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Structure prediction

Add hemes to cytochrome structures

Category: 
Structure prediction

Dear all,

I am using abintio protocol to predict a cytochrome structure. After I generated the model, it did not give HEME locations. The pdb output only contains the regular protein residues, but missing the location of hemes. I am wondering is there anyway to tell Rosetta also predict the hemes? 

Thank you

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Model truncated proteins

Category: 
Structure prediction

Dear all,

I just started to use Rosetta and I am trying to model my protein with truncated sequence (First ~200 aa). I have pdb file of the full sequence and I would like to know the structure will look with first ~200 aa. Which protocol is better for me to use? Comparative modeling or Ab initio modeling? I am also curious about what that input native proteins is doing? Should I just provide my full sequence pdb file?

Post Situation: 

Threading with Ligand

Category: 
Structure prediction

Hi everyone,

I'm trying to use the partial_thread application to fill in some gaps in a PDB crystal structure, 2hko.  This structure has an FAD ligand and a key water I'm trying to keep during threading.  I've cleaned the file as recommended, changed the FAD ligand atom types to match the canonical Rosetta atom types, and made similar changes to my water.  While the threading runs, the ligand gets thrown out.

This is the command I used:

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Weighted scores??

Category: 
Structure prediction

Hi all,

Recently, I used the one point mutation on Rosetta Backrub server for getting predicts of mutation.  What I got are weighted scores after calculations.

My questions are 1.) what's the units of these weighted scores?

2.) what's the relationship between weighted scores and delta delta G (delta G of mutation - delta G of wild type)?

3.) In the output file, these weighted scores (total) are positive for both wild type and mutation. Are they correct? 

I'll appreciate for any help from you.

 

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Relax output mmCIF file to a particular path

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/"

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AbinitioRelax - Error with flags

Category: 
Structure prediction

Hi folks,

I am attempting to run the AbinitioRelax application and when I use the -abinitio:relax option it returns an error.

Here are my commands: /home/xxxx/Documents/rosetta/main/source/bin/AbinitioRelax.default.linuxgccrelease @flags

where flags file contains:

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denovo_density don't output a pdb file

Category: 
Structure prediction

I run the command :

./denovo_density.linuxgccrelease -mode consensus -in::file::silent 1/assembled.*silent -consensus_frac 0.1 -energy_cut 0.05 -mute core -database /home/advanced/rosetta/main/database -out::path::pdb 2

successfully but there is no pdb file generate

the result:

Post Situation: 

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