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Constraints

Explanation of constraint functions?

Category: 
Constraints

Hello,

Can someone explain or show me where to find information about the variables in the constraint function types? For example, in the harmonic function, what are the variables s and dhttps://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/constraint-file

Thanks!

Amanda

Post Situation: 

Cannot create cst files from upl files

Category: 
Constraints

Hi,

I am trying to do structure calculations with CS-Rosetta/Rasrec. Test data from the Rosetta Toolbox work perfectly fine, but my own data make trouble: I am not able to set up a run with NOE data. The .upl files were already trimmed corresponding to trimming the termini as well as renumbered, but converting the cyana .upl files into rosetta .cst files fails, since "there is not enough information to determine the offset". It looks like the sequence information from the upl files cannot be matched with the fasta sequence.

Post Situation: 

heads up for constraints using GAUSSIANFUNC

Category: 
Constraints

The documentation tells that the TAG field is NOT optional for the function type GAUSSIANFUNC.
However, this is not demonstrated in the samples given in the same page: 

https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/de/d50/constraint_file.html

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Freezing arbitrary backbone dihedral angles...

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.

Post Situation: 

Can't read constraint type

Category: 
Constraints

Hello everyone,

I am running Abinitio protocol with some experimental constraints and I have encountered the following message in the log file:

core.scoring.constraints.util: (2) Constraint choice: {file name}
core.scoring.constraints.ConstraintsIO: (2) read constraints from {file name}
core.scoring.constraints.ConstraintsIO: (2) can't read constraint type
core.scoring.constraints.ConstraintsIO: (2) Read in {n} constraints

Post Situation: 

autoNOE peak lists

Category: 
Constraints

Hello.
I am using autoNOE and RASREC Rosetta to try to calculate a protein structure using sparse NMR NOESY data. I am wondering if there is a way I can input a partially (manually) assigned NOE peak list into the autoNOE setup, not just a completely unassigned list. I know I can give RASREC cyana-style upl constraints, but that's not what I'm looking for. I'd like to see if I can improve the accuracy of the autoNOE sampling by giving it a few manually-determined, unambiguous noe assignments, I just don't know how to properly format that input peak list.

Post Situation: 

docking with constraints and flexible bb

Category: 
Docking
Loop Modeling
Constraints

Hi,
I am doing unbound docking and i believe I have enough biological info to locate the binding interface and rough orientation. Doing the docking manually (or with the low res protocol) suggests that there's some conformational change in the interface that I would like to model. I'm guessing this is not something that I can accomplish with the old docking_protocol commandline app. I did see a flexible_bb_docking option but that appears to be undocumented? Maybe I can do this via the ensembles options?

Post Situation: 

AtomPair and SPLINE

Category: 
Constraints

based the function from SplineFunc.cc, it seems different number of columns are required when using AtomPair and SPLINE (see code below). But the documentation only says "replace <filename> with EPR_DISTANCE". This would definite leads to compaint of Rosetta. 

 void SplineFunc::read_data( std::istream &in)

{

 

utility::io::izstream potential_file;

 

// If constraints::epr_distance specified, read in histogram from database

if( basic::options::option[ basic::options::OptionKeys::constraints::epr_distance]() )

{

Post Situation: 

auto_setup_metals flag with loop modeling application fails

Category: 
Loop Modeling
Constraints

I'm trying to make a homology model for a Zn-binding metalloenzyme based on some other members of the same family that have been crystallized. My general strategy has been to do comparative modeling first with limited redesign of the loops to get the main structural features in place, and then use the loopmodel appliation to refine the structure a bit more. I had trouble incorporating the Zn residue into the comparative modeling application, so I inserted the Zn into the PDB result and now I'm trying to include it in the loop modeling step.

Post Situation: 

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