Reply To: How to input constraints?

[Anonymous]

After looking at the code I figured it was a simple index. The problem with renumbering is that it makes it harder to reference back to the original PDB structure. So I manually did the index. As you stated earlier it does not appear that Dock in 3.0 considers constraints which is a big negative. Is there a way to formally request features or see what is being worked on for the next release is some sort of formal bug tracking system?

Thanks for clarifying that the dock_pert values are probably max range values where I assume that the nstruct would then be evenly spaced in the range of values. This makes it hard to run in parallel assuming nstruct is a large value to cover all possible docking positions.

I just finished a 10,000 -randomize1 -randomize2 run and looked at a couple structures with the lowest energy and they are not even close to what should be the docking interface. I am probably going to write some code that will go through and find models from the low resolution run where the predicted structure matches a set of distance constraints and then work from those models.

I started up 20 jobs with -nstruct 500 each and I assume that rosetta is using a good random seed so that the 20 jobs are independently random.