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the link 'https://cdn.rcsb.org/resources/sequence/clusters/bc-95.out' in data_collection.sh can't work ,can you give me some guidance?
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Hi,
I hope my question is not too silly (I'm a webdev, not a biologist)
I'm currently testing the usage of `mmtf` files instead of `pdb` ones, and I noticed differences in cartoon representatio…
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Hi there,
thanks for the script! I am using to generate pdb with missense mutations. It works except for this:
`pymissense O95477 abaca1 --maxacid 2224 --pdbpath 7tc0.pdb --tsv /tmp/alpha.tsv`
…
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The mmCIF file format allows auth_asym_ids to be up to 3 characters long while the PDB format limits them to 1 char. This fundamental difference seems to require refactoring all the chain logic from c…
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ERROR: invalid or damaged sequence database to be searched by hhblits: /home/rpearson/Structure_Prediction_Tools/RaptorX-3DModeling/UniRef30_2020_03_hhsuite
ERROR: failed to run /home/rpearson/Struct…
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Hello. I produce the train data from RCSB PDB recently. And I get 7604 samples(6701 proteins, 6341 peptides) and get a low performance on AUROC and AUPRC. It is inconsistent with the data in your pape…
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```
Analogous to Bio::Align:: data structures, but generic interface for structural
alignments.
Might be better on GitHub, with Bioperl.
Need tools to generate these:
Bio::Tools::Run::STAMP
Bio::Too…
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How can I show specific residues, such as space fill, size theme uniform, and colour theme cartoons, after selection?
import React, { useEffect, useRef, useMemo } from 'react';
import …
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```
What steps will reproduce the problem?
1. Running pdb_bfactor with a pdb file that is not deposited in rcsb
2.
3.
What is the expected output? What do you see instead?
What version of the produ…
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In the showcase notebook there's a `mda.fetch_mmtf` command, but fetching from rcsb can sometimes be problematic with firewalls. Better to download and include the mmtf locally in the repo.