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Some wrong with the flag "-l" for score_jd2.linuxgccrelease

Category: 
Structure prediction

Dear friends,
I am not sure what is wrong with the flag "-l" for score_jd2.linuxgccrelease. When I use:

~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score_jd2.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -l /mnt/hgfs/Downloads/PDBLIST.txt

I got prompt:

Post Situation: 

Syntax to extract PDB files from a silent file

Category: 
Structure prediction

Dear friends,
I think there is nothing incorrect in my command line to extract PDB files from a silent file:

~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score_jd2.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -in:file:silent /mnt/hgfs/Downloads/silent.out -in:file:fullatom -in:file:silent_optH -out:output

The prompt goes well and completes successfully:

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Syntax to build a silent file

Category: 
Structure prediction

Dear friends,
Can I ask the syntax to build a silent file?

1) My purpose is to create a silent file based on all the PDB files in /mnt/hgfs/Downloads/

I am trying:

~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -in:file:s *.pdb /mnt/hgfs/Downloads -out:file:silent /mnt/hgfs/Downloads

After several prompts, I got the error of

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"score vs RMSD plots" & "cluster models"

Category: 
Structure prediction

Dear friends,
After obtaining multiple (e.g.100) models from relax.linuxgccrelease, I think I need to select the most likely one for further design work. By looking at

2) Is this Model Good.pdf
3) Preparing Your Structure.pdf

in Meiler Lab's tutorials, I think I need to do "cluster model" and "score vs RMSD plots" to determine the best model.

I can find cluster protocol in
https://www.rosettacommons.org/docs/latest/cluster.html

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Fixing and Building disulfide bonds in homology modeling

Category: 
Structure prediction

Dear Friends!

I am new to rosetta and I would like to become proficient in running it. As a start I need to find out if it is feasible to force disulfide bonds on the N and C terminal of a protein that does not have any disulfide bonds in nature but will be relevant for fusing into another protein structure that forms disulfide bonds such as the fusion occurs at the disulfide bond branch. My template sequence and target are of different length and so i ran into the this error

"core.conformation.Conformation: [ERROR] Residue 246 is out of range."

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Syntax for relax.linuxgccrelease

Category: 
Structure prediction

Dear friends,
I am trying to use relax.linuxgccrelease to remove any clashes in my PDB file.

Can I ask
1) As I understand from "3) Preparing Your Structure.pdf" in the "introduction" tutorial from Meiler Lab, I should use
relax.linuxgccrelease -database <database> -s <structure> -ex1 -ex2 -relax:sequence -nstruct 100

However, I have been told that:
ERROR: Unused "free" argument specified: -database

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clean_pdb.py of Rosetta VS cleanATOM of PyRosetta

Category: 
Structure prediction

Dear friends,
I am dealing with a PDB file missing some residues. I think I should clean it by clean_pdb.py of Rosetta or cleanATOM of PyRosetta.

In Rosetta, the clean_pdb ignores the missing positions and renumber all the residues from 1 to the end regardless of the missing gap.

In PyRosetta, the missing gap can still be remained.

Can I ask can I get the result similar to cleanATOM by using Rosetta's clean_pdb.py? I think I should clean the PDB first, then do loop modeling for the missing residues. Is that correct?

Thank you very much.

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Questions for "modeling_instructions.pdf" in "Homology or Loop Modelling"

Category: 
Structure prediction

Dear Sir or Madam,
I am trying to following "modeling_instructions.pdf" in "Homology or Loop Modelling".

http://www.meilerlab.org/index.php/jobs/resources

The first thing I need help is
Section "2. Run ROSETTA Comparative Model protocol".
After typing the COMMAND FOR COMPARATIVE MODELING PROTOCOL (attached) into terminal, I got "Exit 255" in the prompt and "ERROR" in the comparative_model.log (attached). The options file is also attached.

Post Situation: 

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