Comments (2)
After further investigation, I identified the cause of the behavior I described. When RFdiffusion parses the PDB files using the parse_pdb_lines
function, it only considers the sequence numbers, excluding any insertion codes. As a result, in my example, (Gly, 52), (Ser, 52A), (Ser, 53) becomes (Gly, 52), (Ser, 52), (Ser, 53). Then, duplicate sequence numbers are removed, leading to the final sequence being (Gly, 52), (Ser, 53), with the insertion (Ser, 52A) discarded.
To address this, I have opted to renumber my files without insertion codes.
from rfdiffusion.
I'm unsure how well RFdiffusion works with insertion codes. You can try explicitly including things in the contig (something like [B1-52/B52A-52A/B53-94/14-20/B103-111]
), but I haven't tried that at all. You may be better off just renumbering the input file to remove the insertion codes(*). RFdiffusion will renumber/relabel the output structure anyway.
*) Automated methods exist. I'd personally use Rosetta to do it, because that's what I'm familiar with. Other programs will also do it, though.
from rfdiffusion.
Related Issues (20)
- Question in lab experiment
- why default pdb db is set to examples/input_pdbs/1qys.pdb
- installation on read only directory :: problems
- Numpy 2.0
- Multiple active site scaffolding is possible?
- Installation doesn't recognize CUDA (due to numpy upgrade to v2.0.0)
- FileNotFoundError: HOT 2
- Fine tuning by using my own dataset
- Using sequence in potentials
- ImportError: cannot import name 'SE3Transformer' HOT 2
- pixi dependencies information for newbie.
- Binder design - clarification on number of binders per target
- diffuser.T is being ignored HOT 1
- Crashing when trying to run "design_motifscaffolding.sh" HOT 1
- RFDiffusion Partial Diffusion Error: Mismatched Contig Length HOT 4
- RF to refine PDB HOT 1
- Discrepancies in Absolute Coordinates & Missing Side Chains in Output
- Problem about design_ppi_scaffolded.sh in the example HOT 1
- Error in latest commit
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from rfdiffusion.