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

Submitted by lanselibai on Sat, 2015-01-17 04:53
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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Rosetta 3 - Applications

extract_pdbs fails to open silent file when -auto_setup_metals enabled

Submitted by attesor on Thu, 2015-01-15 03:22
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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Rosetta 3 - Applications

Good baseline settings for side chain packing

Submitted by pachecoj on Tue, 2015-01-13 19:25
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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Rosetta 3 - General

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

Submitted by lanselibai on Tue, 2015-01-13 14:49
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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Rosetta 3 - Applications

ddg_monomer: if MPI executable is reproducible and efficient?

Submitted by lanselibai on Sun, 2015-01-11 09:48
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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Rosetta 3 - Applications

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

Submitted by lanselibai on Thu, 2015-01-08 03:23
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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Rosetta 3 - Applications

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

Submitted by cossio on Fri, 2014-12-26 13:11
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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Rosetta 3 - Applications

score application

Submitted by Hongtham on Tue, 2014-12-23 06:38
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

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Rosetta 3 - Applications

Combine flags file with command line arguments?

Submitted by cossio on Mon, 2014-12-22 13:52
Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

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Rosetta 3 - General

Segmentation fault

Submitted by Hongtham on Mon, 2014-12-15 20:21
Category: 
Structure prediction

Hi everyone,
I tried to run protocol AbinitioRelax to predict the structure of a sequence amino acid.
Howerver, I just could run this protocol with less than 11 cores (CPU processor). If I increased the core number more than 11, the protocol couldn't be run, even my PC has 12 or 16 processor. It returned the "Segmentation fault (11)" and cancel the job.
It doesn't happen the same problem when I run the protocol Flexpepdock.
Did anybody meeting the same problem with me?
Can anybody help me solve this problem?
Thank you so much.

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