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No Space

Submitted by jrcf on Mon, 2016-01-11 16:18

Category:

Structure prediction

No space

I had a server problem that use is ejecting my job. The server adm sent me an email explaining the problem.

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Generating Protein/NA decoys

Submitted by rbeier1 on Mon, 2016-01-11 03:25

Category:

Docking

Nucleic Acids

I tried to generate Protein/Nucleic acid - Decoy structures using Rosetta, but failed in the low-resolution docking protocol. It seems to be a similar problem as already mentioned in no-output-pdb-files-after-docking-protein-and-dnarna.

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I've got two doubts

Submitted by jrcf on Sun, 2016-01-10 07:45

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

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LIGAND APPEARS TO BE DOCKED INTO EMPTY SPACE

Submitted by gabeliluo1 on Wed, 2016-01-06 16:23

Category:

Docking

Hello All,

My docking results, when viewed together with the input protein structure, appear to be docked into open space.

I have confirmed that the hint coordinates I supplied are correct.

Any ideas why this is happening?

Thanks!

Gabe

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ROSIE - General

xyzVector error in Enzyme design

Submitted by ajmbarbosa on Tue, 2016-01-05 09:46

Category:

Enzyme Design

Dear all,

I'm using rosetta's enzyme design app from build "rosetta_bin_linux_2015.31.58019_bundle". The problem is that the calculation stops very frequently with the following error:

...

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

Submitted by achambe on Tue, 2016-01-05 09:39

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:

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Symmetry definition for apolar helix

Submitted by vanrooyenjason on Tue, 2016-01-05 05:20

Category:

Symmetry

Hi,

I am struggling to generate a symmdef file for a helical model and I am hoping someone can help.

The helical parameters are as follows: rise = 17 Angstrom with 4.674 subunits per turn. The helix is apolar i.e. the ends of the helix are the same as related by 180 degree rotation. The repeating unit is a dimer with C2 symmetry. In the attached pdb (ca only to avoid upload limit) the A and B chains form the dimer which is related to the next C/D pair by the helical symmetry I mentioned.

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ROSETTALIGAND: How to prepare data to plot ROC curves using rosettaligand docking result???

Submitted by Ryhon Wang on Mon, 2016-01-04 22:36

Category:

Docking

Hi everybody: how to prepare data and generate ROC curves after running rosettaligand molecular docking ???

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

Submitted by achambe on Mon, 2016-01-04 11:26

Category:

Design

Loop Modeling

Hi, I am trying to replace the C-terminal segment of a designed protein with that taken from a crystral structure using the Remodel module with the DomainFusion flag turned on. I have tried several different tweaks to the arrangment however the gist of it is that I use the following command.

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