RosettaCommons / RosettaCommons/rosetta
using identify_cdr_cluster with pyigclassify2
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Description
Hi all
I'm now trying to label CDR in my antibody structure using identify_cdr_cluster command in rosetta
I heard that Pyigclassify2 database can be used in rosetta and to use Pyigclassify2 DB
just download pyigclassify2 DB and put all of them in rosetta/main/database/sampling/antibodies.
but even after I download and put pyigclassify2 DB into rosetta/main/database/sampling/antibodies,
identify_cdr_cluster used rosetta/main/database/sampling/antibodies/cluster_center_dihedrals.txt which was used without pyigclassify2 DB
the downloaded pyigclassify2 DB is like below
pyig_ab_mmcif.tar.gz pyig_cluster_mmcif.tar.gz pyig_domain.fasta pyig_readme.txt
pyig_cdr_data.txt.gz pyig_domain_data.txt.gz pyig_mmcif.tar.gz
to use pyigclassify2 in rosetta, should I do some kind of editing of this file ?
or is there any other thing that I miss ?
Thanks in advance
reagards
croshong
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by tracing identify_cdr_cluster and checking rosetta/main/database/sampling/antibodies, especially cluster_center_dihedrals.txt, alongside the listed Pyigclassify2 files. Determine whether the command is expected to read those files or needs a separate configuration or conversion step; done means the supported setup or missing integration is clearly identified.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- cpp
- Domain
- cli, data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100