# Unsolved

The problem hasn't been solved

## Problems installing Rosetta in linux 32 bits

Hi,
I am trying to install PyRosetta v2.0 (beta) in Ubuntu Linux 32 bits. I installed python 2.5 and manage to put it as default (2.7 was default in Ubuntu). But, when I tried to import PyRosetta ("from rosetta import" * or "import rosetta") I got the following answer:

Traceback (most recent call last):
File "", line 1, in
File "rosetta/_init_.py", line 11, in
import utility
File "rosetta/utility/_init_.py", line 1, in
from _utility_all_at_once import *
ImportError: libpython2.6.so.1.0: cannot open shared object file: No such file or directory

Post Situation:

## Energy of individual loop/region

Hi All,

I have an experiment that I did loop modeling on for 6 loops in each PDB. Energy vs. to_native_RMSD of the lowest energies are awful, so I now need the individual energies for each loop.

What I am trying to get is basically the total residue energy and the 2 body contributions of each of the loop residues' neighbors. Having trouble in a few different areas.
First, using score.eval_ci_2b and observing the non-zero energies gives the same scoretypes, with different energies as eval_cd_2b. This makes no sense...VDW, fa_pair, hack_elec are all ci_2b energies...

Post Situation:

## How can i introduce hydrogen bond as constraint?

Hi everyone,

i need you help~

i am trying to introduce hydrogen bond constraints.

something like this:

Let O on residue 1 and N on residue 10 form hydrogen bond.
Let N on residue 1 and O on residue 20 form hydrogen bond.
etc.

i had tried to place the two hydrogen bond atoms close as distance constraint.

but mostly the distance constraint is not enough

so i want to calculate hydrogen bond as a constraint.

i had tried to use hbonds.HBondSet().

but i can only display hydrogen bond state uwing hbonds.HBondSet().show()

Post Situation:

## General Protein Folding Question

Hello. I have a few questions about abinitio structure prediction.

1) Can abinitio predict secondary structure as well, or does it just take secondary structure as a given based on inputs for fragment picker?

2) Is it worth using Rosetta to fold an 800 AA long protein? Are there some tips/tricks needed to run predictions for such a large protein?

Thanks.

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## PyRosetta Folding.py script

I am trying to run the folding.py sample script using the test_in.pdb, frag3 and frag9 files, but I am getting this error:

AttributeError Traceback (most recent call last)

/usr/local/src/pyrosetta/input/folding.py in ()
508 kT , long_inserts , short_inserts , cycles ,
509 jobs , job_output ,
--> 510 PyMOL_Mover_ip , disulfides )
511
512 ################################################################################

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## Rosetta 3.4 installation on fedora core 14

Hi,

I am trying to install Rosetta3.4 on fedora 14 platform. I am getting the following error after issuing the command : scons bin mode=release

ObjexxFCL -lz -lcppdb -lsqlite3
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
scons: *** [build/src/release/linux/2.6/64/x86/gcc/4.5/libutility.so] Error 1
scons: building terminated because of errors.

Pls guide ??

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## how to use AbinitioRelax.mpi.linuxgccrelease?

hello:
I've compiled Rosetta with MPI option and I am trying to use AbinitioRelax.default.linuxgccrelease by command:

mpiexc -n 8 AbinitioRelax.mpi.linuxgccrelease @flags>log &

and I found that there are eight score for each model(eg: model001 model001 ... model001, model002, model002...model002). It seems that Rosetta use eight CPU to generate eight pdb file with the same name and each one overwrite the previous one and we only get the last one in the end.....

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## Membrane folding - blastpgp error.

I know that there have been a number of posts about this problems but none of them post solution to this so hopefully someone can help.

I am attempting to run_lips.pl with the following command

/home/eliza/rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl eliza.FASTA eliza.span /home/eliza/ncbi/blastpgp /home/eliza/ncbi/nr /home/eliza/rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl

But I get the error....

Error in alignblast.pl: blast output file eliza.FASTA truncated:
readline() on closed filehandle MSA at /home/eliza/rosetta/rosetta_

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## Error getting MinMover attributes

Hi,

I’m experiencing some very strange behavior on part of PyRosetta.

I'm running pre-built PyRosetta v2.011 for ScientificLinux (64 bit, r47657) on Linux 3.0.3 ( x86_64) with Python 2.6.6. I’ll use MinMover as an example, but this happens with many other object types.

I can instantiate, configure and run a MinMover without a hitch, e.g. min_mover.tolerance(0.025) works fine. But when I try to access that information using a getter, i.e. min_mover.tolerance(), I get an ArgumentError.

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