You are here

Home

Solved

The problem has been solved

Relax output mmCIF file to a particular path

Submitted by AJVincelli on Sun, 2018-11-25 11:04
Category: 
Structure prediction

Hello, how can I specify the path of a Relax output mmCIF file?

I know that I can specify the path of a Relax output pdb file using the flag "-out:path:pdb Sample/Subdirectory." I can specify the Relax output to be an mmCIF file with the flag "-out:mmCIF." However, the flag "-out:path:mmCIF Sample/Subdirectory" doesn't work. When I do this, I get a pdb file in the current working directory, and a message that says "The following options have been set, but have not yet been used: -out:path:mmCIF Sample/Subdirectory/"

Post Situation: 
Solved
Forums: 
Rosetta 3 - General

InterfaceAnalyzer packstat score = 0.000

Submitted by vmc99 on Fri, 2018-11-16 11:30
Category: 
Scoring

Hello

I am using the InterfaceAnalyzer to obtain packing scores of antibody-antigen strucutres from the PDB database but the packstat score always ends up being 0 for some reason. I am specifying for the activation of packstat calculation as can be seen in my flags.txt file below

-in:file:s 1A14_atomlines.pdb
-interface HL_N
-compute_packstat = 1
-out:file:score_only 1a14_interface.out

The output file is attached below. 

Post Situation: 
Solved
Forums: 
Rosetta 3 - General

Rosetta-based projects using and licensing

Submitted by SergeyP on Fri, 2018-10-26 15:45
Category: 
Compilation

Dear Rosetta Team,

Is it possible to share a code of my Rosetta-dependent non-profit research project and upload it to a publicly accessible GitHub repository licensed under open source license? Is Rosetta License restricts that?

For example, I have "project" like this:

1. Source files that links to Rosetta headers:

Post Situation: 
Solved
Forums: 
Rosetta 3 - General

SPLINE EPR_DISTANCE Constraint Error

Submitted by mmw88 on Tue, 2018-09-18 14:39
Category: 
Scoring

Hello,

I'm getting an unusal error when using SPLINE EPR_DISTANCE constraints with the score.linuxgccrelease function. I generated some structures ab initio using SPLINE EPR_DISTANCE constraints with rosetta_scripts.linuxgccrelease and I wanted to rescore the binary output file with some different constraint weights using score.linuxgccrelease. However, if my input constraint file (cst_fa_file) to the score.linuxgccrelease release function contains any SPLINE EPR_DISTANCE constraints, I get:

Post Situation: 
Solved
Forums: 
Rosetta 3 - Applications

known disulfides in Remodel sequence

Submitted by matteoferla on Mon, 2018-09-10 06:43
Category: 
Constraints

I have a protein structure solved by iTasser against a distant relative. But it has a loop that was not solved correctly and it has two cysteines that probably form a disulfide, so I want to remodel the loop with a disulfide (Rosetta Remodel 3.9 on Linux).

I want to keep the sequences as is, so the disulfide scanner is not for me.

I tried with a PDB template with the following lines:

Post Situation: 
Solved
Forums: 
Rosetta 3 - General

Reading chloride anions

Submitted by Martin Floor on Mon, 2018-08-27 14:29
Category: 
Small Molecules

Hi everyone, 

I am trying to read a pdb file that  has a chloride anion important for its structure. The error is that it is not recognized by rosetta, as sometimes happily happen with other small ions. Looking through the database file I found a params file for a chloride ion model, located at: $ROSETTA_HOME/main/database/chemical/residue_type_sets/fa_standard/residue_types/anions/CL.params. The file reads:

Post Situation: 
Solved
Forums: 
Rosetta 3 - General

Introducing N/C-terminal residues to a pose

Submitted by MNP1986 on Thu, 2018-08-23 06:09
Category: 
PyRosetta

Hello everyone,

I work with a protein where the crystal structure does not include the first 14 amino acids, which are intrinsically disordered.

I would like to add the missing 14 residues using PyRosetta, and I have therefore looked into the FAQ and tried to find the relevant methods in the documentation.  After some considerations I have come up with strategy:

Post Situation: 
Solved
Forums: 
PyRosetta - Applications

Pages

Subscribe to RSS - Solved