RosettaCommons / RosettaCommons/RFdiffusion
Contigmap in Motif Scaffolding
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Description
Hi everyone,
is it possible to specify multiple contigs like: 'contigmap.contigs=[12-20/B14-16/1-5/B18-20/1-5]' when scaffolding a motif?
I have an active site which is made by non continous amino acids and I'm trying to fix those residues and diffuse the other.
From the instructions seems possible, but I get the following error. Any help is very much appreciated:
_File "/home/shared/RFdiffusion/rfdiffusion/contigs.py", line 258, in expand_sampled_mask
int(subcon.split("-")[1]) + 1,
IndexError: list index out of range
Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace._
Thanks a lot!
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Research direction
Start in rfdiffusion/contigs.py at expand_sampled_mask, line 258, and reproduce the reported command with contigmap.contigs='[12-20/B14-16/1-5/B18-20/1-5]'. Run with HYDRA_FULL_ERROR=1 to inspect the complete traceback and trace how each contig segment is parsed. Done means the requested non-contiguous motif-scaffolding input is handled consistently or its supported syntax is made explicit.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100