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add missing residues into rna

Submitted by galvaner on Tue, 2015-09-15 16:41
Category: 
Structure prediction

Hi,

I have an rRNA pdb file (up to few hundred residues)  with missing segments of residues (from 3 to 10 residues in one missing segment; about 10 segments ) and I need to add(predict) the missing parts of structure and get a complete pdb.

1)Is it possible to do it  by PyRosetta?

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PyRosetta - General

Use NMR ensemble in protein-protein docking?

Submitted by cossio on Sun, 2015-09-13 07:57
Category: 
Docking

I want to dock two proteins, A and B. I have pdb files for both of them, A.pdb and B.pdb. Now, A.pdb is an X-ray structure, while B.pdb is an NMR ensemble. Is it possible to run a docking simulation with these inputs? How can I do it?

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Rosetta 3 - Applications

Fnat and Irms are nan in score.sc from docking_protocol?

Submitted by cossio on Sun, 2015-09-13 07:34
Category: 
Docking

I am running a docking_protocol for two proteins. Inspecting the score.sc file, I find that the columns Fnat and Irms are "nan" (Not A Number, I suppose). Why could this be happening? I can post more details if needed.

(BTW, what does Fnat mean?)

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Rosetta 3 - Applications

Is it possible to restart the ddg_monomer.linuxgccrelease?

Submitted by lanselibai on Mon, 2015-09-07 03:46
Category: 
Structure prediction

Dear friends,
 
I am trying to use “ddg_monomer.linuxgccrelease” in our university cluster.
However, since my protein is too large (a dimer, each monomer contains 663 residues), the calculation ends because of the wall-time (72 hours) before it finishes.
I am here to ask if it is possible to restart the program. Or is there a method to make the program faster, like using MPI?  

Thanks. 

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Rosetta 3 - Applications

Antibody Docking application

Submitted by Maryam_tabasinezhad on Sat, 2015-09-05 09:58
Category: 
Docking

Hi, 

I want to do docking antibody-antigen complex. Understanding from literature, ensemble docking and snug dock is better for Ab-ag. But I didn’t find a complete tutorial or documentation for snug dock. I found just the page in the following link that is some confusing:

https://www.rosettacommons.org/docs/latest/application_documentation/antibody/snugdock

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Rosetta 3 - Applications

ERROR: Rosetta does not recognize the property: SIDECHAIN_THIOL, when running minimize_with_cst.linuxgccrelease

Submitted by cossio on Thu, 2015-09-03 08:46
Category: 
Design

This is the command I am trying to execute (taken from here: https://www.rosettacommons.org/docs/latest/application_documentation/ana..., in the Preminimization of the Input Structures paragraph, in High Resolution Protocol):

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Rosetta 3 - Applications

Freezing arbitrary backbone dihedral angles...

Submitted by Mon on Thu, 2015-09-03 07:45
Category: 
Constraints

Dear PyRosetta staff,

I'm using your set_bb_true_range() method of the MoveMap class to define the mobile degrees of freedom for some loop. Then, I use a MinMover (min_type="dfpmin") to minimize the loop according to some score function. I want that both backbone dihedral angles (PHI and PSI) were frozen at the Nt end. Unfortunately, it seems that PyRosetta only freezes the PHI angle while keeping mobile the N-terminal (Nt) PSI. In the C-terminal end, the PHI angle is mobile and the PSI is frozen.

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PyRosetta - Scripts

InterfaceAnalyzer dSasa calculation

Submitted by mintseris on Wed, 2015-09-02 09:43
Category: 
Docking

Hi,

I had previously run InterfaceAnalyzer in Rosetta 3.5 but then had to re-run it with a more recent version (2015.19.57819) and was surprised to notice that the dSASA numbers were quite a bit different. This is not a calculation I expected to change much and it shouldn't depend on scoring functions.

I just ran the following on 1brs in the integration tests folder:

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Rosetta 3 - Applications

Models which are not recorded (Abinitio protocol)

Submitted by allan.ferrari on Fri, 2015-08-28 13:39
Category: 
Structure prediction

Hello everyone,

I was running Abinitio protocol and I have noticed that a certain sequence yield sequeced models (S_000001, S_000002, S_000003) in the absence of the secondary structure predicition file. Conversely, in the presence of this file in the protocol some models where not generated (or, at least, not recorded). In fact, I have something like the sequence: S_00002, S_00009, S_00013, etc. From 100,000 models required only around 10,000 were possible to be extract. Is there any resonable reason for this fact?

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Rosetta 3 - General

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