You are here

Unsolved

The problem hasn't been solved

mpi / jd2 with AbinitioRelax and relax (3.2)

Hi,

I have a working mpi compile of Rosetta 3.2, and intend to use AbinitioRelax and relax on a cluster.

Things are currently working:
- with NO EXTRA PARAMETERS in my flags file (so same flags file as for single processor). Note that I have "-run:constant_seed" and "-run:jran 1111111" in my flags file.
- using "mpirun -np 8 scriptfile" (looks like one core is used for management, and 7 used for computations, and speed improvement is ~6X versus non-mpi version)

My question relates to potential JD2 parameters I could use in my flags file.

Post Situation: 

Domain Insertion equivalent in Rosetta 3.2

Hi,
I'm trying to get something like the domain insertion mode in 3.2. For example, I have a 100 residue protein and I'd like to remodel the 50 residues between residues 25 and 75. Should I add a jump between residues 25 and 75 and have rosetta read a movemap to fix the backbone angles of residues 1-25, and 75-100?

Thanks

Post Situation: 

Protein design - PyRosetta Script problem

Hi,

I am running the script for protein design downloaded from http://pyrosetta.org/scripts.html.

It makes design of the last 10 aa of the protein while the rest of the protein remains unchanged.
When I calculated 100 decoys, in 99 cases I obtained the same sequence of the designed fragment (different from the native one).

When I allowed for changes of sidechains rotamers in the rest of the protein I also obtained sets of the same decoys.

It is strange... Is it ok???

Post Situation: 

PyRosetta 2.0 Beta Strand Build

I'm having a strange issue with the beta version of PyRosetta (using 64bit Ubuntu). The phi,psi dihedral angles corresponding with an alpha-helix, when applied to a 20-mir polyA structure (this is simply from the tutorial) returns an alpha-helical structure as expected. But the dihedral angles corresponding with a beta strand (-135,140) returns a completely incorrect, wheel like structure. It's as if the changes weren't applied. Could someone confirm this with their 2.0 build?

Post Situation: 

questions about ab init membrane protein

Hello
I am trying to use the membrane ab initio modeling application by the following command:

    run_lips.pl (fasta file) (span file) (path to blastpgp) (path to nr database) (path to alignblast.pl script)

    example: (path to mini)/mini/src/apps/public/membrane_abinitio/run_lips.pl BRD4.fasta BRD4.span /work/bjornw/Apps/blast/bin/blastpgp /scratch/shared/genomes/nr ~bjornw/mini/src/apps/public/membrane_abinitio/alignblast.pl

Post Situation: 

Installation of rosetta 3.2 of fedore core 6 platform

Hi ,

I am trying to install rosetta 3.2 on fedore coer 6 platform but I am getting the following errors after giving scons bin mode=release command :-

[root@bmel rosetta_source]# scons bin mode=release
scons: Reading SConscript files ...
svn: '.' is not a working copy

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/usr/local/rosetta-3.2/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.

Post Situation: 

Performance improvement in AbinitioRelax and relax 3.2 ???

I got the following benchmarks for AbinitioRelax and relax (version 3.2). The speed improvement I observed compared to 3.1 are so important that I am wondering if they are real. I would appreciate if someone could confirm that such improvement (3.2 vs 3.1) is really to be expected.

System : 90 residues protein

Protocols tested :

1. "AbinitioRelax -abinitio -out:nstruct 100"
2. "relax -relax" (3.1) or "relax -relax:thorough" (3.2) on above abinitio structures
3. "relax -relax:fast" on above abinitio structures

Post Situation: 

NMR / NOE related tools in 3.2 ?

Is there an increase in NMR functionality in 3.2? Although I saw nothing in the 3.2 documentation to suggest this, the 3.2 version of "relax -help" and "score_jd2 -help" now suggests a wide array of NMR-related options (see attachment with partial output from "relax -help". So, are there really new NMR-related tools in 3.2? Are those documented somewhere?

Stéphane

Post Situation: 

Pages

Subscribe to RSS - Unsolved