which works reasonably well and should be relatively robust across cross-linux platforms. I'd be delighted if there were a simpler way, so please pull-request and update this if/when a better solution emerges. I wanted to write this so that someone with a minimal background in Linux could still get this up and running, as many people who use VMD may be new to Linux computing. If this describes you and things remain unclear, please
Setting up run_scaled

run_scaled is a simple but incredibly helpful bash script written by Alexander Kauer. It can be downloaded from here and added into your $PATH. If you know what this means, jump ahead to the Dependencies section.
$PATH is a list of location that the shell checks for executable files when you type something into the terminal. To see which directories are currently in your $PATH variable type
echo $PATH

# on ubuntu 18.04 this reveals
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

Now you have two options for adding things to your $PATH. One is to select one of those directories and copy the file run_scaled into that directory. To do this you may need to copy as root. A better option, however, is to create a new directory in user space where you can add any/all executable files you might want to use.
To do this, we'll create a file in our home directory called bin
 cd ~           # cd to the home directory
 mkdir bin      # make the directory bin

Then copy run_scaled into this directory and make sure the permission is set to executable - i.e. if you downloaded run_scaled into your home/<username>/Downloads folder and were currently in your home directory, this would look like
 cp Downloads/run_scaled bin/ 

To check this has worked, type
  ls ~/bin    # list all the files in the newly created bin directory 

This should print the name run_scaled to the terminal prompt. Note that '~' is shorthand for your 'home' directory.
Finally make sure run_scaled is executable by running
  cd ~/bin
  chmod +x run_scaled

This moves us to the ~/bin directory and adds the eXecutable permission stamp to the file (if it's already executable nothing bad will happen).
Finally, we have to add the directory /home//bin to the $PATH. The easies way to do this is to edit your shell configuration file. To check what shell you're running type
echo $SHELL

If this prints out either /usr/bin/zsh or /usr/bin/bash then great! If it prints out something else you may need to do some Googling to check how to add a directory to the $PATH in your shell.
For zsh or bash this is easy though.
If you're using zsh...

If you're running zsh (echo $SHELL = /usr/bin/zsh) then enter the following into your terminal:
echo "export PATH=\${PATH}:~/bin" >> .zshrc

If you're using bash...

If you're running bash (echo $SHELL = /usr/bin/bash) then enter the following into your terminal:
echo "export PATH=\${PATH}:~/bin" >> .bashrc

What do these do?

Both of these commands add the line
export PATH=${PATH}:~/bin

To your .zshrc or .bashrc files, respectively, adding the directory ~/bin into the $PATH. To check this has worked start a new terminal and typ
echo $PATH   

and, HOPEFULLY your /home/bin directory is now the last directory in the $PATH.
Dependencies

run_scaled actually uses a few other bit of software to work. These are

xvfb
xpra >= 2 https://xpra.org/
xrandr

Ubuntu (tested on 18.04)

For Ubuntu 18.04 these dependencies can be installed via
sudo apt install xpra 
sudo apt install xvfb  

Using run_scaled with VMD

Finally, to use runscaled with vmd simply type
run_scaled vmd

Or
run_scaled --scale=3 vmd

Where the '3' can be any number and defines the scaling factor
This format can still pass arguments to vmd; e.g.
    run_scaled --scale=3 vmd my_pdb.pdb

The interface may be slightly laggy, but not to a extent that is problematic. However, the window text can now be easily scaled without issue, making everything legible.
Postscript

I wanted to put this in one place because in all my Googling of VMD with small font, small text, can't read, I didn't find an example where someone had discussed the VMD-issue with run_scaled