RosettaCommons / RosettaCommons/foundry
Confusion regarding RFD3 inputs
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Description
Hi! I was playing around the input options for RFD3. I think that it is not entirely clear what could the outcome of some combinations mean.
I have a particular example. Consider this input:
{
"test_2": {
"input": "./init_pdbs/start.pdb",
"contig": "A1-263",
"select_unfixed_sequence": "A69-76,A153-154,A172,A174,A202,A204,A207,A208",
"select_fixed_atoms": {
"A1-263": ""
},
"length": "263-263"
}
}
What I expect it to do: diffuse everything from scratch while preserving the sequence in all positions except for ones I specified. However, I see that, for example, Arg92 clearly turns into Phe, despite its number not specified in "select_unfixed_sequence". It is still called "Arg" in the file though. Please see a figure:
How should I specify the input to achieve what I stated - to diffuse everything from scratch while preserving the sequence in all positions except for ones I specified?
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Research direction
Start by tracing how RFD3 interprets the provided input block, especially contig, select_unfixed_sequence, select_fixed_atoms, and length, using ./init_pdbs/start.pdb as the concrete input. Clarify which residues are diffused or sequence-preserved, explain the observed Arg92/Phe result, and document the configuration that produces the requested behavior.
Written by the indexing model from the issue text.
Assessment
- Domain
- documentation, machine-learning
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100