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Regarding the Documentation of Rosetta and PyRosetta

Dear members,

i m very new user of rosetta and pyrosetta i have idea about the algorithms of various molecular simulation programs like Gromacs autodock and other.

i want to know is there any documentation available about all the algorithms and methods used in Rosetta ? more precisely rather then hard core scientific notation i am looking for an easy and more descriptive documentation which can provide the information of various methods available in Rosetta.

Post Situation: 

using MonteCarlo to fold a random structure into a helical structure

I want to use MonteCarlo to fold a random structure into a helical stucture.But I have some troubles.
This is my script:from rosetta import *init()
p=pose_from_pdb("output3.pdb")
scorefxn=ScoreFunction()
scorefxn.set_weight(hbond_lr_bb,1.0)
scorefxn.set_weight(vdw,1.0)
ncycles=60000
KT=1.0
mc=MonteCarlo(p,scorefxn,KT)
movemap=MoveMap()
movemap.setbb(True)
small_mover=SmallMover(movemap,KT,5)
for i in range(1,ncycles):
small_mover.apply(p)
mc.boltzmann(p)
if(i%1000==0):
mc.recover_low(p)
mc.recover_low(p)
dump_pdb(p,"mc_output1.pdb")
But it told me:

Post Situation: 

loop modeling error 'CcdLoopClosureMover' object is not callable

I am using the current release "PyRosetta v2.012" it stucked, error is given bellow
the "loops.py" script which i m using have been attached with this post this script is provided online its not my own script: thanks

from where i can get the reference for all the available methods and function of Pyrosetta so that i can use that as per my requirement and it seems that scripts are written for different versions may not work for all the versions so how can i get the version specific details of various pyrosetta functions

Post Situation: 

loop modeling error 'CcdLoopClosureMover' object is not callable

m using the current release "PyRosetta v2.012" it stucked, error is given bellow
the "loops.py" script which i m using have been attached with this post this script is provided online its not my own script: thanks

Error Log++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++Error Log
core.chemical.ResidueTypeSet: Finished initializing centroid residue type set.
Created 1980 residue types
set up job distributor
randomizing loop
low res loop modeling
Traceback (most recent call last):
File "loops.py", line 89, in
ccd(p)

Post Situation: 

Error in loop modeling protocol its showing error "NameError: name 'ccd_closure' is not defined"

I stuck again loop modeling protocol test file is not running. its showing error "NameError: name 'ccd_closure' is not defined"

Log+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++log

setting up movers
core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments fr
om file test_in.frag3
core.chemical.ResidueTypeSet: Finished initializing centroid residue type set.
Created 1980 residue types
set up job distributor
randomizing loop
low res loop modeling
Traceback (most recent call last):

Post Situation: 

Error in loop modeling protocol

I m trying to run the the given script loops.py its showing error

Traceback (most recent call last):
File "loops.py", line 35, in
ccd = CcdLoopClosureMover(my_loop, movemap)
NameError: name 'CcdLoopClosureMover' is not defined

Here is full log

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

C:\Users\Zebrafish\Desktop\LOOPmodeing\loop_modeling\loop_modeling>python loops.
py

Post Situation: 

rosetta compile with mpi options

Hello

I am trying to compile rosetta with mpi options on our linux based university cluster but the compilation fails with the following error,

Before compiling, I copied the site.settings.tacc.lonestar.intel into site.settings in /tools/build/, since in one of the posts it was mentioned that this is suitable for compiling on intel based clusters.

$ ./scons.py bin mode=release extras=mpi
scons: Reading SConscript files ...
Running versioning script ... fatal: Not a git repository (or any of the parent directories): .git

Post Situation: 

pmut_scan does not produce log file

Hi all,

I am trying to get ddG estimates for mutations on a interface. I run successfully pmut application with several different parameters, but contrary to what I understand should happen no log file is produced with the ddG info. The mutated pdb file is indeed produced with a lot of information after the coordinates are written.

But I cannot find the ddG info there....

Should a log file be produced then?

Everything seems to run fine, but as I said I cannot find the ddG info.

Post Situation: 

profit program in antibody design

I am running /tools/antibody/sample_data/command to test the functions of rosetta antibody building. Everything seems fine until

Running ProFit...
profit < grafting/details/profit-H.in > grafting/details/profit-H.out sh: profit: command not found

My question is where can I get this "profit" command?

Thank you and best wishes,
Ting

Post Situation: 

MaxSub and MaxSub2.0

Dear all,

The definition of the "MaxSub" is the maximum number of residues that fit "well", and according to the original paper, the default cutoff distance is 3.5A.

Q1: Does Rosetta use the same cut-off?
Q2: what about MaxSub2.0?

Q3: Why some web servers give me different "maxsub" form Rosetta's?

Thank you so much for your continuous support.

Jad

Post Situation: 

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