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Add hemes to cytochrome structures

Submitted by BuddySphinx on Sun, 2018-12-16 13:46
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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Rosetta 3 - General

Model truncated proteins

Submitted by BuddySphinx on Wed, 2018-12-12 10:32
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?

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Rosetta 3 - Applications

Threading with Ligand

Submitted by ekwan on Thu, 2018-12-06 15:10
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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Rosetta 3 - Applications

Weighted scores??

Submitted by sizhang on Wed, 2018-12-05 15:22
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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Rosetta 3 - Applications

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/"

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Rosetta 3 - General

AbinitioRelax - Error with flags

Submitted by jmschu on Wed, 2018-11-21 17:36
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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Rosetta 3 - Applications

denovo_density don't output a pdb file

Submitted by ylwang on Sun, 2018-11-18 17:51
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:

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Rosetta 3 - Applications

Using residue patches in AbinitioRelax

Submitted by kent on Fri, 2018-11-02 11:19
Category: 
Structure prediction
Chemically Modified Residues

I am hoping to 'fold' short phosphorylated peptide sequences, and started by generating fragments with SS predictions on the unphosphorylated peptides. For example, I ran this sequence through a local installation of PSIPRED and picked 200 3- and 9-mers:

>1
MKGDAHRYLAEFATG

I checked that the TYR_p:phosphorylated patch was active in the full-atom patches.txt, then created a centroid patch and added it to the patches.txt by analogy to existing patches:

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Rosetta 3 - Applications

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