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Snugdock+ensembledock usage

Submitted by Anouk on Mon, 2014-09-22 08:09
Category: 
Docking

Hi all,

I have a quick question:
i have submitted 5 antibody sequences to Rosie and for each of them got ten lowest-energy structures. I have the solved structure of a protein X. I read the paper of Snugdock, got excited by the idea of using snugdock with ensembledock together and now want to perform a docking of my protein X using the models i got from Rosie.

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Rosetta 3 - Applications

Help for a Beginner Needed! Installation on Win 8 Computer

Submitted by wushufury on Sun, 2014-09-21 14:21
Category: 
Compilation

Hi- Being very new to this, I've only had a chance to skim through the forums. I did have a few questions, though. As I'm new to using python and RC, I want to thank whomever for answering for their patience in helping me understand this.

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Rosetta 3 - Build/Install

Questions for "modeling_instructions.pdf" in "Homology or Loop Modelling"

Submitted by lanselibai on Sun, 2014-09-21 09:02
Category: 
Structure prediction

Dear Sir or Madam,
I am trying to following "modeling_instructions.pdf" in "Homology or Loop Modelling".

http://www.meilerlab.org/index.php/jobs/resources

The first thing I need help is
Section "2. Run ROSETTA Comparative Model protocol".
After typing the COMMAND FOR COMPARATIVE MODELING PROTOCOL (attached) into terminal, I got "Exit 255" in the prompt and "ERROR" in the comparative_model.log (attached). The options file is also attached.

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Rosetta 3 - Applications

flexpepdock_score_only

Submitted by ays on Sun, 2014-09-21 06:17
Category: 
Scoring

Hi,
I used flexpepdock_score_only find the rmsca between 2 complexes. I also caculated the rmsca between the 2 complexes ((deltax^2+deltay^2+deltaz^2)^0.5) but the rmsCA score I got was different than the one I got using flexpepdock_score_only. Why is that happening?

Note - both complexes have the same sequence of aa.

Thanks!

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Rosetta 3 - Applications

Viewing and modifying hydrogen bond detection criteria

Submitted by promero on Tue, 2014-09-16 15:26
Category: 
Scoring

Hello! I have been working with PyRosetta for a while to model protein-ligand interactions. I was getting hydrogen-bond information from other software, but wanted to use PyRosetta's Hbond set for my pose. Rosetta did not find all the expected hydrogen bonds, so I wanted to check what criteria was used by Rosetta to find the HBs, and also see whether I could tweak these criteria in any way (things like maximum distance, or maximum angles, etc.).

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PyRosetta - General

Rosetta membrane blastpgp/psiblast database problem for lips4 generation

Submitted by fbarrera on Tue, 2014-09-16 11:45
Category: 
Membrane

I have run Rosetta membrane successful in the past, but it seems that now the blastpgp database necessary to run the run_lips.pl script is obsolete.
In the lastest BLAST release, blastpgp has been dropped entirely in favor of psiblast.
I am then blocked and I cannot generate the lips4 file using:
run_lips.pl <fasta file> <span file> <path to blastpgp> <path to nr database> <path to alignblast.pl script>

Is there a way of the run_lips.pl connecting the psiblast, or does it need to be modified?

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Rosetta 3 - General

Atom_.cc line 304

Submitted by fred on Thu, 2014-09-11 12:04
Category: 
Structure prediction

Hi list,
I'm running the minirosetta.mpi threading protocol and everything seems to be working fine.
The query silent is been regularly updated and I can extra pdbs from it.
However, from time to time get the following error message on screen.

ERROR:: Exit from: src/core/kinematics/tree/Atom_.cc line: 304

Any ideas?
Best.
Fred

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Rosetta 3 - General

Missing residue coordinates in PDB files

Submitted by lanselibai on Thu, 2014-09-04 07:34
Category: 
Structure prediction

Dear Sir or Madam,
I got a PDB file, in which some of the residue coordinates are not resolved (shown below, missing from 136-139). But I can still know the amino acid sequence. Can I ask what is the best way to estimate those missing coordinates?

I am thinking manually copy the coordinates of same type of residue to the PDB file, followed by minimization to some extent. Is this okay? What particular minimization protocol/restrain should I use?

Thank you very much.

Yours sincerely
Cheng

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PyRosetta - General

system requirements (python and scons versions, etc) for Rosetta 2014.3x?

Submitted by megirvin on Wed, 2014-09-03 08:50
Category: 
Compilation

Hello,

I'm having trouble compiling rosetta 2014.34 on a red hat machine, and it looks like the problem may be with one or more missing features/attributes in one (or more) python modules. What versions of python (and I guess scons) are needed?

Thanks, - Mark

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Rosetta 3 - Build/Install

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