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RMS determination using Rosetta 3.3

Submitted by adraney on Thu, 2011-12-08 12:44

To give some context, I have a set of decoys that I've run cluster analysis on and now I'm trying to look at analyzing the clusters to see what similarities there are within the cluster. The long term goal is to analyze the 0th cluster, which contains the most structures, which is hypothesized to be the most likely place for where the true structure will be. That being all fine and dandy, I've isolated the poses that I need and was trying to determine the rms of each pose against the middle pose of the cluster.

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Rosetta 3 - Applications

Pair potential

Submitted by jadolfbr on Thu, 2011-12-08 08:06

Does anyone know if the pair term has changed since it's introduction? Does it use the same pdb statistics and bins as described in:
Simons, K. T., Ruczinski, I., Kooperberg, C., Fox, B. A., Bystroff, C. & Baker,D. (1999) Proteins Struct. Funct. Genet. 34, 82–95.

It seems as though the term is the same for centroid and full-atom scoring. Is this true?

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Rosetta 3 - General

Re: Multigraft

Submitted by bharat_46010 on Wed, 2011-12-07 17:24

Is is possible to graft a continuous site such as P-loop onto a known scaffold instead of searching a new one using Multigraft approach. The p-loop occurs between a helix and a beta-sheet . I want to graft the same onto the surface loops of my protein , maintaining the geometry of those residues that occur in P-loop. Hope my question is clearly understandable .

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Rosetta 3 - General

Creation of core.* file in current running directory

Submitted by alejandro on Tue, 2011-12-06 06:19

Good afternoon,

I'm using Rosetta as a library inside my own code and I'm running several instances of my programs on a cluster. It happens that, sometimes, a file named core.* is created in the directory where the programs are launched where * is a number (e.g. 1041, 15897, etc.). This file can weight up to 2GB but its size varies.

Can anyone explain this behavior, tell me if it's normal and give me some clues to avoid the creation of this file?

Thank you in advance for your help

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Rosetta 3 - General

Rosetta 3.3 installation error

Submitted by bharat_46010 on Tue, 2011-12-06 04:20

Hi,

I am trying to install rosetta 3.3 on fedora core 14 platform. I am getting the following error after executing scons bin mode=release command :-

[pauling@BME rosetta_source]$ scons bin mode=release
scons: Reading SConscript files ...
Traceback (most recent call last):
File "/home/pauling/Downloads/rosetta3.3_bundles/rosetta_source/SConstruct", line 139, in main
build = SConscript("tools/build/setup.py")
File "/usr/lib/scons/SCons/Script/SConscript.py", line 614, in __call__
return method(*args, **kw)

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Rosetta 3 - Build/Install

ddg with ligands

Submitted by bhaines1 on Mon, 2011-12-05 14:32

Could someone please recommend a way to include ligands in a ddg calculation (using ddg_monomer or otherwise)? I'd like to estimate the effect of mutations to the protein domain on the stability of the interface between said protein domain and the enzyme substrates.

Thank you in advance for any response!
Brandon

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Rosetta 3 - Applications

problems in InterfaceAnalyzer analysis

Submitted by chenchaozhao on Fri, 2011-12-02 23:36

Hi, everyone!

Now I met a samll bug during InterfaceAnalyzer analysis as follows.

`core.io.silent: Reading all structures from 1-46wt.out
core.io.silent: bad format in sequence line of silent file
core.io.silent: line = SEQUENCE:
core.io.silent: tag = SEQUENCE:
terminate called after throwing an instance of 'utility::excn::EXCN_BadInput'

And the starting lines of my silent file are:
`SEQUENCE:

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Rosetta 3 - Applications

Can one use a non-write privileged rosetta executable?

Submitted by jhbrown on Tue, 2011-11-29 12:15

I am trying to do a comparative modelling using /sware/rosetta3.3/linux/rosetta_source/bin/minirosetta.linuxgccrelease.
The program didn't run, and the last few lines of the log file are:

Warning: Unable to locate database file Dunbrack02.lib.bin
core.pack.dunbrack: Dunbrack library took 8.4 seconds to load from ASCII
Warning: Unable to locate database file Dunbrack02.lib.bin
Warning: Unable to locate database file Dunbrack02.lib.bin
core.pack.dunbrack: Opening file /sware/rosetta3.3/linux/rosetta_database/dun02bwtPgW for output.

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Representing Cross-linked nitrogens

Submitted by jjlee2 on Sat, 2011-11-26 18:42

I am trying to use Rosetta 3.3's Ab-initio relax program to fold a protein with cross-linked lysines. I am trying to use distance constraints to represent the cross links, but every time I try to run Ab-initio on the following constraint file, I get the error "Exception : Atom NZ 26 not found". Does anyone know why this might be happening?

Thanks

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