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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

ratio of conformers and docking output

Submitted by pramod on Fri, 2014-12-12 12:54
Category: 
Docking

Hi,

I am performing docking claculations using RosettaLigand. I have two questions regarding RosettaLigand docking:

1. How does Rosetta ligand process the ligand conformers fed to dock a structure? I mean does it try all the ligand conformers sequentially in the input file or does it pick them randomly, if so on what criteria?

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Rosetta 3 - General

Checkpoint with rosetta3.4

Submitted by AmelieH on Mon, 2014-12-01 15:51
Category: 
Docking

Hello,

I would like to use checkpoints in order to restart a job if it ends because of a wall-time before he finishes.
I tried the flags:
-in:file:checkpoint true
-run:checkpoint true

But no file is generated, it doesn't look to work.
Anyone knows how I can use checkpoint in the docking protocol?

Thanks

Amélie

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Rosetta 3 - Applications

Docking2: Mismatch between score file and graph

Submitted by Ashafix on Sat, 2014-11-29 07:44
Category: 
Docking

When looking at the graphical docking output (Interface score I_sc / RMSD) the values shown when hovering over the dot do not match the values on the graph itself (see screenshot, ScoreGraph.png). The lowest scoring decoy has a I_sc of ~-6 while the value shown is -4.5. The numbers of the decoy do not match either, the lowest scoring decoy from the result list is 0927 and has a I_sc of -6.228 (which would fit the graph), but on the graph the number is 0836. In another run the values and numbers matched.

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ROSIE - General

Docking flags

Submitted by AmelieH on Thu, 2014-11-13 08:46
Category: 
Docking

Hi all,

I'm trying to change the filters for the docking protocol.
I tried :
dock_lowres_filter 15 5
This option is supposes to set manually the interchain_contact and the interchain_vdw cutoff.

However my log file still says that the cutoff have the default value 10 1.
protocols.docking.DockingProtocol: Scoretype: interchain_contact score: -12.5, cutoff: 9.99
protocols.docking.DockingProtocol: Scoretype: interchain_vdw score: 1.30527, cutoff: 1

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Rosetta 3 - Applications

Rescoring protein docking decoys to get Irms

Submitted by lj269 on Thu, 2014-10-23 13:23
Category: 
Docking

Hi,

I'd like to rescore protein docking decoys to calculate the Irms (interface rms) against the lowest energy decoy. If I rescore using the scoring application, I can get the overall rms but not the Irms. I've tried including flags like -evaluation:Irms but can't seem to get it to work. Also, although less important, is there away to apply the same scoring as the docking application does - without specifying any scoring patches or weights or anything the overall score is completely different to the docking output score.

Cheers.

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Rosetta 3 - General

ERROR:: Exit from: src/core/fragment/ConstantLengthFragSet.cc line: 116

Submitted by phanvy on Wed, 2014-10-08 22:28
Category: 
Docking

Dear all,
when I run the ab_initio Flexpepdock protocol, I got this error :src/core/fragment/ConstantLengthFragSet.cc line: 116
Can someone give me some comments?
this is my flag:
-s eq_1_0001.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database

-out:file:silent decoys.silent
-out:file:silent_struct_type binary

-pep_refine
-lowres_abinitio
-rep_ramp_cycles 10

-ex1
-ex2aro
-use_input_sc
-constant_seed
-jran 12456

-frag3 ../NullFragments0/output_files/frags.200.3mers

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Rosetta 3 - General

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