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error when compiling on ubuntu-10.10

Submitted by Rustaman on Fri, 2011-04-29 21:46

I had tried to compile (build) rosetta-3.2 on PC running Ubuntu-10.10 (64 bits),
I have conducted downgrade of gcc to version 4.1,
with this command:

$/> ./scons bin mode=release

but, after approx. half an hour compiling, I got the following errors:

-Lsrc -L/usr/local/lib -L/usr/lib -lObjexxFCL -lz
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
scons: *** [build/src/release/linux/2.6/64/x86/gcc/libutility.so] Error 1
scons: building terminated because of errors.

What should I do to resolve this errors?

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Rosetta 3 - Build/Install

maxsub calculation in scoring app

Submitted by abdullah on Thu, 2011-04-28 06:47

Dear Rosetta,

I'm trying to calculate maxsub values between a native PDB structure and a set of ab-initio predicted decoy structures using score.linuxgccrelease. According to the manual score.linuxgccrelease should print out maxsub if a native structure is provided. However, running the following command:

score.linuxgccrelease -in:file:s S_00000006_58.pdb -native 1ctfA.pdb -score_app::superimpose_to_native

returns only a RMSD value:

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Rosetta 3 - General

SequenceRelax on a loop

Submitted by jtmacd on Mon, 2011-04-11 07:53

Hi there,

Is there a way of doing SequenceRelax on a loop?

So far I have managed to do simple energy minimization with the attached script:

from rosetta import *
rosetta.init()
pose = Pose("test_in.pdb")
mm4060 = MoveMap()
mm4060.set_bb_true_range(15,24)
loop = Loop(15,24,20)
set_single_loop_fold_tree(pose, loop)
minmover = MinMover()
minmover.movemap(mm4060)
scorefxn = create_score_function('standard')
minmover.score_function(scorefxn)
print scorefxn(pose)
minmover.apply(pose)
print scorefxn(pose)
minmover.apply(pose)
print scorefxn(pose)
minmover.apply(pose)

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PyRosetta - General

membrane ab-initio modeling, is the quality comparable to comparative modeling of 20% id template?

Submitted by fglaser on Thu, 2011-04-07 07:57

Dear All,

I would like to try your membrane ab-initio modeling protocol of rosetta, to model a membrane protein of 6 TM regions. But I am not sure how your protocol should perform compared to homology modeling, this protein has 370 aa and has a distant template of about 20% id for 300 aa region. I wonder if rosetta ab-initio method could produce equivalent or better results than the comparative modeling based on the template we have, and what is the best course to follow. And wether or not the results will be comparable.

Best regards and thanks a lot,

Fabian

--

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Rosetta 3 - Applications

How to build a parallel version of rosetta++(Rosetta 2.3.0)???

Submitted by ice_flame on Fri, 2011-03-25 22:24

Hi Rosetta users,

I'm using Rosetta 2.3.0. I want to build a parallel version. I installed MPICH and scons and modified some lines of basic.setting which is in rosetta++/tools/build/. I added the mpi bin, include amd lib path to the file and added a flag "Wno-long-long" to make mpicc and mpiCC work (since the cpmpiler always complains about that it doesn't support 'long long' type). I also installed the rsh-version and configured it to make the work.

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Rosetta++ - Build/Install

How to build a parallel version of rosetta++ (Rosetta2.3.0) ?

Submitted by ice_flame on Fri, 2011-03-25 22:20

Hi Rosetta users,

I'm using Rosetta 2.3.0. I want to build a parallel version. I installed MPICH and scons and modified some lines of basic.setting which is in rosetta++/tools/build/. I added the mpi bin, include amd lib path to the file and added a flag "Wno-long-long" to make mpicc and mpiCC work (since the cpmpiler always complains about that it doesn't support 'long long' type). I also installed the rsh-version and configured it to make the work.

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Rosetta++ - General

the meaning of total_score in docking

Submitted by libai2098 on Mon, 2011-03-21 05:46

Now,I use Rosetta for protein-protein docking.But I do not understand the meaning of total_score .-270 is better than -280?I think the Rosetta manual is not very perfect.What is more,Fnat , I_sc ,Irms, fa_ hack,interchain_contact are not write in manual.I will look forward to your response.Thank you.

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Rosetta 3 - Applications

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