You are here

Home

Solved

The problem has been solved

Rosetta numbering with missing occupancies

Submitted by ShaneOConnor on Fri, 2011-10-07 16:18

Hi,

I've a short question so it should only require a short answer :-).

How does Rosetta numbering work with missing occupancies? For example, say we have a PDB structure containing three residues A6, A7, and A8. If all atoms of the second residue A7 have zero occupancy, does Rosetta map A6 to residue 1 and A8 to residue 2, omitting A7?

Post Situation: 
Solved
Forums: 
Rosetta 3 - General

minimize_with_cst problems (ddg_monomer)

Submitted by alexn on Tue, 2011-09-20 13:46

Hi all,

I'm trying to use the ddg_monomer application as described in the rosetta3.3 manual. It gives a command for preminimization of your input pdb structure using the application "minimize_with_cst". Trying this exact code with my pdb, or even with 2ci2.pdb found with the integration test, ends with "using -l option" as the last line of the output. Anyone else having similar problems or have a solution?

Post Situation: 
Solved
Forums: 
Rosetta 3 - Applications

Abrelax - Dunbrack02.lib.bin missing

Submitted by omirus on Sun, 2011-09-18 06:30

Hi,

I've installed Rosetta 3.3 (yes, downloaded after 9/6/11) and started some abinitio runs with the second method described in Wang et al. 2011 (PLoS ONE). After a few minutes Rosetta stops with the following warning:

"Warning: Unable to locate database file Dunbrack02.lib.bin"

I've checked the database directory, the file is not present. I have also checked Rosetta 3.2.1; the old version contains the files Dunbrack02.lib.bin and Dunbrack08.lib.bin, which are both missing in Rosetta 3.3.

Post Situation: 
Solved
Forums: 
Rosetta 3 - Applications

Pepspec - random runtime segfaults (rosetta 3.3 database replaced) [solved]

Submitted by loreseeker on Wed, 2011-09-14 08:13

Hello.

When running pepspec (pepspec.linuxgccrelease) I encounter random runtime segmentation faults, occurring at different "places"/times in consecutive runs with the same input and .args files.

I'm running Rosetta 3.3 on Ubuntu 11.04 workstation (quadcore, 4GB RAM) which has (seemingly) successfully compiled.
The pepspec demo test runs without problems.
Rosetta 3.3 database is replaced with the working version.

I've tried several different .pdb files, processed with fbb and otherwise and several different .args files. Segmentation faults occur with all.

Post Situation: 
Solved
Forums: 
Rosetta 3 - Applications

how to use constrains in PyRosetta?

Submitted by ast on Mon, 2011-09-05 07:22

Hi all,

I know this has been asked in some ways before, but never conclusively answered (at least for me ;-):
I do a design approach using the PackRotamersMover(). Now I want to have him use a constrain (e.g. AtomPair).
They way I think it should work:
1. tell the SF about the constrain: I tried "SF.set_weight(cst_weight, 2)" ... that doesn´t work because he does not know "cst_weight" ... so what is the correct description for the constraints in set.weights?
2. somehow load my constraint file as an object that I add in step 3 .... I have no clue how to do that.

Post Situation: 
Solved
Forums: 
PyRosetta - General

Compiling Rosetta 3.3 on Linux Mint

Submitted by proteinproteindock on Thu, 2011-09-01 16:05

I'm relatively new to programming, and this is the first time I'm learning a new software on my own so please bear with the possibly stupid question.
I'm having trouble reformatting my protein. All I have typed so far, just to check that I'm doing it right is: ./ligand_rpkmin.linuxgccrelease

and my error message is: bash: ./ligand_rpkmin.linuxgccrelease: No such file or directory

I'm in the correct directory, scons is installed, and I see the file ligand_rpkmin.cc...
So I tried to instead run: gcc ligand_rpkmin.cc

Post Situation: 
Solved
Forums: 
Rosetta 3 - Applications

Rosetta3 Tutorials Beta Release

Submitted by smlewis on Fri, 2011-08-19 13:35

At RosettaCON2011, many of the developers and users got together to write documentation for an afternoon under the beautiful, central Washington sunshine. I've put up a beta release of the tutorials that we assembled at RosettaCON2011 at
http://rosettadesign.med.unc.edu/collaborators/RosettaCon2011/RosettaCON....

Post Situation: 
Solved
Forums: 
Rosetta 3 - General

rosetta 3.3 Installation failed by Segmentation fault

Submitted by xpzhang on Wed, 2011-08-03 10:48

I downloaded Rosetta3.3_bundles.tgz, but file failed to be uncompressed. I downloaded rosetta3.3_source.tgz and rosetta3.3_database.tgz packages and tried to install it on my Fedora 13, which supported Rosetta 3.1, 3.2 and 3.2.1. Unfortunately, the compilation of Rosetta 3.3 failed by Segmentation fault. My system uses scons-2.0.1-1.fc13.noarch. I used "scons bin mode=release" command line.

The second question concerning the new release is: apart from the new functions, is there any change/improvement on the old programs (for example AbinitioRelax) exist in release 3.2.1?

Post Situation: 
Solved
Forums: 
Rosetta 3 - Build/Install

P(Res | phi,psi )

Submitted by jadolfbr on Thu, 2011-07-21 08:49

I would like to use a specific library for design using new distributions of P (Res | phi, psi). I found 7 files in the rosetta_database directory that seem to be exactly what I'm looking for: Paa, P_AA, Paa_n, P_AA_n, Paa_pp, P_AA_pp, P_AA_pp_08.2009
Our lab is in the process of becoming a Rosetta developer officially once again, but that will take some time.

First, can anyone point me in the right direction as to the format of each of these files/how each of them are used?. Some, like P_AA seem fairly obvious, but some of the others I have no idea.

Post Situation: 
Solved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Solved