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How to install Rosetta in Redhat Linux ?

Submitted by ajaniharesh on Fri, 2012-02-24 02:32

Hello everyone,

I am new user in Rosetta. I have downloaded academic rosetta software from website.

I am using Redhat linux.

Can anyone give me simple installation steps of rosetta in redhat linux.

Thanks in advance.

With warm Regards
HARESH AJANI
NIPER

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Rosetta 3 - General

frelax relaxation with constrains

Submitted by ast on Fri, 2012-02-24 01:44

Hi.
Is there experience with using frelax with constrains, like "frelax.constrain_relax_to_native_coords" or "frelax.constrain_relax_to_start_coords". The first uses a defined pose I guess (frelax.set_native_pose), while the latter tries to keep the situation at the begin of relax? Is there any possibility to restrict this constrains to a subset of amino acids... that is: keep a motive more or less fixed while relaxing the rest? Like in the packmovers using the .res file with NATRO.
Thanks
ast

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PyRosetta - Applications

partial alignment in pyrosetta

Submitted by ast on Thu, 2012-02-23 04:16

Hi everybody,

can someone tell me how I get the superimpose_pose function working. It requires besides the two poses an "(object)atom_map"n specifying a set of atoms to superimpose i guess?
So, how does this object look, or how do I generate it. I would like something equal to the "structural_alignment.py" of EH Baugh (input: pose1, pose2, residues1, residues2) from the Pyrosetta site. Or does the existence of this .py tell me there is no build in function in PyRosetta that works this way?
Thanks

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Relax a structure with >1 copy of a modified residue fails [Solved]

Submitted by franfdez on Wed, 2012-02-08 00:47

Dear all,

I am relaxing a dimer structure which contains one modified residue per subunit. Relaxing a monomer with one modified residue is OK, as is relaxing a dimer where the modified residue has been removed from the input PDB file. However, as soon as there are two copies of the modified residue in the input PDB or during relax run (a dimer or a monomer with C2 symmetry enabled) then the calculation run into this dead end:

ERROR: dis==0 in pairtermderiv!
ERROR:: Exit from: src/core/scoring/methods/PairEnergy.cc line: 468

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Rosetta 3 - Applications

NC atom type [Solved]

Submitted by franfdez on Tue, 2012-02-07 16:05

Dear all,

Apologies if this is a well-established feature or if answers to this or similar questions have already been posted in the forum; a search for 'atom type' did not yield a precise answer.

I want to use NC atom types for the pyridine ring nitrogen atom but this particular atom type (along with a few others) are systematically commented out in all Rosetta database files. My pyridine ring is actually functionalised so it is not exactly a bare-and-bones pyridine ring.

For example, in ${ROSETTA_DATABASE}/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt file:

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Rosetta 3 - General

Garbled Ligands from docking_protocol

Submitted by skovacs on Tue, 2011-12-20 07:55

Greetings,

I'm trying to construct a homo-dimer of a protein+ligand (so a total of two peptide chains and two ligand chains) using docking_protocol with the -docking::partners flag.
I've parameterized the ligand using molfile_to_params.py and docking_protocol runs without generating any fatal errors (although there are numerous warnings about discarding atoms, missing heavyatoms, can't find atoms, etc.).
However, when I check the output structures, I find that both peptide chains are intact but both ligands have completely come apart.

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Rosetta 3 - Applications

How do you implement phosphoserine in ab -initio folding?

Submitted by smiruthi on Fri, 2011-12-16 14:45

I would like to substitute one of the serines (S43) in my sequence to be phosphorylated. How would I do that?

I tried substituting [SER_p] in the fasta sequence and -residues:patch_selectors phosphorylation but that did not work. Any suggestions?

Thanks!

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