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Error in using “loopmodel” for selective rebuilding

Submitted by sushreet on Mon, 2014-07-14 11:57
Category: 
Loop Modeling

Hi,

I am new to rosetta. I am trying to build the missing residue loops in 4hna sturcture. But I am getting error while generating the input file for the loopmodel application.

My input command is: loops_from_density.linuxgccrelease -database /util/rosetta/rosetta-3.2/rosetta_database/ -in:file:fullatom 4hna_9_his.pdb -edensity::mapfile apo_cut12.mrc -edensity::whole_structure_allatom_wt 1.0 -edensity::realign min -edensity::sliding_window 9 -edensity::mapreso 8.9 -edensity::grid_spacing 2.12 -max_helix_melt 1 -max_strand_melt 1 -frac_loop 0.026

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Rosetta 3 - Applications

Argument error when running D120_Ligand_interface.py

Submitted by piladam on Wed, 2014-07-09 10:43
Category: 
Docking
PyRosetta

Hi,

I am trying to run D120_Ligand_interface.py sample script with the provided test_lig.pdb and ATP.params. I have placed the ATP.params file into (in PyRosetta main directory) /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types and added the path of the ATP.params file to the file /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt. When I run the script (in ipython - run D120_Ligand_interface.py) I get the following error message.

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PyRosetta - General

FloppyTail vs. Remodel for linkers

Submitted by attesor on Mon, 2014-07-07 08:36
Category: 
Design

I have a 11aa long linker (known sequence) connecting two parts of a protein (NOT two independent domains). I want to model the linker before some downstream Rosetta analysis on the protein. It seems FloppyTail is often suggested for the modeling of linkers.

My question is: how is FloppyTail compared to Remodel + Fixbb? What if I just insert some 11aa long extension (of any sequence) between the two parts using Remodel, then I use fixbb to mutate this newly inserted extension to the sequence of my linker? How would this compare to FloppyTail?

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Rosetta 3 - Applications

Question about wrong homology design

Submitted by mony2182 on Fri, 2014-07-04 10:26
Category: 
Structure prediction

Hi everyone, I have been using rosetta 3.4 and 3.5 to build an homology model of a protein and the result is the same, the structure is broken just in one of the amino acids. I made a control test and made the homologue model of the same template and also the structure is broken. In figure A is the template an in figure B is the homologue model where appears the some fragments of one residue outside of the structure, How can I solve that?
there is my script:

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Rosetta 3 - General

Evaluate Docking Result

Submitted by byin on Thu, 2014-07-03 11:31
Category: 
Docking

Hi,
I have a set of outputs conformation from rosetta after hotspot placement. It's a docking of antigen and antibody. So, how should i evaluate the results? I filtered out the top100 lowest ddG, but, when proceeding to SASA, shape complementarity score and number of hydrogen bond, the results varied. Some having more H-bond with lower Sc score ( around 0.3-0.4). Some with no H-bond but better Sc score.

For example:
A: -31 ddG, 3 H-bond, 2641 SASA, 0.565 Sc
B: -29 ddG, 0 H-bond, 2050 SASA, 0.610 Sc
C: -20 ddG, 5 H-bond, 2039 SASA, 0.323 Sc

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Rosetta 3 - General

Supercharge server

Submitted by alva on Wed, 2014-07-02 17:36
Category: 
ROSIE

When I looked up the supercharge queue, I found many jobs have been holding since June.
Most of them are not even started yet. I know rosie is getting busier, and I am wondering how long it will take to run one project these days.
Is there a technical problem with the supercharge program (the server is down for some reason..?)?

Thank you for your attention,
YC

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ROSIE - General

Symmetric assembly and output reconstruction

Submitted by felipet on Wed, 2014-07-02 10:23
Category: 
Symmetry

Hi

I am modeling an helix assembly and I was wondering how to reconstruct the assembly from SymDock output pdb. The output only includes the chains that are in direct contact with the master subunit, and hence I don't have the next chain along the fiber/helix to include in the command line (make_symmdef_file.pl)

Thanks in advance!

felipet

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Rosetta 3 - Applications

Problems when inserting spin-label R1A

Submitted by ajasja on Fri, 2014-06-27 04:14
Category: 
Non-Canonical Peptides
PyRosetta

Dear all,

I would like to use the spin-lable R1A (implemented as part of Rosetta EPR).
In database/chemical/residue_type_sets/fa_standard/residue_types.txt I activated the needed lines

## Spin label types
# kills my unit tests???
residue_types/spin_labels/R1A.params

Although the “kills my unit tests???” comment is not very encouraging:=)

The problem is:

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PyRosetta - General

Failed glycine check when running RosettaRemodel to build disulfide

Submitted by cheyuk on Fri, 2014-06-27 02:31
Category: 
Design

Hi Rosetta users,

I was recently running RosettaRemodel to build a disulfide between two residues. The first residue is a gly and the second is tyrosine. I ran into this error:

"Failed glycine check. Cysteines cannot replace glycine positions in the native pose."

Is this because gly doesn't have a CB atom so that the CB-CB distance cannot be measured? I can think of mutating the gly to other residues as a workaround. But is there any other way to build a disulfide bond involving a gly using RosettaRemodel?

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Rosetta 3 - Applications

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