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Bug in cluster?

Submitted by nitroamos on Mon, 2011-11-21 12:53

When I run the cluster application with the following command:

cluster.linuxgccrelease -database ~/rosetta3.3//rosetta_database -in:file:s *.pdb -in:file:fullatom -cluster:radius -1 -cluster:gdtmm -cluster:limit_clusters 25 -cluster:limit_total_structures 100 -cluster:sort_groups_by_energy

I'm getting lines with:

protocols.cluster: Adding struc: 2.32622e-310

in the output... There's nothing suspicious about the rest of the output, and it seems to be giving me reasonable results...

Is this a bug, or am I doing something wrong?

thanks!

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Rosetta 3 - General

PyRosetta version 2.011 for Mac/Linux is ready to download!

Submitted by Sergey on Mon, 2011-11-21 08:51

Hi Everyone,

PyRosetta version 2.011 for Mac/Linux is ready to download!

Release notes:
- PyRosetta - PyMOL integration.
- All Rosetta classes can be subclassed in PyRosetta.
- It’s now possible to define custom energy terms in PyRosetta (Examples can be found in test/*Subclassing*)
- Rosetta libraries updated to r45995 (Nov 2011)

For download links for various distribution visit: http://www.pyrosetta.org/

Sergey.

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PyRosetta - General

Rosetta releases and revision numbers

Submitted by ShaneOConnor on Thu, 2011-11-17 13:55

Hi mini,

It's happened to me a few times that I've needed to check out older versions of Rosetta for compilation. Sometimes it's also handy to know the revision numbers of the releases quickly. I've not yet found a list of releases and their SVN revision numbers so I created the following. Please correct it if I've made any mistakes. To add to Rocco's comment below, please note that the corresponding trunk revisions are approximate i.e. tThey correspond to the point of branching from the trunk but the releases may include bugfixes from later trunk revisions.

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Rosetta 3 - General

Can not build the parallel version of rosetta-2.3.1 (the SnugDock). Help!!

Submitted by ice_flame on Fri, 2011-11-11 07:53

Compilation
Hi all,

I was trying to build a parallel version of Rosetta-2.3.1(SnugDock) on my workstation. My OS is RHEL 5.4(32-bit), and I use Openmpi-1.4.3.

I tried to compile it as I did to Rosetta2.3.0 on the same computer and the very same OS and MPI compilier, but it didn't work.

I got the following errors:

######################
job_distributor.cc:(.text+0x5ada): undefined reference to `pathways::pathways_generator_main(bool&)'
collect2: ld return 1
make: *** [rosetta.mpilam] error 1

######################

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Rosetta++ - General

InterfaceAnalyzer -resfile

Submitted by gw on Wed, 2011-11-02 16:01

The InterfaceAnalyzer documentation leads me to think that resfiles are fully supported for design purposes. However InterfaceAnalyzer does not seem to recognize my resfile. The structure output is identical to the input. Here is my protocol

$rosetta3.3/rosetta_source/bin/InterfaceAnalyzer.linuxgccrelease
-database $rosetta3.3/rosetta_database/
-s input.pdb
-use_resfile true
-resfile ala.res
-add_regular_scores_to_scorefile

# ala.pep
NATAA
start
1 C PIKAA A
2 C PIKAA A

Thanks in advance

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Rosetta 3 - Applications

Rosetta3.3 installation error

Submitted by lzx32 on Wed, 2011-10-26 08:40

Dear developers,

I have downloaded Rosetta3.3 and run Scons bin mode=release. Everything seemed to be fine till I ran the tenzyme_design protocol.

Here is what I got:

/usr/local/rosetta3.3/rosetta_source/bin/enzyme_design.linuxgccrelease -database /usr/local/rosetta3.3/rosetta_database/ @flags >first_try.log

/usr/local/rosetta3.3/rosetta_source/bin/enzyme_design.linuxgccrelease: error while loading shared libraries: libprotocols.so: cannot open shared object file: No such file or directory

I can find the liprprotocols.so file in one of the directories:

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Rosetta 3 - Build/Install

How to get PyRosetta on OS X 10.6.6 working successfully

Submitted by ara on Mon, 2011-10-24 15:22

Hello all,

I thought I would post this here to help other folks installing PyRosetta.

My system is as follows:
OS X 10.6.7
Intel Core 2 Duo - 64 bit (To find out if you have a 64 bit machine go here http://support.apple.com/kb/ht3696)
X-Code installed
Native OSX python

1) After you have installed X-code and download PyRosetta open up your terminal and type:
$ which python

You should see something like this:
/usr/bin/python

Then at the command line type:
$python

Your output should look like this:

Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49)

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PyRosetta - Build/Install

Scoring issues - differs from command line vs .py file - for a simple ddG loop

Submitted by ara on Mon, 2011-10-24 13:16

Hello all,

I was able to get PyRosetta up and running on my mac under OS X 10.6.6 . I am working on what I think is a simpler version of the ddG script (we don't need the docking feature). What I am trying to do is bring in a pdb file, score it using the ddG paramters, and then mutate each residue (basically cycle through all the possible combinations)to see what happens to the ddG values are. The start of the script is here: (The loop is a mess at the moment)

from rosetta import *
init()

pose = Pose()
pose_from_pdb( pose , "2O2X_clean.pdb" )

pymover = PyMOL_Mover()

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PyRosetta - Scripts

prepack_example.sh error message

Submitted by sacch on Sun, 2011-10-23 23:22

Dear all,

I am running pre pack_example.sh while using FlexPepDocking. I have used almost the same commands and flags as what I have used in the example 2b1z (where 2b1z runs fine) on a new antibody-peptide pair, 2hfg, but I got the following error while running

FlexPepDocking.linuxgccrelease -database $PATH_TO_DB @../prepack_flags. Could someone point out what have I done wrong please?

Error message:

ERROR: this_pose.total_residue() == residue_packstat_.size()
ERROR:: Exit from: src/protocols/toolbox/pose_metric_calculators/PackstatCalculator.cc line: 164

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