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When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

- Python version
- Python arch (32 or 64bit) if different from OS

- Version of PyRosetta including SVN revision number.

Thank you!

Post Situation: 

antibody.linuxgccrelease- output models don't have the same sequence as the input fasta

Category: 
Structure prediction

hi,

I am using antibody.linuxgccrelease aplication in order to model camiled heavy chain only antibodies.

when using the command:

antibody.linuxgccrelease -exclude_homologs true -vhh_only -fasta my_fasta.fa | tee grafting.log

 

for example with my_fasta.fa:

Post Situation: 

ValueError: can only read V2000 format files

Category: 
PyRosetta

I'm providing the molfile_to_params.py with the enzyme-ligand complex of my molecule but unfortunetly it gives the "ValueError: can only read V2000 format files" error. Previously i gave it the individual ligand file and it processed with no problems. But when i try to process this file it doesn't seem to work. I suspect the problem is about the chemical table file formats and something in my code is from V3000 but i'm a begginer so i don't know what.

I will attach the text files of both the ligand .mol file and the complex .mol file. 

Post Situation: 

CoupledMoves not altering backbone coordinates?

Category: 
Design

HI All,

I'm beginning to play around with CoupledMoves for flexible backbone design and I am unable to get it to alter the protein backbone coniguration.

When I run the tutorial here (https://github.com/Kortemme-Lab/coupled_moves-tutorial) it works. But when I try and apply that (or similar) command to another protein it will deisgn the sequence, but all the output pdbs have no coordinate changes. 

Post Situation: 

RosettaAntibody - No matching templates for CDR1

Category: 
Structure prediction

hi,

I am trying to use RosettaAntibody in order to model a camiled heavy chain only antibody (pdb code: 1YC7_1).

when using the following command:

antibody.linuxgccrelease -exclude_homologs true -vhh_only -fasta 1YC7_1.fa | tee grafting.log

(I am using exclude_homologs in order to test its preformance, because this antibody structure is already solved and found in the database).

I get the following error:

Post Situation: 

relax.linuxgccrelease in multiple processors

Category: 
Structure prediction

Hi, sorry if my question is naive.  But I would like to aks if it is possible to run  the next command in multiple processors and not in just one?

relax.linuxgccrelease -s model1.pdb -nstruct 1000

 

regards

and thank you

Post Situation: 

Error in Ubuntu 20.10

Category: 
Compilation

Hi, sorry for disturbing you but  I have problems installing Rosetta.  In Ubuntu 20.10.

I have also tried with clans, but it did not work.  I follow all the classical error list, but still no success. Also I am not sure what is the error. 

Could someone help me, please?

regards

JP

Post Situation: 

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