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RosettaDesign error with Option file open failed

Category: 
Design

Dear users and developers,

I was running RosettaDesign and an error was reported as "[FILE]: src/utility/options/OptionCollection.cc

[LINE]: 536

[START_MESSAGE]

Option file open failed for: '/**/general_FD.flags'".  

This flag file worked on other server previously. Is this an error with compiling Rosetta or with the flag file? Could anyone please give some suggestions about how to fix this? Thank you so much.

Best,

Post Situation: 

Breaking fastDesign into more stages or writing something custom

Category: 
Design

I know that rosetta_scripts XML protocols can be run in PyRosetta, and I think there is also a specfic PyRosetta version of fastDesign.  But I'm wondering to what extent the underlying functions used in fastDesign (e.g. modifying constraint strengths, modifying vdw repulsion terms) can be written in PyRosetta directly such that some customization would be possible?

 

Post Situation: 

application for affinity optimization

Category: 
Design

Hello

Which application is suited for increasing affinity between 2 proteins? I would like to specify ranges of residues to be mutated in only 1 of the proteins/chains, e.g. in a resfile. 

Essentially I want to do something like the opt-dG application in RAbD, but with ranges of residues a protein domain that is not an antibody. Can the opt-dG do this?

Post Situation: 

Rosetta changing Atom Name in PDB ATOM record?

Category: 
Design

Looking at an output PDB file from Rosetta Design, I've noticed that some of the hydrogens have a numeric prefix attached to their atom name in the ATOM record of the PDB file (picture attached).

Does anybody know what this prefix indicates? According to the PDB website, that particular column (column 12) should just be empty, so it is surprising to see a numeric value there.

I believe this is also causing errors for me trying to use another software which analyzes PDB files, by not recognizing the atom name.

 

Post Situation: 

nstruct vs. trials?

Category: 
Design

In RosettaScripts,

we can specific the number of target structures for the script to design via the

-jd2: ntrials X 

flag where X is the number.

However, in the GenericMonteCarlo mover used for iterative design, we can also specify the number of iterations via the "trials" argument.

My question is, are there any advantages/disadvantages to setting the nstruct number low but setting the trials number high, and vice versa? 

Post Situation: 

Filter for fixed-bb design using RosettaScript?

Category: 
Design

Hello,

If I want to implement fix-bb design (or a slight variation of it) using RosettaScripts, what filter should I use?

Can I not use a filter if I'm just interested in generating a library of designs from multiple input structures with different backbone conformations?

Does it make sense to not use a filter, since (to my understanding) the packer will generally pick rotamers that have less energy than the original residue anyways and output a final score for the designed pose?

Post Situation: 

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