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Can I use the relax mode application for removing clashes in a membrane protein homology model?

Submitted by doranhen on Thu, 2012-12-20 05:45

Hi,
I am trying to fix the clashes in a homology model structure I have created of a membrane protein. I tried fixbb to fix only the sidechains, yet I still get clashes ):. Therefore, I want to try to use the relax application in rosetta3.1 to remove clashes. My questions are:
1. Is it O.K to use relax for a membrane protein? If so, what flags should I use to indicate in relax that I want the calculations done on a membrane protein (for instance, would adding -score:patch no_solvation be enough?)

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Rosetta 3 - General

fragment_picker problem

Submitted by adva on Tue, 2012-12-18 01:15

Hi,
I'm trying to run fragmet_picker on my sequence using this commnad:

/home/advas/tools/rosetta3.4/rosetta_source/bin/fragment_picker.linuxgccrelease -database /home/advas/tools/rosetta3.4/rosetta_database -in::file::vall /home/advas/tools/rosetta3.4/rosetta_tools/fragment_tools/vall.jul19.2011 -in::file::fasta 2anna.fasta -frags::ss_pred 2anna.psipred_ss2 predA -frags::scoring::config simple.wghts -frags::bounded_protocol -frags::frag_sizes 9 3 -frags::n_candidates 200 -frags::n_frags 200 -out::file::frag_prefix frags -frags::describe_fragments frags.fsc

my sequence is
>2anna

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Rosetta 3 - General

Symmetric Minimization

Submitted by aroop on Mon, 2012-12-17 11:45

Hi!

Two questions:

1) Is it possible to minimize specified residues? I do not want different rotamers? So I do not want to use NATAA in the resfile, but if I use NATRO then specify minimize_rotamer - will that have the expected behavior?

2) Secondly, does symmetry work with minimization. For example, can I do something like this:

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Rosetta 3 - Applications

Can only relax one structure at a time

Submitted by lah435 on Wed, 2012-12-12 01:55
I have never been able to give the relax application more than one structure at a time, but now I have hundreds and doing each individually just isn't an option. How can I do this? my flags file contains: -in:file:l inputs the inputs file contains: 00_wildtype_0016_0001.pdb 00_wildtype_0016_0002.pdb ... 00_wildtype_0016_0203.pdb all the input files are in the current directory. The error is: protocols.jd2.PDBJobInputter: pushing 00_wildtype_0016_0201.pdb nstruct index 1
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Rosetta 3 - Applications

Specifying sidechain NOE restraints in Relax!

Submitted by kalabharath on Mon, 2012-12-10 16:44

Hi,
I have both backbone NOE and sidechain NOE data for a small protein. When I specify the backbone NOE data during Abinito simulation it works fine with scoring penalties displayed in atom_pair_constraints column. But when I modify the constraints file for sidechains and supply it Relax or Score with "-constraints" flag it doesn't seem to make any change in the energies, I seriously doubt that It takes those constraints into account during relax. So my questions are:
1. Can relax take sidechain restraints?
2. Is there any special flag to supply during relax?

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Rosetta 3 - General

adding nucleotides to a dna model

Submitted by jadolfbr on Wed, 2012-12-05 11:40

Hi all.

I am trying to add nucleotides to the 3 and 5 prime end of a dna strand. I have used this code to grab a nucleotide residue, thanks to smlewis and sergey:

chm = rosetta.core.chemical.ChemicalManager.get_instance()
set = chm.residue_type_set('fa_standard').get()
ade = rosetta.core.conformation.ResidueFactory.create_residue(set.name_map("ADE"))

I used prepend_polymer_residue_before_seq_pos and append_polymer_residue_after_seq_pos to add the nucleotides to the pose.

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