You are here

Home

Unsolved

The problem hasn't been solved

Generate structural fragments

Submitted by kingljy on Tue, 2011-05-10 20:18

Hello everyone,when I run "/rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta",I got the error follow:
[root@localhost input]# /rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta
Run options:
be verbose.
don't run psipred.
don't run prof.
don't run jufo.
don't run sam.
FILENAME: trhl2.fasta
no id specified. parse filename instead.
INTERMEDIATE: trhl2.fasta
ID: trhl CHAIN: 2
Warning: can't find executable file /work/chu/src/shareware/psipred/bin/psipred!

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Dunbrack Library

Submitted by jadolfbr on Tue, 2011-05-10 13:59

Hi All;

I'm trying to import a new Dunbrack library into PyRosetta.
I've found the RotamerLibrary class in core.pack.dunbrack._dunbrack_all_at_once and a method create_fa_dunbrack_libraries(), but I am unsure how to call it or setup an instance. Can anyone help? Thanks.

-Jared

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

abinitio - is there a way to limit number of CPU cores the program uses?

Submitted by burkheadlab on Mon, 2011-05-09 16:37

So the lab I'm working in has access to a 16 core server but we were told to use no more than 8 cores for any one application. So I was wondering if there is a way to limit the number of cores that abinitio uses while it runs its folding simulations? I looked through the help but didn't see anything that looked like it was what I'm looking for. Thanks for the help.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pyrosetta energy function

Submitted by somayyehzangooei on Mon, 2011-05-09 08:20

I am considering various conformations of a given protein and I should compare their corresponding energy values. I have used Pyrosetta to compute the energies using the "scorefxn = create_score_function('standard')" command. I was under the impression that the PDB structure of a protein should have the minimum energy.

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

'DockingProtocol' object has no attribute 'setup_foldtree'

Submitted by karelk on Wed, 2011-05-04 06:24

Hi around, sorry for disturbing with my problem that I haven't found posted or solved and if it has been solved I didn't find it. I recently downloaded PyRosetta and would like to use it for docking. The easiest, I thought, is to take an example script that comes with PyRosetta - docking.py, taking the test_dock.pdb that also comes with PyRsoetta and run it to get an idea about computational time. But it doesn't work by writing:
=========
docking.py in ()
15 print "setting up docking fold tree"

Post Situation: 
Unsolved
Forums: 
PyRosetta - Scripts

Problem readin .ccp4 map file

Submitted by jljbbc on Tue, 2011-05-03 11:29

Hi all,
I have bin trying to run the electron_density/molecular_replacement demo at step 4 run_rosetta_mr_nogap.sh and I get the following error. There is nothing wrong with the ccp4 map file (opens fine in other programs)but it appears to be looking for a MRC format map. How do I get the program to accept the ccp4 map?

core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ ERROR ] Error opening MRC map MR.1_2mFo-DFc.ccp4. Not loading map.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Version of VALL Database and Corresponding Constraint Coordinate File for Fragment Generation

Submitted by jurkm on Mon, 2011-05-02 03:00

Dear all,

I realized that the latest vall database that comes with Rosetta 3.2 is version 2006-05-05. Unfortunately, there is no corresponding constraint coordinate file ("vall_cst_coord.dat.") for that database. Both database files are only available for the 2001-02-02 version. Is there a way to get the constraint coordinate file also for vall 2006-05-05?
The 2001 version contains only one-third of entries in comparison to the 2006 version.

I want to use this for fragment picking using also my experimental NMR data (can't rely on Robetta).

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Problem with the -dock_ppk flag

Submitted by lzx32 on Sat, 2011-04-30 00:21

Hey everyone,

I have been running protein docking with two monomeric proteins by using Rosetta3.2. Everything seemed to be fine with the docking runs except when I added the -dock_ppk line into the flags file.

Instead of having the -dock_ppk line in the flags file, I also tried to prepack the proteins by using the command line:

/usr/local/rosetta3.2/rosetta_source/bin/docking_protocol.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ -s input1.pdb -dock_ppk

It did not work either. Here is the last portion of the log file:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Problem with symmetric docking

Submitted by saxen on Fri, 2011-04-29 15:15

Hello everyone,
I'm trying to refine a homotrimer by using symmetric docking in Rosetta 3.2.1. I built the symmetry definition file and ran the following command:

~/rosetta_bin/docking_protocol.linuxgccdebug -database ../rosetta_database -in:file:s INPUT.pdb -in:file:fullatom -ex1 -ex2 -symmetry:symmetry_definition symdef.txt -symmetry:initialize_rigid_body_dofs -symmetry:perturb_rigid_body_dofs 3 8 -nstruct 1 -out:file:fullatom

Which yielded the following output

core.init: Mini-Rosetta version exported from unknown

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Pages