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[LoopModelerMover] ERROR: Can't build a fold tree from a loop with an unspecified cut point.

Category: 
Loop Modeling

Hello,

I am trying to use the LoopModelerMover to relax a couple of loops in a protein complex. I would like to let Rosetta select cutpoints automatically so I leave the cutpoints set to 0. An example script is attached as a text file. I have tried specifying the loops as loop subtags and as a loops file, and in both cases I get this error. 

ERROR: Can't build a fold tree from a loop with an unspecified cut point.

 

Post Situation: 

getting a3m files

Category: 
Structure prediction

Hi,

I want to use RoseTTAfold on the Robetta.new server but it requires an a3m file I dont know how to generate.

I saw a script on the github page (https://github.com/RosettaCommons/RoseTTAFold/blob/main/input_prep/make_msa.sh) that to my understanding is supposed to convert fasta to a3m but it dosent seem to work and I get the following error:

Post Situation: 

C-termini remodelling of dimeric structure removes second chain

Category: 
Loop Modeling

Dear Rosetta Community,

I am trying to remodel a short C-terminal loop into  a docked dimeric structure consisting of 2 identical proteins and while the modeling itself worked, the output contains only the first protein.  The flags I used are the following:
-in:file:s bestp1.pdb
-remodel:blueprint c-term.remodel
-no_optH false
-ex1
-ex2
-remodel:num_trajectory 1
-remodel:quick_and_dirty

Post Situation: 

Rosetta Enzyme design cst block raises error

Category: 
Enzyme Design

Hi All,

I'm trying to run the Rosetta Enzyme Design protocol and I wrote a cst file for the matching step.

My cst file includes two blocks (I pasted below), they use the exactly same format but when I add the second block the match program starts to report an error.
 

Post Situation: 

Compilation and unit test failures

Category: 
Compilation

Hi all,

I installed Rosetta 3.13 in KISTI supercomputor 5 (Nurion) (https://www.ksc.re.kr/eng/index/main).

And, I ran the unit tests. It is showing 85% success rate. 

Below is what I did and I have attached the relevant documents.

$ cd rosetta/main/source

$ module purge

$ module load craype-network-opa python/2.7.15 gcc/8.3.0 mvapich2/2.3.1 craype-mic-knl

Post Situation: 

Internal error while running AbinitioRelax

Category: 
Structure prediction

I am trying to learn Rosetta without any background computer science or bioinformatics. I tried to run the AbinitioRelax.default.linuxrelease program with the proper input files and got the following internal error -

[FILE]: src/core/chemical/GlobalResidueTypeSet.cc
[LINE]: 149
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to open file: /home/rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types.txt


[END_MESSAGE]
[END_CRASH_REPORT]
 

Post Situation: 

Rosetta Double changing mmCIF chain ID

Category: 
Design

Hi everyone!

Perhaps a beginner question. I am having problems with Rosetta changing the default chain ID (double letter) when reading and writing as mmcif. Specifically I am relaxing a long list of proteins into cryo-em density using rosetta scripts and and the resulting mmcif files written by rosetta have the "auth_asym_id" truncated from ex. "Ac" -> "c" or "Xm" to "m". Does Rosetta not support double letter chain IDs internally? Is there any solution to this problem?

Best and thank for any help,

Victor

Post Situation: 

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