[chimerax-users] usage for multimer
Dennis Poh
pohdennis90 at gmail.com
Wed Oct 5 09:35:21 PDT 2022
Hi Eric
1. It seems that I don't have sufficient GPU memory in colab.
I have the following error message:
INFO:colabfold.batch:Running model_1
/usr/local/lib/python3.7/dist-packages/haiku/_src/data_structures.py:195:
FutureWarning: jax.tree_flatten is deprecated, and will be removed in a
future release. Use jax.tree_util.tree_flatten instead.
leaves, structure = jax.tree_flatten(mapping)
/usr/local/lib/python3.7/dist-packages/haiku/_src/data_structures.py:203:
FutureWarning: jax.tree_unflatten is deprecated, and will be removed in a
future release. Use jax.tree_util.tree_unflatten instead.
self._mapping = jax.tree_unflatten(self._structure, self._leaves)
/usr/local/lib/python3.7/dist-packages/haiku/_src/stateful.py:457:
FutureWarning: jax.tree_leaves is deprecated, and will be removed in a
future release. Use jax.tree_util.tree_leaves instead.
length = jax.tree_leaves(xs)[0].shape[0]
/usr/local/lib/python3.7/dist-packages/alphafold/model/geometry/struct_of_array.py:136:
FutureWarning: jax.tree_flatten is deprecated, and will be removed in a
future release. Use jax.tree_util.tree_flatten instead.
flat_array_like, inner_treedef = jax.tree_flatten(array_like)
/usr/local/lib/python3.7/dist-packages/alphafold/model/geometry/struct_of_array.py:210:
FutureWarning: jax.tree_unflatten is deprecated, and will be removed in a
future release. Use jax.tree_util.tree_unflatten instead.
inner_treedef, data[array_start:array_start + num_array])
/usr/local/lib/python3.7/dist-packages/alphafold/model/mapping.py:50:
FutureWarning: jax.tree_flatten is deprecated, and will be removed in a
future release. Use jax.tree_util.tree_flatten instead.
values_tree_def = jax.tree_flatten(values)[1]
/usr/local/lib/python3.7/dist-packages/alphafold/model/mapping.py:54:
FutureWarning: jax.tree_unflatten is deprecated, and will be removed in a
future release. Use jax.tree_util.tree_unflatten instead.
return jax.tree_unflatten(values_tree_def, flat_axes)
/usr/local/lib/python3.7/dist-packages/alphafold/model/mapping.py:129:
FutureWarning: jax.tree_flatten is deprecated, and will be removed in a
future release. Use jax.tree_util.tree_flatten instead.
flat_sizes = jax.tree_flatten(in_sizes)[0]
ERROR:colabfold.batch:Could not predict af1819. Not Enough GPU memory?
INTERNAL: cublas error
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
2. Would it be possible to run this in jupyter? Or are there alternatives?
3. " Prediction may fail with total sequence length over 1000 residues due
to limited GPU memory." - this total sequence length meaning all the
sequences in the list to be concatenated?
4. I seem to also have some pdbxx.m8 and afxxxx.csv files - may I know what
these files are for?
Thanks!
-Dennis
On Thu, 6 Oct 2022 at 00:25, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Also, if you are copying the sequence from a text editor, make sure the
> editor is displaying the sequence as plain text or that you are copying as
> plain text, otherwise invisible formatting characters may be embedded in
> what you paste.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> > On Oct 5, 2022, at 9:14 AM, Elaine Meng via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Well, the message says there is an invalid character, so all I can say
> is to make sure that you are pasting plain text, and check to see that you
> have only standard amino acid codes and commas.
> >
> > WIthout seeing exactly what you pasted, we can't tell which part caused
> the problem.
> >
> > Elaine
> >
> >
> >> On Oct 5, 2022, at 9:09 AM, Dennis Poh <pohdennis90 at gmail.com> wrote:
> >>
> >> 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
> >>
> >
> >
> > _______________________________________________
> > ChimeraX-users mailing list
> > ChimeraX-users at cgl.ucsf.edu
> > Manage subscription:
> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>
>
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