A run on the Haddock server generates a few graphical charts and a web page with the results. Am I missing something? I can’t find this anywhere.
Thanks
Provided your run completed without any errors (you must have been notified otherwise), here is an example of the typical results page generated by the web server:
http://haddock.science.uu.nl/services/HADDOCK2.2/Files/E2A-HPr-demo/index.html
The first information you will get is a detailed description of the clusters of models generated by HADDOCK. If you scroll down the web page, you can find seven plots showing the distribution of the models with respect to standard criteria used in the field (fraction of common contacts, interface and ligand RMSDs). The various structural analyses are made with respect to the best HADDOCK model (the one with the lowest HADDOCK score).
My mistake.
What I meant was I am using a local installation of Haddock and the programs to generate the charts and results pages don’t seem to be anywhere in the package. Is there any way to get this software?
You will have to generate those by yourself I am afraid… Check our manual analysis part in the online HADDOCK manual.
Is there any way to get the ligand and interface RMSD values in a local Haddock run?
In order to do that you will need to know the structure of the complex you are docking.
And then write your own script to do it… We typically use Profit for this.
Example scripts can be found in the ana_scripts directories of the various examples provided with HADDOCK.