Re: [DIYbio] Re: Protein Shop Help!

I am quite interested in assisting you in any way you need.  I am a  computer scientist that has studied synthetic biology for a number of  years.  You can download and run protein shop effortlessly using the  virtual appliance I created here:    http://www.graysonconsulting.biz/    All tools to run this virtual appliance are free.  All you have to do is  download virtual box and .ova from that website and start the ova  appliance.  Proteinshop will come up automatically with the ubiquitin  protein.  Let me know if you have questions :>  

I have taken this as a reference point and set up a Vagrant/Virtualbox/Chef arrangement:

https://github.com/exratione/protein-shop-vagrant

This should be a push-button setup for most of you after you get Vagrant, Virtualbox, Chef, and Librarian-chef installed. The docs are hopefully comprehensive enough.

These are 64-bit VMs, so you'll need a 64-bit host OS.

I'm not done with the Ubuntu version yet, so if you want to try it out, use the CentOS box. That works for me: I can get the pretty picture of purple Ubiquitin to show up. More than that I'm not prepared to vouch for.

The issues with g77 are legion, it's a horrible mess trying to get it onto any modern platform, so don't even try to use it. Use gfortran instead and alter the Makefile accordingly. That works fine for me on both Ubuntu and CentOS.

William: I do need to know how, if at all, you altered the ProteinShop codebase from the original so I can add that to the docs. Did you replace the geometry section, as was mentioned earlier in the thread, for example? The ProteinShop code I'm using is pulled from your example VM.

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