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compile pyrosetta under redhat 5.9 with g++ 4.1.2 and python 2.7.4

Submitted by coomteng@gmail.com on Sun, 2014-08-31 09:53
Category: 
Compilation

Hi,

the compilation was successful but when I run the TestBindings.py it always shows the following error.

rosetta-3.5/rosetta_source/src/python/bindings/rosetta/core/scoring/methods/__methods_all_at_once_.so: undefined symbol: _ZN4core7scoring7methods15PBLifetimeCache7set_pbpERKSsN7utility7pointer10owning_ptrINS0_25PoissonBoltzmannPotentialEEE

g++ version: 4.1.2 or 4.4.7 the same error.
python version 2.7.4
boost_version: 1.46 or 1.5.6

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PyRosetta - Build/Install

Problem in using "loopmodel" application to add missing residues

Submitted by sushreet on Wed, 2014-08-27 12:43
Category: 
Loop Modeling

My problem is with flags -max_helix_melt and -max_strand_melt while creating the loopfile. If I take the default values (-1), it is creating the loopfile with no LOOP information. I have tried with other values which did not give me the correct LOOP information. How should I determine the correct values for these flags to get the correct loopfile. Please suggest.

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Rosetta 3 - Applications

Getting chi rotamers

Submitted by ajasja on Tue, 2014-08-26 12:11
Category: 
Non-Canonical Peptides
PyRosetta

Hi!

Is there a way to get rotamers in PyRosetta? I googled around and found this old post, but the conclusion seemed to be, that it might be easier to implement the parsing of the rotamer libraries again. Is this still the case?

I tried to explore on my own (see ipython notebook), but the most promising function

pose.residue(6).chi_rotamers(1)

returns

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PyRosetta - General

Error when using next-gen KIC (Signal 6)

Submitted by janwp on Tue, 2014-08-26 08:36
Category: 
Loop Modeling

Dear all,

I keep receiving a very strange error message when using NGK on a 24-core (48 mpi threads) workstation. The error occurs normally around the ~ 180 output file (once i made it to > 600 but I am aiming for at least 2000). I am trying to model up to 4 loops simultaneously but the error also appears sometimes if I model only one loop. I also tried reducing to no more than 20 threads but the error would still appear.

After googling a bit I tried to set:

ulimit -s unlimited

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Rosetta 3 - General

Can I export command line & result from iPython PyRosetta shell to a text file?

Submitted by lanselibai on Mon, 2014-08-25 04:05
Category: 
PyRosetta

Dear Sir or Madam,
I know we can use cmd.exe to export command line by using

python name.py > name.txt

However, we cannot see anything in the cmd.exe if we do that.

I am thinking can we export result from iPython to a text file? I was trying

run name.py > name.txt

But I think the file of "name.txt" has not been created.

Can you please help me? Thank you very much.

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PyRosetta - General

Large Memory usage in Windows r10 Build

Submitted by ajasja on Fri, 2014-08-22 09:09
Category: 
PyRosetta

Dear all,

When running simple scripts such as these, the memory usage of the python interpreter under windows goes to about 5.5 GB. Im using the r10 version of PyRosetta.Is such high memory usage normal?

Under linux (version '56891:56891:6efc58f8abb54611ace5a6cdd7e69e6c970a01ef') the same script takes about 1 GB.

Does this perhaps have something to do with the monolith (win) vs namespace (linux) release?

Best regards,
Ajasja

 

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PyRosetta - General

Adding 'virtual' residues for N- and C-terminal optimisation

Submitted by Derek Smith on Thu, 2014-08-14 23:18
Category: 
Structure prediction

Dear All,

I would like to optimise the N- and C-termini of a model, and would like to use some of the loop modeling protocols to do so. I have read in the documentation that virtual residues are required for this. How do you add these? Are there examples in the tutorials?

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Rosetta 3 - Applications

Incorporating iron-sulfur cluster into ROSETTA applications

Submitted by Derek Smith on Thu, 2014-08-14 23:12
Category: 
Small Molecules

Hello,

I am working with an enzyme that uses Fe4S4 iron-sulfur clusters as co-factors. I recently built a model (using other software) and want to use ROSETTA for optimisation and enzyme design. I am very new to the software suite, and have managed to relax the protein together with the substrate ligand, for which I have a mol2 file. I would also like to include the iron-sulfur cluster, for which I have PDB coordinates, as well as AMBER PREP and FRCMOD files.

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Rosetta 3 - Applications

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