Tag Archives: windows

Computing, Science

Python, Windows and PyMol

So I was chatting with an ex-colleague who had been having some fun getting PyMol to install on Windows. So I thought I’d do a quick write-up.

To start with, you need four things:

  1. The latest (C)Python installation package (AMD64 for 64-bit Windows 10)
  2. The NumPy+MKL wheel from Christoph Gohlke’s collection for AMD64
  3. The PyMol wheel from the same for AMD64
  4. The PyMol Launcher wheel from the same (optional) for AMD64

Install Python:

Make sure to tick “add to path” also, disable the pathlength limit, since it’s an option:

Open a commandline: (shift+right click)

Use pip to install wheel:

Then install NumPy+MKL:

Then PyMol: (this will also pull in Pmw)

Then PyMol Launcher (if you want)

Then find where PyMol is installed: (a ‘cheat’ here is %appdata% in the address bar!)

And create a shortcut on the Desktop/Start Menu/Task Bar (to your taste)…

Protein loaded is 5XA7, a recent submission and nothing whatsoever to do with me. I just picked it for demonstration purposes.

And now it should work! In all honesty, I find the pip install system far more trouble than just finding and installing the relevant libraries used to be…

Computing

Dodgy Internet Connections: Ping Script

I’m having some fun at the minute with a dodgy internet connection. It really is driving me to distraction, I must admit. It’s quite frustrating.

It manifests as a connection that drops in and out almost at random. In fact, if I heavily load the connection, rather than doing what I expect and dropping out, it seems to stabilise. But I can’t really download hundreds of GB all the time, can I? Also, it does likewise drop out occasionally at high loads – that’s the worst issue anyone has to try to troubleshoot: an intermittent one.

Regardless, I’m trying to collect evidence for the flakiness (although tonight it doesn’t seem to be playing – I’ve had a largely painless experience online this evening) so need some way of proving that something is up.

Note that I’m in Windows 10 most evenings, due to Skype, Word and Visual Studio. Yup, spend all day at work on Linux, move to Windows of an evening. Insert moaning about no good Office suites on Linux here.

So, anyway, a quick Windows (non-Powershell) script to ping a site at regular intervals, and log if not successful. Right now I’m not interested in when it is working – only when it’s not.

@echo off
setlocal enabledelayedexpansion
set hostIP=[put an IP address here]
:loop
set pingline=1
for /f "delims=" %%A in ('ping -n 1 -w 250 -l 255 %hostIP%') do (
    if !pingline! equ 2 (
        set logline=!date! !time! "%%A"
        echo !logline! | find "TTL=">nul || echo !logline! >> pinglog.txt
        )
    set /a pingline+=1
    )
timeout 10
goto loop

All credit due, I found this here and modified slightly so I didn’t have to download something from Windows Server 2003. OK, so timeout is slightly less accurate than sleep, but for my purposes it is sufficient. It will run until you kill it. Closing the command line is sufficient.