- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] usage for multimer
by Tom Goddard 05 Oct '22

05 Oct '22

Hi Dennis, Are you asking about fetching AlphaFold database models? Those are only of monomer proteins. With AlphaFold predictions energy minimization is done using OpenMM and the Amber force field -- it has nothing to do with binding affinity. I don't know what you mean by a contact map. Maybe you are interested in the ChimeraX interfaces tool that shows contact residues at an interface. Please give enough details in your questions so they are clear, otherwise we will not be able to spend the time to answer. Tom > On Oct 5, 2022, at 7:41 PM, Dennis Poh <pohdennis90(a)gmail.com> wrote: > > Hi Tom > > Thanks, also in the chimerax GUI software, I can fetch my separated sequences delimited with a comma, but does the overall structure that appears the most energy-minimized model or just a superimposition simply based on sequence similarity? > > How is the energy-minimization done (is it based on deltaG = G(bound complex) - G(protein1) -G(protein2)) ? > Could a contact map be produced (if 2 sequences are compared pairwise) too? > > -Dennis > > On Thu, 6 Oct 2022 at 01:43, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Dennis, > > AlphaFold on Google Colab will only work for total sequence length of about 1000 because the old Google Colab GPUs only have 16 Gbytes of memory. Modern GPUs for machine learning like an Nvidia A40 (48 GB) or A100 (40 or 80GB) or A6000 (48 GB) can handle more than 3000 residues but those GPUs cost $5000-$15000. A consumer Nvidia RTX 3090 (24 GB, $1500) can manage up to 2000 residues. Setting up AlphaFold on your own machine is a bit of work. I see from your output file name "af1848" you tried to run total sequence length 1848 which certainly will fail on Google Colab. For examples of AlphaFold runs at different sequence lengths see > > https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> > > Also AlphaFold has a minimum sequence length for each individual sequence is 16 so your example ACCCC and ALLPAAAA will not work. This minimum length is because AlphaFold uses a sequence alignment made by searching a billion database sequences and searching shorter sequence produces millions of hits that are not evolutionarily related. > > The sequence length limits are described in the ChimeraX documentation > > https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#caveats <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#caveats> > > Tom > > >> On Oct 5, 2022, at 9:35 AM, Dennis Poh via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> 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(a)cgl.ucsf.edu <mailto:pett@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(a)cgl.ucsf.edu <mailto:chimerax-users@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(a)gmail.com <mailto:pohdennis90@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(a)cgl.ucsf.edu <mailto:meng@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 <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(a)cgl.ucsf.edu <mailto:chimerax-users@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(a)gmail.com <mailto:pohdennis90@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(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> > Manage subscription: >> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

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combining executable html commands
by Krishnan Raman 05 Oct '22

05 Oct '22

I have large presentation with several html executable commands . is there a way I can run them with one click single command for all of them? thanks Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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usage for multimer
by Dennis Poh 05 Oct '22

05 Oct '22

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

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Using ChimeraX to predict protein-protein interaction/binding via Alphafold.
by Tan, Wei Ren 05 Oct '22

05 Oct '22

Dear Sir/Mdm, Sorry to disturb you with regards to this matter, as I am unable to find any resources online, or on your YouTube channel to solve my problem. I am William, a medical student at King's College London, UK, who have been using your software, ChimeraX, for the past few months to elucidate possible protein structure for one of the protein I am currently studying. I have faced a problem with predicting a protein interaction between a heterodimer (6z1n) and a novel protein that I am studying now. When I loaded both pdbs, I am unable to run the alphafold via the command: alphafold predict #1&#2 (where #1 is 6z1n and #2 is my protein of interest) Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead? Thank you very much and sorry to disturb you! Sincerely Yours, William Tan

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ligand not showing up
by Dr. Eddie 05 Oct '22

05 Oct '22

Hi all, I've got a pdb and I can't seem to get ChimeraX to recognize the ligand (resname STR) at the end of the pdb. I've modified the ATOM to be HETATM but it still does not show up. I hide solvent and the lipids and I know where it should be (from seeing it in vmd) but only a void is there. Any ideas what is wrong with the pdb? Thanks, Eddie

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alphafold contacts output file
by McClean, Phillip 04 Oct '22

04 Oct '22

Hi Everyone- I used the following command to obtain a file with the contacts between two chains: alphafold contacts /B to /C output contact_pae.txt I cannot seem to find where the output file is located. Thanks for any help. Phil McClean

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ChimeraX for multimeric prediction
by Dozic,Abdul-Vehab 03 Oct '22

03 Oct '22

Greetings, Firstly, I wanted to say that ChimeraX is excellent software, and it can definitely be helpful to enhance our research experience. I wanted to ask about using ChimeraX to predict whether a protein occurs in a multimeric form. I ran Alphafold for multimeric simulations and I have analyzed the predicted aligned error qualitatively, but I was wondering if ChimeraX had some built-in package for fast error analysis such as that it can tell us automatically whether it is likely to find a protein in a particular multimeric state that was modeled by Alphafold. Thanks, Best, Abdul-Vehab

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morph question
by Krishnan Raman 29 Sep '22

29 Sep '22

The morph creates a new model; when i display this new model the last(frame) with final conformation shows up on the screen. is there a way to show the first frame when i play the morph using an executable command? i do have to show the model to play the morph using coordset command. thanks Krishnan CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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Question about resfit command
by Mary Liu 28 Sep '22

28 Sep '22

Dear Chimera X users, Is it possible to show the fit of each nucleotide (not amino acid residue) in density using the resfit command or something like that? Thanks

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Re: [chimerax-users] alphafold contacts output
by Elaine Meng 28 Sep '22

28 Sep '22

> On Sep 27, 2022, at 1:59 PM, McClean, Phillip <phillip.mcclean(a)ndsu.edu> wrote: > > Hi Elaine, > > I am using output data from alphafold2 multimer as provided by Colabfold. Following the video (https://www.youtube.com/watch?v=TMcjEecFHaI&t=6s) I use the following command: > > > alphafold contacts /b to /c distance 8 > > For my complex, the links at the distance are all blue (good results). What is confusing is that the distance of some of the contacts are greater than 8 angstroms. Those distances are between backbone carbon atoms, I assume. The fact that the command asks for amino acid pairs that are less than 8 angstroms apart suggest that other atoms than those in the backbone are less than 8 angstroms. Is my conclusion correct. > > Thanks as always for the advise. > > Phil Hi Phil, Yes, your conclusion is correct - the distance cutoff applies to any atom in the residue within any atom in the other residue, whereas the pseudobond is drawn between alpha-carbons, as mentioned here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts> We generally recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) since many heads are better than my one, unless you are including some data that needs to remain private. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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