Changes between Version 1 and Version 2 of Ticket #7970, comment 4


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Timestamp:
Nov 8, 2022, 5:11:11 PM (3 years ago)
Author:
Tom Goddard

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  • Ticket #7970, comment 4

    v1 v2  
    11The esmatlas server only allows sequences lengths less than or equal to 400.  Found this trying PDB 7soi chain A, 839 residues.  Returns message "Sequence is longer than 400." instead of a PDB file.
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    3 The web page interface
     3The web page interface (https://esmatlas.com/resources?action=fold) also limits sequence length to 400.
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    5     https://esmatlas.com/resources?action=fold
    6 
    7 also limits sequence length to 400.
     5I could allow predicting subsequences or even automatically chunking to length 400 with specified overlap.  It would be nice if "esmfold predict /A:1-400" worked but current the sequence specifiers do not allow specifying a subsequence.  This is because it returns a Chain instance (which allows aligning to the residues), but it does not look like our Python Chain instance can be created from Python.  I could do it in a slightly hacky way with another option "subsequence 1,400" and for chunking "chunk 400 overlap 10".