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Ways to improve ROSIE docking2 jobs

Submitted by AdoCbl on Wed, 2015-09-23 15:12
Category: 
Docking

(1) By the images of various output pdb files, be more clear that these are ones with the ten lowest I_sc (interface energy) scores.

(2) In the instructions, give more details about the differences between local_docking and docking_local_refine protocols.

(3) For each docking_local_refine job, please let every output pdb file listed in score.sf have a unique name and include all these pdb files in the tar archive file for the job.

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ROSIE - General

Ways to improve both docking2 and symmetric_docking jobs

Submitted by AdoCbl on Wed, 2015-09-23 14:43
Category: 
Docking

(1) When you click on a point in a plot, a window appears listing data for that point. Often the cursor blocks the top line of this window. Could you add a blank line to the top of this window so the cursor doesn't block any important data?

(2) Could you prevent job names from ending with blanks, /, or \ characters? I have tried automatically fishing results out of the resultant tar files using Matlab, but Matlab has given trouble when the job names end with blanks. I'd imagine job names with / or \ in them could cause similar problems.

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ROSIE - General

Transitioning from ROSIE to Rosetta

Submitted by AdoCbl on Wed, 2015-09-23 11:49
Category: 
Compilation

I have been using ROSIE for a while now and am wondering what is the easiest way to transition to Rosetta. For example, is the code needed to make all the files in the tar archives for ROSIE docking2 and symmetric_docking jobs available? If so, where can I find this code? Is this code included in some of the many files included in the tar archives ROSIE makes for each job? If so, which files? It would be great if I could start with this code and adapt it as desired to do more complicated things in Rosetta.

Thanks!

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ROSIE - General

compile error on OS X Yosemite

Submitted by jlburkhead on Sun, 2015-09-20 16:27
Category: 
Compilation

I amt trying to install the lastest release of Rosetta on Mac OS Yosemite. 

The build quits on the following error:

src/utility/thread/backwards_thread_local.hh:19:9: error: keyword is hidden by macro definition [-Werror,-Wkeyword-macro]

#define thread_local

        ^

1 error generated.

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Rosetta 3 - Build/Install

RNA add/modify residues

Submitted by galvaner on Fri, 2015-09-18 05:49
Category: 
Structure prediction

Hi,

I wnated to solve this in PyRosetta because of the possibility of easy Windows instalation, but I recieved advice to do it in Rosetta ( https://www.rosettacommons.org/node/9517 ).

So what I need (also described in a link above) is that I have RNA pdb file with hundreds of residues in witch I miss usually about ten segments each max 40 but often 3-4 residues ( I have only FASTA sequence of the missing parts). I want to predict the missing parts and insert it into my pdb.

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Rosetta 3 - General

add missing residues into rna

Submitted by galvaner on Tue, 2015-09-15 16:41
Category: 
Structure prediction

Hi,

I have an rRNA pdb file (up to few hundred residues)  with missing segments of residues (from 3 to 10 residues in one missing segment; about 10 segments ) and I need to add(predict) the missing parts of structure and get a complete pdb.

1)Is it possible to do it  by PyRosetta?

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PyRosetta - General

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