I'm using an ab initio script to preform a structure calculation with NOE restraints (i,i+3 or longer). The _fa NOE file, as I understand it, only activates at one stage. Is it better to create a centroid file for earlier stages of the calculation? Is it necessary ?
As well, would someone be willing to share a structure generation script with me ? I'm sure I could be doing it better. As things go, I have method to generate a little protein structure from NOEs and coordinate a Zn ion with 3xCys/1xHis, below. I would appreciate the help to make it better and more efficient.
thank you (again, since I just posted a cst question)
Constraints: it is definitely better to use centroid constraints than fullatom constraints. (Using both is fine.) Centroid mode is made for allowing large conformational sampling; fullatom mode only samples within whatever potential well centroid mode found. Therefore, the constraints will work much better in centroid mode. Just be careful to only constrain on centroid-present atoms (which includes the amide hydrogen and all backbone heavyatoms, but usually not HA).
(I don't have a script for this other than the resources we discussed - hopefully someone else will.)
There is a are two scripts in the CS_ROSETTA distribution, cst_map_toCB.py and cst_map_toCEN.py. The CB script outputs HA atoms but I think the CB/CEN atom mapping table can be modified to account for that.
My molecule folded well when I included some centroid restraints. Oliver Lange has graciously offered his help to suggest improvements to my method.
There is a patch file that adds HA atoms to centroids, I'm just not sure how it's activated - if you have need for HA we can look it up.