The problem hasn't been solved
hi,
is it possible to restrict a space in Rosetta Design... like use some dummies guaranteeing that positions in this area are not to large thus blocking space... or do I have to restrict the surrounding amino acids going for small ones and just hope that´s enough.
Thanx!
Hi,
I've searched for details of what exactly the relax protocol does. I know that it does "agressive sampling" and basically just minimises the Rosetta energy. Is there anywhere I can get more detail than that? I've looked through the Rosetta publications and many describe different aspects of Rosetta but I haven't found any that describe specific protocols or applications. I understand that these protocols keep evolving and therefore cannot be described "for once and for all" so, is my search in vain?
Hi, fellows:
We have two transmembrane peptide from two separate membrane proteins and we would like to see how they pack. The conformation of helix 1, i.e., tilt angle w.r.t the membrane etc, is determined by NMR. For the second helix, we currently take it as an ideal helix. The tilt angle for helix 2 is also known. This problem is similar to the glycophorin A packing problem addressed in "Toward high-resolution prediction and design of transmembrane helical protein structures".
The make_fragments.pl script for Rosetta3.3 now refers to a runPorter.pl script that uses Porter (http://distill.ucd.ie/porter/) to generate a PsiPred style output. I've been able to get the Porter executables, but where is the runPorter.pl script?
Hi,
does anybody have experience or ideas on how to involve waters in a packing/design process?
I want to repack a protein but want to make sure to include some water filled cavities. Is there a way to define waters or a sort of placeholder, though explicite waters would be better, so that the design-packer can generate a suitable surrounding.
Thanks!
can someone suggest if there are demos or tests for running multigraft design? it would be great help..
dear all,
Does anyone know if RosettaMatch can allow the same residue to satisfy two constraints in RosettaMatch?
thanks for the help!
Is there any way to read (write) structures (pdbs) using a python stream?
Couldn't find any clue in PyRosetta's documentation, so I guess its not a standard feature.. but I'm wondering whether there's a hack people use to in order to enable it..
Thanks!
Lior Z.
Good Afternoon,
We were wondering if Rosetta3.3 had the ability to use scoring as described in
RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation by Will Sheffler and David Baker
We have searched the forum for how to utilize it but were not able to find a solution.
Any help would be greatly appreciated.
Best,
George
hello,
is there any possibility to create a pose from a pdb style string in pyrosetta?
from the "PyMOLPyrosettaServer.py" script I can see that pymol can be made to listen for a pdb string sent from pyrosetta. i would like to go in the other direction directly passing a pdb string to pyrosetta in order to generate a pose. is this possible? and if so what is the necessary code for this?
i know that one can generate a pose from a pdb file but i would like to skip this step in order to save the time it costs to read/write from/to disk.