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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!
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:
[ 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.
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
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.
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:
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:
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
and thank you
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: