[chimerax-users] usage for multimer

[Dennis Poh]

Hi Elaine,

Thanks, I was trying to predict a multimer or the overall structure of many
subunit chains using individual sequences, each separated with a comma in
colab.
But it seems that there was some error and no pdb file was generated; the
error message is as follows:

ERROR:colabfold.batch:Could not generate input features af1848: Invalid
character in the sequence:
Traceback (most recent call last):
  File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line
1357, in run
    model_type,
  File "<ipython-input-1-d6881d38b934>", line 122, in
generate_input_feature_wrapper
    (input_features, domain_names) =
batch.generate_input_feature_orig(*args, **kw)
  File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line
1018, in generate_input_feature
    sequence, input_msa, template_features[sequence_index]
  File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line
869, in build_monomer_feature
    sequence=sequence, description="none", num_res=len(sequence)
  File "/usr/local/lib/python3.7/dist-packages/alphafold/data/pipeline.py",
line 43, in make_sequence_features
    map_unknown_to_x=True)
  File
"/usr/local/lib/python3.7/dist-packages/alphafold/common/residue_constants.py",
line 580, in sequence_to_onehot
    raise ValueError(f'Invalid character in the sequence: {aa_type}')
ValueError: Invalid character in the sequence:
INFO:colabfold.batch:Done
Downloading structure predictions to directory Downloads/ChimeraX/AlphaFold
cp: cannot stat '*_relaxed_rank_1_model_*.pdb': No such file or directory
cp: cannot stat '*_unrelaxed_rank_1_model_*_scores.json': No such file or
directory

-Dennis

On Wed, 5 Oct 2022 at 23:36, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Dennis,
> Your sequence input is wrong - it should contain only the sequences pasted
> as plain text, with only a comma between them (NOT the ">description" line
> because it is not supposed to be in fasta format).  How to input
> sequence(s) is explained in the AlphaFold help page.
>
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict>
>
> "For predicting a complex (multimer), the sequences of all chains in the
> complex must be given. The same sequence must be given multiple times if it
> occurs in multiple copies in the complex. The sequences can be specified
> either collectively as a model number chosen from the menu of currently
> open models (e.g. when that model contains multiple chains), or
> individually within a comma-separated list of UniProt identifiers or
> pasted-in amino acid sequences."
>
> E.g. something like
>
> ACCCC,ALLPAAAA
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 5, 2022, at 4:12 AM, Dennis Poh via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Sorry, I couldn't generate the pdb from chimera colab - is there
> anything that i may have missed?
> >
> > -Dennis
> >
> > On Wed, 5 Oct 2022 at 17:11, Dennis Poh <pohdennis90 at gmail.com> wrote:
> > Hi
> >
> > I encounter a problem in multimer prediction with the sequences I use as
> input.
> > It's always indicating:
> > "Missing or invalid "sequences" argument: Sequences argument"
> > and " is not a chain specifier, alignment id, UniProt id, or sequence
> characters"
> >
> > The input format is always something like a fasta format:
> > >seq_id
> > ACCCC
> >
> > >seq_id2
> > ALLPAAAA
> >
> > May I know how I can rectify this?
> >
> > Thanks!
> > - Dennis
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20221006/06d839e7/attachment.html>