The problem has been solved
Hi,
As the manual of PyRosetta just introuces some simple
movers like small mover and shear mover.
I want to know how to use backrub mover on PyRosetta.
thx.
Hello,
I'm using Rosetta 3.4 and I want to make a homology model of a GPCR protein -> I know very well how the model should look like.
This is the input I'm using:
/opt/soft/rosetta3.4/rosetta_source/bin/minirosetta.linuxgccrelease \
-database /opt/soft/rosetta3.4/rosetta_database \
-in:file:fasta mc4.fasta \
-in:file:fullatom \
-in:file:native s1p.pdb \
-in:file:template_pdb s1p.pdb \
-in:file:psipred_ss2 mc4.psipred_ss2 \
-frag3 mc4_03 \
-frag9 mc4_09 \
-out:file:fullatom \
Hi Everyone,
Our ROSIE server now have new Erraser protocol mode: Erraser single-residue. Please visit http://rosie.rosettacommons.org/ for documentation and job submission.
Best,
Rosetta@cloud is formed as a joint venture between University of Washington and Insilicos to offer the Rosetta molecular modeling software as a cloud-based, pay-per-use service to the biotech and pharmaceutical industry. Rosetta@cloud is hosted on Amazon Web Service, allowing customers access to the massive computer resources for a fraction of the cost normally required while eliminating the annual software licensing cost.
Hi Everyone,
Our ROSIE server now have Erraser protocol (developed in Das Lab http://www.stanford.edu/~rhiju/ ) open for public. Please visit http://rosie.rosettacommons.org/ for documentation and job submission.
Best,
Hi everybody,
I have taken the example on simultaneous stub placement, and modified it a bit.
In this example, one sidechain is forming a hydrogen bond. I don't need this
part so I removed it from the script. I just need to transplant two hydrophobic hotspots.
The original script works great, but when I modify it, I get problems with
the hotspot constraints. Basically, it seems they are not applied anymore.
The message I get in the output is:
"protocols.hotspot_hashing: Applied 0 hotspot constraints to the pose".
Hi all,
My cluster situation has changed, and my sysadmin needs to install a new OS on the cluster I'm currently using. He asked me if I could verify Rosetta's compatibility with the new OS he is planning on installing so we can recompile Rosetta on the new OS. I know the supported builds page of the documentation is a bit outdated from the last time I checked, so I thought it would be safer to run it past the devs first...the OS he's planning on running is OpenSUSE Linux 12.2.
Thanks,
Alex
Hi there,
I am running into problems with pmut using openmpi. We successfully compiled Rosetta3.4 with mpi support, but now that we run pmut with the openmpi command 'mpirun -np 8', the job does not distribute 'the work of creating and scoring all mutants evenly across all available CPUs' (as it says in the manual), but instead calculates every mutant 8 times: the log file lists every entry 8 times (see below). Am I doing something obvious wrong? Or did the compilation with openmpi fail?
Thanks a lot for your help in this matter.
Rene
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Hi,
I am a newbie in working with Rosetta. I used a flexpeptdock protocol to dock a peptide into protein. I tried to use scoring protocol and extract information from a silent file (result from docking) with 100 poses. After running "score.linuxgccrelease" with the default commands, rosetta starts and freeze with:
protocols.jobdist.JobDistributors: (0) Master Node -- Waiting for job request; tag_ = 1
Before I started Rosetta I compiled it with the mpi option. Is it possible this to be the reason for freezing?
Thanks.
Hello everybody,
I want to model some loops and the n-terminus of a protein.
The n-terminus is 45 residues long and I know the positions of the residues 14-20.
So I have created a homology model of my protein with these residues in correct position and now want to use Rosetta to improve the loops and the n-terminus before and after these 6 residues that I know.
