You are here

Structure prediction

Ca-RMSD

Category: 
Structure prediction

Hi.

I'm with a doubt in relation to setting the alpha carbon to the CaRMSD. Analyzing the tutorial(Mailerlab) understand: that fixed points are used, and in the case of an ion channel (from a RosettaCM) Ca of the first residue of the alpha helix and Ca last residue alpha helix.
You are correct my deduction?

Post Situation: 

Space Swap!!!

Category: 
Structure prediction

Hello people.


it is normal for cluster.py occupy much space in the swap? I am following this tutorial, I had problems occupy the entire swap, and the program stops running, it increased to 54Gb, and still is using almost entirely.
It is running for more than 22 hours, and apparently will take all of the memory again and crash the program.

the script is:

Post Situation: 

Missing CS-HM-Rosetta Binary files

Category: 
Structure prediction

Dear All,

I try to determine protein structures using CS-HM-Rosetta.

It is stated in the supporting information (http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1202485109/-/DCSupplem...) that we need  execution of "cm_scripts/bin/predict_distances.pl sequence.fasta sequence.aln –aln_format grishin –outfile sequence.dist_csts" in order to generate the homology constraints.

Post Situation: 

Antibody Modeling Question

Category: 
Structure prediction

I'm trying to model a structure of an antibody.  I have an initial starting structure, which I have generated using a separate online server, and I have prepared the structure for modeling with rosetta.  I've been using the application "antibody_model_CDR_H3" which simultaneously docks Vh-Vl and samples loop conformations for HCDR3.  

Post Situation: 

Error message: ArchiveManager spinning down

Category: 
Structure prediction

Hi Rosetta community! 

The first run I created worked perfectly, but for some reason creating another run for the trimed sequence is not working! I got this error message after about 1min of starting the run: 

ERROR: error detected in ArchiveManager -- spinning down

ERROR:: Exit from: src/protocols/jd2/archive/ArchiveManager.cc line: 426

--------------------------------------------------------------------------

MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD 

with errorcode 911.

Post Situation: 

I've got two doubts

Category: 
Structure prediction

Hello guys.

I've got two doubts.


First: someone tell me of an article that explains why for example be between 100,000 and 200,000 decoy to abinitio or 15000 decoy for comparative modeling?


Second: to see the articles in the case of e.g. abinitio is informed that were N decoy, if 100,000, my doubt; was produced a total of 100,000 or 100,000 was requested in the script?

Thank you all for the help

Post Situation: 

Fusing C-terminal or N-terminal segments onto proteins using Remodel

Category: 
Structure prediction
Design
Loop Modeling

Hi I am trying to fuse a structure onto a designed protein structure at the C-terminus using the following command:

remodel.linuxgccrelease -s model3.pdb -remodel:RemodelLoopMover:bypass_closure -remodel:domainFusion:insert_segment_from_pdb model4.pdb -remodel:blueprint model3.blueprint -use_input_sc -num_trajectory 3 -save_top 1 -database <PATH> -overwrite -out:file:scorefile model3.sc

model3.pdb covers the range: 1-393

model4 covers the range: 290 - 393

Where the blueprint has the following general format:

Post Situation: 

Error score_scatter_plot.py

Category: 
Structure prediction

Hi guys,

I'm using a tutorial for analysis my results of abinitio, in the step for "identify the best socring models" using this script  "~/rosetta_workshop/Rosetta/main/source/bin/combine_silent.default.linuxgccrelease -database ~/rosetta_workshop/Rosetta/main/database/ -in:file:silent 2LZM_0*.out -in:file:silent_struct_type binary -in:file:fullatom -out:output -out:file:silent 2LZM_all_models_silent.out -out:file:silent_struct_type binary -out:file:fullatom"

I has this error

Post Situation: 

cluster.linuxgccrelease Killed error

Category: 
Structure prediction

Dear Rosetta's users,

I'd run my score analysis employing the score options below [1]. But after some minutes the programs gave me this error message: killed. As I'm interested to cluster my 50 000 structures generated by Rosetta3.5, I wonder to know what I'm doing wrong with this cluster analysis.

Kind regards.

Post Situation: 

Pages

Subscribe to RSS - Structure prediction