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Structure prediction

FloppyTail as a rosettascripts file

Category: 
Structure prediction

Hello rosetta community,

I was wondering if anyone has a RosettaScripts xml file that emulates de FloppyTail application. I´m currently generating decoys of a two domain protein
with a big disordered linker with the objective of modeling it to saxs data.
I just wanted to gain more control over the process and to see exactly what the application is doing.

Thank you,
Tiago

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How to build disulfide bond between two cysteine, i.e. change two "-SH" (sulfydryl) into "-S-S-"?

Category: 
Structure prediction

Dear friends,
I have a Fab (antibody fragment of antigen binding) with two chains(LC 1-214, HC 215-442). An interchain disulfide bond is supposed to form between LC-214-cysteine and HC-434-cysteine. I am using 4KMT as its homology template. In the 4KMT structure, the interchain disulfide bond does exist. However, after replacing the residues with my own residues, the interchain disulfide bond has lost and become "-SH" instead of "-S-S-".

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remodel: what are the exact meanings of notations for secondary structure?

Category: 
Structure prediction

Dear friends,
On the website of remodel

https://www.rosettacommons.org/docs/latest/rosettaremodel.html

It is said:

"By replacing the "." to "E", "L", "H", or "D", Remodel will build residues with secondary structure of extended strand, loop, helix, or random, respectively."

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extract_pdbs fails to open silent file when -auto_setup_metals enabled

Category: 
Structure prediction

I have tested the new option -auto_setup_metals ( https://www.rosettacommons.org/docs/latest/Metals.html ) when relaxing an enzyme containing a Zinc ion, corrdinated by four cysteine residues. The weekly build version used for test was downloaded at the end of 2014 from Rosettacommon website.

The relax program finished successfully. However, the extract_pdb program fails to read the silent file generated by relax with -auto_setup_metals. It complains:

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Good baseline settings for side chain packing

Category: 
Structure prediction

Hi,

I'm trying to compare another method to Rosetta's side chain packing. My first pass is just using default options for the PackMover, and the results I'm getting out of Rosetta are pretty bad by comparison. Are there good rule of thumb settings for establishing a baseline over a set of proteins?

I am setting up a PackMover in C++ code, as opposed to running the command line fixbb application. Looking through the fixbb code I see the following options, some of which aren't mentioned in the documentation:

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ddg_monomer: what is the meaning of "total score" and "score"?

Category: 
Structure prediction

Dear friends,
After using a PDB of -740 REU to run ddg_monomer, I use score_jd2.linuxgccrelease to score the silent output. In the score file (attached), the first two elements are "total_score" and "score". The scale of "total_score" is close to the talaris2013, i.e. -700 to -730; the scale of "score" is -1000, much lower than -700.

Can I ask
1) What is the difference of "total score" and "score"?

2) Why cannot we just use one score?

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ddg_monomer: if MPI executable is reproducible and efficient?

Category: 
Structure prediction

Dear friends,
It is my first time using an MPI executable to run the ddg_monomer. I tested it to mutate the first residue from D to A with different cores, which is compared to a serial job. The following is the results:

Core number, time, ddg prediction
1 (serial), 32 hours, -0.362
2, 25.433 hours, -1.722
4, 29.766 hours, 0.055
8, 24.68 hours, 0.239
24, 25.13 hours, -3.080

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Does relax.linuxgccrelease fully relax the structure compared to ddg_monomer.linuxgccrelease?

Category: 
Structure prediction

Dear friends,
I was using relax.linuxgccrelease to relax my protein (442 residues) with 100 outputs:

~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/relax.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -s /home/lanselibai/Cheng/relax/input/C226S_raw.pdb -out:show_accessed_options -nstruct 100 -relax:quick &> /home/lanselibai/Cheng/relax/output/record.log &

Then I score it using score_jd2.linuxgccrelease:

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ddg_monomer with -ddg::local_opt_only true, will it affect other chains that are close?

Category: 
Structure prediction

I have a .pdb file containing two chains. I do a mutation on one residue on one of the chains, using ddg_monomer. If I set the flag "-ddg::local_opt_only true" in the ddg_monomer run, and if some residues on the OTHER chain (the one I didn't mutate) are very close to the mutated chain (less than 8 angstroms), does that mean that the residues on the other chain are optimized too?

Thanks.

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score application

Category: 
Structure prediction

Hi everyone,
I want to ask a question.
I have some protein structure and i want to calculate their score and chose the one which has lowest score. I used "score_jd2.mpi.linuxgccrelease" to get score.
But the output file pdb has different Hydrogen coordinate even I used the command "no_optH true" to keep the Hydrogen atom position.
I dont understand why it happened.
and which structure should I use for following job? the inital structure of the output pdb after running score command?
Thank you so much.
Hongtham

Post Situation: 

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