The problem hasn't been solved
Hi Everyone,
I want to create fragments given a query sequence of any length and the fragment extracted should be of same sequence. So just picking fragment without applying scoring scheme.
How can I do this?
Thanks in advance.
Hi All/Rocco,
Just a quick question. I am running a few (thousand) structures through score_jd2 using the command below, and I am occasionally seeing this message I've never seen before:
No structure mods allowed during scoring!
Any idea how this would be tripped? Some of these structures may have missing atoms and need some rebuilding of side chains during pose construction, but shouldn't that occur before scoring? The structures themselves look fine, and can be loaded into PyRosetta with no issues.
Command:
Dear ALL,
I have a complex with two chains. Now I am going to design the binding interface of Chain A while fix everything in the chain B.
Which application should I use? Thank you!
Hello,
I've been attempting measure some structures RMSDs by using the PyRosetta's functions all_atom_rmsd() and CA_rmsd(). I've also seen the function native_CA_rmsd(), and used it but I can't tell the diference between this one and CA_rmsd().
So far the functions I use are the ones I've been able to find by tabbing for iPython's autocomplete. I know that there is a native RMSD for all atom, but I've not been able to find it. Are these PyRosetta exposed methods listed somewhere?
What's the sign of ddG score in rosetta 3?
I think the ddG here is dG(mut)-dG(wild). so a lower score of mutant means better structure. So negative ddG means stabilize?
But in the paper "Role of conformational sampling in computing mutation-induced changes in protein structure and stability". It looks like ddG from rosetta has same sign as protherm database, which negative sign means destabilize.
So I am confused. Can anyone explain a little bit? Thank you!
rosetta.init()
pose = pose_from_sequence("AAAAAAAAAAAAA", "fa_standard")
pose_symm_data = core.conformation.symmetry.SymmData(pose.n_residue(),pose.num_jump())
pose_symm_data.read_symmetry_data_from_file("c2.sym")
core.pose.symmetry.make_symmetric_pose(pose, pose_symm_data)
it fails with an error:
"\core/pose/PDBInfo.hh PDBInfo::natoms( Size const res): res is not in this PDBInfo!"
The assert is coming from PDBInfo.hh, line 363:
The fragments file:aat000_03_05.200_v1_3
position: 1 neighbors: 200
1pg4 A 309 W L -108.068 162.569 -178.328 0.102 4.369 116.235 3 0.000 P 1 F 1
1pg4 is the name of protein.But what is the "A 309 W L -108.068 162.569 -178.328 0.102 4.369 116.235 3 0.000 P 1 F 1"?What's the meaning of those?
"{series}{pdb}{chain}{size}_{strategy}.{depth}_{version}" is mentioned in Rosetta user guide.But it is different.
I've noticed that they are some modifications in talaris2013 in energy terms in comparison with score12.
There appear new hack_ele energy term. What is more now I can see rama and omega - in score12 as default they weren't visible.
My question is : what's stand for hack_ele? And why can I see now rama and omega energy terms? Is there any docuemnation for talaris2013?
Hi,
Sorry for this duplicated topic. I posted it to the wrong place (PyRosetta Script) I think.
I wrote a simple script to calculate the free energy. The PyRosetta was successfully initiated, but returned me nothing.
This is my script:
import rosetta
rosetta.init()
import sys
def deltaG(interface):
comp = rosetta.pose_from_pdb(interface)
f = rosetta.ScoreFunction()
f.set_weight(fa_atr,0.59)
f.set_weight(fa_rep,0.05)
f.set_weight(hbond_bb_sc,1)
f.set_weight(hbond_sc,1)
f.set_weight(fa_sol,0.37)
f.set_weight(p_aa_pp,0.29)
f.set_weight(ref,0.48)
Hi,
I wrote a simple script to calculate the free energy. The PyRosetta was successfully initiated, but returned me nothing.
This is my script:
import rosetta
rosetta.init()
import sys
def deltaG(interface):
comp = rosetta.pose_from_pdb(interface)
f = rosetta.ScoreFunction()
f.set_weight(fa_atr,0.59)
f.set_weight(fa_rep,0.05)
f.set_weight(hbond_bb_sc,1)
f.set_weight(hbond_sc,1)
f.set_weight(fa_sol,0.37)
f.set_weight(p_aa_pp,0.29)
f.set_weight(ref,0.48)
print "delta G:", f(comp)
print f.show(comp)
def main():
interface = sys.argv[1]