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Is it possible to specify a custom constraint function in PyRosetta?
Here's a list of all the functions that we can use: https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/constraint-file
However, none of those functions match my use case.
I am relaxing a protein with a chemically bound ligand (attach as C14_SPF). The ligand is composed of Phosphopantethine and acyl together which are bound to ALA (residue 36 of chain B) of my protein. Actually, the residue 36 was originally SER which is bound to Phosphopantethine and acyl, but for modeling I took the OG of SERin Phosphopantethine and converted SER to ALA.
I'm folding a protein which is a trimeric long helix bundle. I started from the main/demos/public/symmetry_examples/fold-and-dock/ and added my info (sequence, fragments etc). This basically works but a lot of the resulting folds are globular not long - the helixes fold over on themselves. I'd like to constrain this to extended conformations only.
I looked at constraints in the Rosetta docs, and tried creating input_files/constraints.cst to give a penalty to any structure which has less than 50-70 A distance between residues 1 and 63:
I need protonation on the epsilon 2 nitrogen (HIE, HSE) and not on the (HID, HSD). The reason for this is that HID is mechanistically wrong and plays havok with my ligand.
Even though MutateResidue in pyrosetta does not accept the `mutate_self` argument it appears it calls HID HIS_D and HIE HIS and the mover thinks of them as not self of each other, so this works with switching and the heavy atoms are kept in place.
Hi, I am using Rosetta 3.7 and the following flags for relax:
relax.linuxgccrelease -s complex.pdb -out:suffix _relax -nstruct 5 -relax:default_repeats 5 -out:path:pdb ./ -out:path:score ./ -ignore_unrecognized_res
I was wondering if there are any default restraints on backbone displacement in this, I believe in principle unconstrained, procedure.
With thanks and best regards,
I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.
I'm docking a small molecule into an enzyme utilizing using match style constraints and the EnzRepackMinimize Mover. The constraint is between my small molecule and a cofactor in the enzyme.
I've generated the params file for both my small molecule and the cofactor. When I run my script with the following distance constraint, everything works fine.
CONSTRAINT:: distanceAB: 1.2 0.1 1000 0 2
When I run my protocol trying to turn on the covalency term as in the following line
I am trying to run Local Relax on an ADP-bound protein structure. I cleared the first hurdle to make a ligand params file, and the program runs fine and includes the ligand. I made the params file by taking ADP from a related structure, converted it to mol2 using iBabel, and made the params file using molfile_to_params.py