Comments (10)
A better workaround should be:
foldseek lndb queryDB_h queryDB_ss_h
foldseek convert2fasta queryDB_ss queryDB_ss.fasta
Note though that we might not keep the state to alphabet letter assignments stable between releases.
from foldseek.
We have recently added the --format-mode 5
option to our software, which generates PDB files with all Calpha atoms superimposed based on the aligned coordinates.
from foldseek.
This gives an error at the moment. The workaround is to
mv db tmp
cp db_ss db
foldseek convert2fasta db db_ss.fasta
mv tmp db
from foldseek.
You can just use foldseek createdb pdbFolder outputDb to generate the _ss files.
from foldseek.
These sequences should be stored in the database with the ending _ss. You can convert it to a fasta file by using
foldseek convert2fasta db_ss db_ss.fasta
from foldseek.
I get the following error:
foldseek convert2fasta queryDB_ss queryDB_ss.fasta
convert2fasta queryDB_ss queryDB_ss.fasta
MMseqs Version: a4983ce31e6e006a29d9d9330ce9f826cd555d3e
Use header DB false
Verbosity 3
Database queryDB_ss needs header information
from foldseek.
Hi! I am running into some issues when trying to find the _ss file. When I run the easy-search command, I believe the command deletes this database. Could you advise me on a different command to run in order to receive this database as an output? I am solely interested in converting pdb files to 3Di sequences.
from foldseek.
Thank you so much! It works! This was very helpful!
from foldseek.
Is it possible to reverse this, ie, from the states generate the 3D structure? As VAEs are generative models, "something" should come out when you decode the states. Is this possible through the current API?
from foldseek.
At least for the foldseek databases we also store the C-alpha coordinates and also implement PULCHRA within foldseek. So you can get a reasonable backbone back from each foldseek database entry.
I donβt think we have looked into getting a structure back out of the 3Di states yet though.
from foldseek.
Related Issues (20)
- Backbone only search returns no hit. HOT 4
- easy-search hangs on scop40 test HOT 9
- precomputed pdb lookup and sequence don't line up HOT 1
- `--taxon-list` option not accepting multiple taxonomy IDs correctly HOT 5
- Can't find exact match in PDB HOT 2
- 3di for multi-chain protein HOT 2
- Comparison of specified structure fragments HOT 1
- Job kept being stucked in the pending state HOT 7
- How to conduct clusters based on global structures instead of local substructures? HOT 1
- Create human-readable taxonomy lookup table from precomputed database HOT 3
- Potential permission issue when trying to create foldseek db HOT 1
- Error std::out_of_range when creating database with specific cif files HOT 4
- Cannot use createdb to merge two existing db HOT 1
- (core dumped) "$MMSEQS" createcomplexreport "${QUERY}" "${TARGET}" "${SCORECOMPLEX_RESULT}" "${REPORT}" ${REPORT_PAR} HOT 18
- No 3D alignment shown in webserver viewer HOT 9
- Retrain Foldseek's VQ-VAE and compile it with the main program. HOT 1
- How to convert the 3D descriptors back to PDB file? HOT 3
- Foldseek-multimer returns non-interacting chains HOT 3
- How to download AFDB clusters? HOT 3
- Input taxonomy database is missing when using createdb HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
π 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. πππ
-
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 β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from foldseek.