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Changing the membrane Thickness (THKN)

Submitted by jlapin on Mon, 2018-11-12 06:32
Category: 
Membrane

Hello (Py)Rosetta community

Currently whenever I add a membrane to my pose the membrane thickness is always 15 A (30 total). I would like to elongate that in order to model different types of phospholipids found in bacterial cells.

My best idea to do this is to change the x-coordinate of the membrane residue in the pose object, using the following commands

>>> AID = AtomID(1, pose.size())

>>> pose.set_xyz(AID, XYZ(30,0,0))

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PyRosetta - General

Membrane protein protocol on PyRosetta

Submitted by jlapin on Sat, 2018-07-28 14:41
Category: 
Membrane

Hello Rosetta community

I need to score a membrane protein using PyRosetta and am having trouble with the implementation.  The 2014 post in the forum has not been very helpful in terms of syntax, and there is little to no documentation. I see a tutorial is in the works on the website, but if anyone has advice right now that would be greatly appreciated. A working (minimal) example would probably be most helpful, something I can work off of. 

Thank you

Joel

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Rosetta 3 - Applications

"caught exception" for PDB with membrane "DUM" residues

Submitted by nitroamos on Wed, 2018-05-30 08:35
Category: 
Scoring
Membrane
Non-Canonical Peptides

If I run this command:

residue_energy_breakdown.static.linuxgccrelease -in:file:s hasDUMresidues.pdb -out:file:silent energy_breakdown.out -ignore_unrecognized_res true

on the attached pdb, I get this error:

caught exception 

 

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Rosetta 3 - General

problem creating lips4 file using run_lips.pl

Submitted by adva on Sun, 2015-02-15 06:22
Category: 
Membrane

Hi,
I'm trying to generate the input files for membrane ab-initio. I already created the span file using OCTOPUS.
However, the run_lips.pl script keeps failing. It creates blast outputs (blast and blast.msa files) but the raw file is empty and the lips4 file contains only the header, and the lipo file is also without values.
I think there's some problem with the part running this script- "http://gila.bioengr.uic.edu/cgi-bin/lips/script.cgi".

Can anyone help me with that?

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Rosetta 3 - Applications

Combine flags file with command line arguments?

Submitted by cossio on Mon, 2014-12-22 13:52
Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

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Rosetta 3 - General

Rosetta membrane blastpgp/psiblast database problem for lips4 generation

Submitted by fbarrera on Tue, 2014-09-16 11:45
Category: 
Membrane

I have run Rosetta membrane successful in the past, but it seems that now the blastpgp database necessary to run the run_lips.pl script is obsolete.
In the lastest BLAST release, blastpgp has been dropped entirely in favor of psiblast.
I am then blocked and I cannot generate the lips4 file using:
run_lips.pl <fasta file> <span file> <path to blastpgp> <path to nr database> <path to alignblast.pl script>

Is there a way of the run_lips.pl connecting the psiblast, or does it need to be modified?

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Rosetta 3 - General

ddg_monomer and membrane proteins

Submitted by afmo on Tue, 2014-05-20 02:37
Category: 
Scoring
Membrane

Dear all,
I am a new Rosetta (3.5) user and I would like to study the effects of some point mutations on a monomeric transmembrane protein.

Can ddg_monomer properly predict the change in stability induced by point mutations in transmembrane proteins? If yes, should I specify a particular score function file using -ddg:minimization_scorefunction option? I would like to study mutations in both, the transmembrane (membrane-facing and not) and the extracellular region of the protein, should I treat them separately?

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Rosetta 3 - Applications

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