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Getting interface residues?

Submitted by JuliusSu on Wed, 2014-04-16 21:58

Hi everyone, I was looking through the source code of D090_Ala_scan.py, which contains code such as:

p = Pose()
pose_from_pdb(p, "aacap1_0290.pdb")
starting_p = Pose()

#parameters
dock_jump = 1
interface_dist = 8.0 #angstroms
DockingProtocol().setup_foldtree(p)

scorefxn = create_score_function('standard')
scorefxn(p) #needed for proper Interface calculation

interface = Interface(dock_jump)
interface.distance(8.0)

interface.calculate(p)

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PyRosetta - General

ERROR: PDB reader is ignoring atom

Submitted by phanvy on Wed, 2014-04-16 17:59

I am using Rosetta 3.4 for docking. but, I do not know how to fix this Error:
core.io.pdb.file_data: (4) PDB reader is ignoring atom N in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pdb.file_data: (4) PDB reader is ignoring atom HT1 in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pdb.file_data: (4) PDB reader is ignoring atom HT2 in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior

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Rosetta 3 - General

Change the number of residues on pdb file!

Submitted by phanvy on Tue, 2014-04-15 23:26

I am a new Rosetta user. I have some problems because I don not understand about how Rosetta work exactly. With docking, I have to prepare a file pdb have 2 chain (in my case :1 enzyme and 1 peptide), and enzyme have to have residues number start at 0, right? how I can change the number of residues on pdb file?
I have to prepacked pdb file before docking, right?
Thank you so much.

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Rosetta 3 - General

Unable to set up interface foldtree because there are no movable jumps - (antibody/antigen docking)

Submitted by snorp on Mon, 2014-04-14 13:01
Hi, I've been using Rosetta to generate models of antibody-antigen interactions. I'm using the 2014wk05 release to do the following: I use an antibody downloaded form pdb (4KVN) remove the chain A, hetatm and waters in pymol then load in the new antigen (generated using I-Tasser and free of heteroatoms etc.), this joined file is then saved and fed in to rosetta scripts with the following flags:
-docking -dock_pert 8 5 -spin 1 -randomize1
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Rosetta 3 - Applications

backrub score different from calculated score

Submitted by attesor on Wed, 2014-04-09 07:34

I have used backrub (Rosetta3.5) and it calculates scores for decoys.
When I recalculate scores using score.linuxgccrelease from the same rosetta version, different values (30% difference) are generated.
Both used score12 and and dun02. Why are the values so different?

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Rosetta 3 - General

Scoring residue vs. organic ligand

Submitted by almeida on Tue, 2014-04-08 12:18

Hi all,

I have a pdb files with coordinates of a residue conformations interacting with a organic molecule. I want to score this conformations with score.linuxrelease app. The program crash when reading the coordinates of the ligand can not identify the name of the ligand (LIG).

There is a way to overcome this? Is necesary some kind of parametrization?

Thanks in advance

Yasser

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Rosetta 3 - Applications

extract silent error - tag mismatch

Submitted by shrutikhare on Thu, 2014-04-03 00:13

Dear all,

I have been trying to extract PDBs from silent file and keep getting this error:

core.init: command: /opt/rosetta3.3/rosetta_source/bin/extract_pdbs.linuxgccrelease -in:file:silent silent.out -database /opt/rosetta3.3/rosetta_database/
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-20988320 seed_offset=0 real_seed=-20988320
core.init.random: RandomGenerator:init: Normal mode, seed=-20988320 RG_type=mt19937
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4218 residue types

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Rosetta 3 - Applications

Replace the rotamer of a particular residue in a pose

Submitted by AyushGoyal on Wed, 2014-04-02 23:45

In a pose, how can I replace the rotamer of a particular residue? I know I can use the pose.replace_residue function to change the amino acid type at the residue at seqpos in the pose sequence.

replace_residue (Size const seqpos, Residue const &new_rsd_in, bool const orient_backbone)
Replaces the residue at with

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PyRosetta - General

how to identify selected interface residues

Submitted by vijayaraj81 on Mon, 2014-03-31 01:40

Hello everyone,

I am using rosetta scripts (Version 3.5) to redesign a protein-protein interface. I use the following taskoperation to restrict the redesign with 8 ang CB distance cutoff from the interface,

RestrictToInterfaceVector name=vector jump=1 CB_dist_cutoff=10.0 nearby_atom_cutoff=8 vector_angle_cutoff=75.0 vector_dist_cutoff=9.0

I would like to see the residues selected by the program that are within 8 ang cutoff distance. Is this information written somewhere in the outfile?

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