I’ve spent over a week trying to get the standalone version of haddock2.2 running on my computer, but to no avail. I mean, I have it running, just the values of what I get from my computer and what I get from the webserver are very different. Is there a way to upload 50+ structures at a time for refinement?
Running on different architectures will lead to differences.
Did you compare the run.cns files from a local run with the one from the server?
To check that your setting are correct.
Also the server does for example assigns automatically the protonation state of HIS, which you have to do manually for the local version.
So first make sure to have a proper refinement setup locally.
Batch submission is not supported, but you can refine an ensemble of 50 models (provided those are the same complex).
But you might write your own script to automate submission to the server…
Dear amjjbonvin,
Could you suggest how to go about writing a script to automate job submission to the server? I know beginner level programming in Perl. Will I be able to use Mechanize to automate form submission? Any hints/suggestions will be very helpful.
Thank you.
Our server is already heavily used, we won’t advertise ways of increasing the load… 
But others might have a solution they might want to share.
As a hint, use the file upload interface, editing on your side the haddockparam files and uploading then then to the server.
You can find such a haddockparam file in the result page of a previous run for example.