ligand docking, how to combine some silent.out files into a silent_all.out file
Submitted by Ryhon Wang on Fri, 2013-12-06 01:53
You are here
Unsolved
The problem hasn't been solved
fragment picking with 100% sequence identity
Submitted by nawsad on Thu, 2013-12-05 07:12
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.
Post Situation:
Forums:
- Read more about fragment picking with 100% sequence identity
- 1 comment
- Log in or register to post comments
No structure mods allowed during scoring! error
Submitted by jadolfbr on Wed, 2013-12-04 14:06
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:
Post Situation:
Forums:
- Read more about No structure mods allowed during scoring! error
- 2 comments
- Log in or register to post comments
how to design binding interface?
Submitted by Lindsay on Mon, 2013-12-02 19:06
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!
Post Situation:
Forums:
- Read more about how to design binding interface?
- 8 comments
- Log in or register to post comments
Alignment and RMSD
Submitted by ñ on Wed, 2013-11-27 12:43
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?
Post Situation:
Forums:
- Read more about Alignment and RMSD
- 5 comments
- Log in or register to post comments
sign of ddG of mutation
Submitted by Lindsay on Wed, 2013-11-27 00:25
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!
Post Situation:
Forums:
- Read more about sign of ddG of mutation
- 2 comments
- Log in or register to post comments
Symmetric pose initialization fails
Submitted by gudmal on Tue, 2013-11-26 06:42
Hi all.
I am using PyRosetta for Windows, and after running the following code sample:
...
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:
Post Situation:
Forums:
- Read more about Symmetric pose initialization fails
- 3 comments
- Log in or register to post comments
Fragments file
Submitted by Run on Tue, 2013-11-26 02:40
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.
Post Situation:
Forums:
- Read more about Fragments file
- 4 comments
- Log in or register to post comments
talaris2013 energy terms modifications
Submitted by peony on Sat, 2013-11-23 02:48
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?
Post Situation:
Forums:
- Read more about talaris2013 energy terms modifications
- 8 comments
- Log in or register to post comments
Script running, but returns no results
Submitted by chinhsutran on Fri, 2013-11-22 06:25
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)
Post Situation:
Forums:
- Read more about Script running, but returns no results
- 1 comment
- Log in or register to post comments
Pages
