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The problem has been solved

We no longer officially support cygwin

Submitted by smlewis on Mon, 2012-03-26 06:53

Cygwin support has been troublesome for the Rosetta community. Nobody in the community uses Windows or cygwin for development work, and generally we don't even have a cygwin build available for testing. We have de facto not supported cygwin for a while, in the sense that most cygwin problems stumped us. Until this situation changes we are no longer supporting cygwin. Feel free to post your questions on this board anyway; perhaps other cygwin users will be able to help.

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Rosetta 3 - Build/Install

core.scoring.rms_util: WARNING: CA_rmsd out of range...

Submitted by mdyini on Sat, 2012-02-25 16:14

Hi, I have some question about how Rosetta3x read PDB files.
I was preparing my pdb files by the relax mode. The protein has 263 residues and another peptide ligand has 11 residues. From the log file, I found it recognized the 274 residues correctly, but somehow is expecting 275 residues for the rms_util and rotamers building. Below is part of the log file:

...
core.import_pose.import_pose: original fold tree: FOLD_TREE EDGE 1 263 -1 EDGE 1 264 1 EDGE 264 274 -1
core.import_pose.import_pose:

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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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PyRosetta - Applications

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

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