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Structure prediction

Error from clean_pdb.py

Category: 
Structure prediction

Dear Rosetta Users,

I'm recently studying the Comparative Modeling tutorial: https://www.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial

When I ran the script: clean_pdb.py, there was an error: /dors/meilerlab/apps/Linux2/x86_64/bin/python2.5: bad interpreter: No such file or directory.

What can I do to fix this? The python on my computer is python 3. Thank you in advance!

Post Situation: 

ERROR: Not complementary at positions

Category: 
Structure prediction

Hi Rosetta team,

    I am trying to generate some tertiary structures for a relatively large RNA (300+ nt) with rna_denovo. But I keep getting a strange error saying the nucleotides are not complementary:

[ ERROR ]: Caught exception:


File: src/core/pose/rna/RNA_SecStruct.cc:286
[ ERROR ] UtilityExitException
ERROR: Not complementary at positions C   48 and G   53
 

    I attached my secondary structure, fasta and ct file for the RNA. I wonder what's the cause of this problem. Thanks much.

Post Situation: 

Modelling humanized camelid like antibody

Category: 
Structure prediction

Dear Rosetta community,

I went over the antibody structure prediction tutorials and now in the process of modeling structures for my custom sequence which has 27 aa's in the CDRH3. When I ran the following command,

antibody.linuxgccrelease -fasta cfab.fasta

I got the following error 

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Question with rosetta AbPredict tutorial

Category: 
Structure prediction

Hi,

I am new to rosetta and just started working on some tutorials. I am currently trying to use AbPredict code to generate sample structures by trying to execute tutorial documents at https://zhuanlan.zhihu.com/p/82235565 and also at rosetta_bin_linux_2020.50.61505_bundle/main/demos/tutorials/AbPredict. However, I am having following questions. 

1. create_run.sh file at the rosetta_bin_linux_2020.50.61505_bundle has a syntax issue and the one with the link works perfectly.

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: 

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: 

[Solved] RosettaAntibody3 - Grafting step is failing to detect H3 from the input sequence

Category: 
Structure prediction

I am trying to run RosettaAntibody3 to build an Fv hhomology model from an input sequence. I am following the documentation form here.

I am using the command: 

antibody.static.linuxgccrelease \
  -database $ROSETTA_DATABASE \
  -fasta /mnt/data/input/myinput.fasta \
  -nstruct 1 \
  -out:path:all /mnt/data/output/output-graft/ \
  -detect_disulf false

 which fails fairly quickly with the error:

Post Situation: 

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