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null rosetta energy/score

Submitted by fred on Tue, 2011-10-18 10:31

Hi there,
I have extracted the 5% best scores structure from 100,000+ decoys and combine them into one single silent file. After clustering I have realized their rosetta energy/score are all null. Of course, I was intend to cluster and sort them by energy. However, the score flag have been lost upon extract process. Is there any keyword to preserve their energy flags when extracting?

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Rosetta 3 - General

error: CPU you selected does not support x86-64 instruction set [SOLVED]

Submitted by UliG on Mon, 2011-10-17 08:03

Dear colleagues,

I am trying to install Rosetta 3.3 on:

- HP ProLiant DL380 G6
- CPU: 2 x Intel Xeon Quad Core
- OS = SUSE SLES 11, kernel 2.6.27.19, x86_64
- compiler: gcc 4.3-62.198-x86_64
- python: 2.6.5
- scons: 2.1.0

command: scons bin mode=release OR additionally arch=x86 arch_size=64

crash + error message:

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Rosetta 3 - Build/Install

Debugging Rosetta under XCode

Submitted by sacch on Sun, 2011-10-16 18:23

Hi all,

I am new in Rosetta. I am planning to add a new empirical force field to rosetta, but I have no idea what is the best cutting point in order to be able to debug it. Here is my question.....
1. What's the size of the memory typically required for debugging Rosetta under Xcode?

The configuration of my machine:

Processor 2.8 GHz Intel Core 2 Duo
Memory 8 GB 1067 MHz DDR3
Software Mac OS X Lion 10.7.2 (11C74)

I have successfully compiled Rosetta using "-j 2 mode=debug bin --". The default compiler is GCC 4.2.

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Rosetta 3 - General

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?

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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?

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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.

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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.

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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.

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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

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Rosetta 3 - Applications

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