Score Function weights
Submitted by thorx020 on Sun, 2012-08-12 13:59
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Making mutations in PyRosetta?
Submitted by thorx020 on Thu, 2012-08-09 09:24
Hi all,
I'm new to PyRosetta and just had a quick question. Is there a way to make mutations to an existing protein structure using PyRosetta? I'm currently doing all the mutations in PyMOL then saving the mutants as new pdb's and calling them into PyRosetta for analysis. If I could just write a short script to mutate the structure using PyRosetta, it would save me a lot of time. Thanks!
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Scoring Electrostatics
Submitted by aroop on Tue, 2012-08-07 11:41
Hi!
I know that there used to be a scoring potential called hack_elec. Does anyone know if this still exists in Rosetta 3.x ? If it does what are the command line flags to invoke it during scoring?
Thanks in advance,
Aroop
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ndruns and nstruct in fixbb
Submitted by Anonymous on Tue, 2012-08-07 01:52
In manual for fixbb in Rosetta 2.x, ndruns is used to specify the number of iterations. In the manual for fixbb in Rosetta 3.x, the parameter ndruns is not introduced anymore. Rather, nstruct is used to specify "The number of iterations to perform per input structure". Does it mean nstruct has replaced ndruns? Or is ndruns the same as nstruct but only one decoy (the best scoring decoy) is returned?
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RNA Denovo RMSD data
Submitted by eremma on Thu, 2012-08-02 01:40
Hi,
I am new to the Rosetta software and I would really appreciate some help from someone with experience in RNA Denovo. I am using the rna_denovo application on a cluster with Rosetta 3.3 and I want to predict 3D structures for a large number of RNA molecules.
Initially I predict 3D structures for which there is NMR data available so that I can determine how well the algorithm works. I am supplying the NMR structure as the native structure in order to plot RMSD vs. energy (score).
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Scoring when the protein is a different length
Submitted by gw on Wed, 2012-08-01 08:53
I would like to truncate a protein (the C terminus). I'm not sure where - the segment is about 70 residues long and is 3 helices with short loop segments of a few residues connecting them. Rather than make 70 truncation mutants in the lab I thought I could narrow it down by comparing the scores of truncated PDBs.
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how to output a structure when scoring it?
Submitted by tianbu on Tue, 2012-07-31 09:38
Dear all,
I use score_jd2 to score a pdb structure. But I also want to output the structure.
I try ~/software/Rosetta_3.4/rosetta_source/bin/score_jd2.linuxgccrelease -s 1f0m.pdb -database ~/software/Rosetta_3.4/rosetta_database -out:prefix 1f0m_test -out:output
But I didn't get the structure. I only get the 1f0m_test.sc which contains the energy of the pdb.
I think I have found the reason. I should use score instead of using score_jd2
But the structure output by score has more H atom than original one. Is that will change the energy score? Thank you!
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how to calc the fa_rep in rosetta2.x?
Submitted by tianbu on Tue, 2012-07-31 08:38
Dear ALL,
I design a structure by rosetta2.3 and score it by rosetta3.4. The energy score is different. And even the fa_rep /fa_atr are different (900 vs 1100). are there any different definitions between two programs? How does rosetta2.3/rosetta3.4 calculate the fa_rep/fa_atr? Thank you!
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ab initio membrane error (frag9 file...)
Submitted by almeida on Mon, 2012-07-30 08:53
Hi all...
I'm running the ab initio membrane app as...
almeida@IDBiotum7:/modelacion/Rosetta$ membrane_abinitio2.linuxgccrelease -abinitio:membrane -in:file:fasta ../P13866.fasta -in:file:spanfile sglt1.span -nstruct 5 -in:path:database /home/almeida/Softwares/Rosetta/rosetta_3.4/rosetta_database/
... and I got this error: 'ERROR: Value of inactive option accessed: -in:file:frag9'
How do I generate the frag9 file for my protein sequence?
Thanks in advance...
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Error Atom_::dihedral_between_bonded_children
Submitted by abiadak on Mon, 2012-07-30 06:34
Hi, I'm running the example homology_modeling_threading_basic from the demos with minirosetta ver. 3.4 and fails whith
ERROR: Atom_::dihedral_between_bonded_children: atoms are not both my children!
ERROR:: Exit from: src/core/kinematics/tree/Atom_.cc line: 407
when setting the flag:
-out:nstruct 10
If compiled with gcc 4.4 (x86_64) it happens while generating fifth model and when compiled with icc 12.1 (x86_64) it happens while generating third model.
Any help would be welcome.
Thanks!
David.
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