- ChimeraX-users - RBVI Mailing Lists

Problem reading ccp4 maps
by Luca Pellegrini 11 Oct '22

11 Oct '22

When I try to read ccp4 maps from Phenix Resolve_cryoEM into ChimeraX, I’ve started getting the following message: "MRC file is truncated. Failed reading 1 values, type int32” It’s ChimeraX version 1.5.dev202210110346 (2022-10-11)/ macOS Monterey/MacBook Pro 2021, M1 Pro. Best wishes, Luca

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Can you do convex hull on ChimeraX?
by Tianming Qu 10 Oct '22

10 Oct '22

Hi dear ChimeraX-Users and developers, Is ChimeraX available for drawing the convex hull of protein structures? Best, Tianming

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Fit in map, save new coords of map
by Nebojsa Bogdanovic 10 Oct '22

10 Oct '22

Hello, I open two maps and I fit #2 into #1. I need to save map #2 at it's new position, but there is no option "relative to model or map". By doing "volume resample #1 onGrid #1, I match the box sizes but the new position is not maintained after saving that new map. Is there any command/function I could do that with? Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Re: [chimerax-users] alphafold contacts between 3 and more subunits
by Tom Goddard 10 Oct '22

10 Oct '22

Hi André, I added two options "replace" (default true) and "name" (default "PAE Contacts") to the alphafold contacts command. The replace option determines if existing contact pseudobonds (in the group with the specified or default name) are deleted. If replace is false the new contacts are just added to any existing ones. The name option gives the pseudobond model the specified name. So you could use alphafold contacts /A to /B alphafold contacts /B to /C replace false alphafold contacts /A to /C replace false to put all the contacts in one pseudobond submodel. If instead you wanted them in 3 different models you could use alphafold contacts /A to /B name "AB contacts" alphafold contacts /B to /C name "BC contacts" alphafold contacts /A to /C name "AC contacts" This will be in tomorrow's (Oct 11) ChimeraX daily builds. Tom > On Oct 10, 2022, at 12:38 PM, Michaelis, Andre Clemens <michaelis(a)biochem.mpg.de> wrote: > > Awesome, > Thank you so much! > > Best > André > > > —————————————————— > > >> Am 10.10.2022 um 20:50 schrieb Tom Goddard <goddard(a)sonic.net>: >> >> Hi André, >> >> The "alphafold contacts" command creates a submodel of the atomic structure containing pseudobonds with the submodel named "PAE Contacts". If you rename that submodel then it won't replace it when you do the second alphafold contacts command on the same structure. For instance, if the structure is model #1. >> >> alphafold contacts /A to /B >> rename #1.1 "AB contacts" >> alphafold contacts /B to /C >> rename #1.2 "BC contacts" >> alphafold contacts /A to /C >> >> This should be easier to do. I should add an option to the alphafold contacts command "replace false" that automatically uses new names for each group of pseudobonds. I've made a request for this. >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770> >> >> Tom >> >>> On Oct 10, 2022, at 5:47 AM, Michaelis, Andre Clemens via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hi, >>> >>> Is it possible to draw contacts (PAE, alphafold) between more than just 2 subunits? >>> e.g.: >>> alphafold contacts /A to /B >>> AND >>> alphafold contacts /B to /C >>> AND >>> alphafold contacts /A to /C >>> >>> Righ now, a new command deletes the old contacts. Not sure about a syntax that would combine/add those >>> >>> Thank you very much! >>> >>> Best André >>> >>> >>> _______________________________________________ >>> 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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alphafold contacts between 3 and more subunits
by Michaelis, Andre Clemens 10 Oct '22

10 Oct '22

Hi, Is it possible to draw contacts (PAE, alphafold) between more than just 2 subunits? e.g.: alphafold contacts /A to /B AND alphafold contacts /B to /C AND alphafold contacts /A to /C Righ now, a new command deletes the old contacts. Not sure about a syntax that would combine/add those Thank you very much! Best André

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mrc to pdb
by Tianming Qu 07 Oct '22

07 Oct '22

Hi, is there any way I can convert a .mrc file to .pdb file in chimera? Best, Tianming

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A question about the level option in volume viewer
by Qu Tianming 06 Oct '22

06 Oct '22

Hi ChimeraX-developers, I got a question about the level option in volume viewer. I think the level represent the isovalue for the density map. So when I set the level as 0.03, I got a density map as following : [?? ???????] When I set the level as 0.01, the density map as following: [?? ???????] So my question is that, does level 0.03 or 0.01 means, all grids with a density value lower than 0.03 or 0.01 will be present? Means when I set the level as 0.01, everything left in the density map is the density value lower than 0.01? Best, Tianming

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Moving molecules in VR
by Dr. Eddie 06 Oct '22

06 Oct '22

Hello, I'm trying to move some waters away from a ligand (and eventually some lipids as well) as they overlap too much for minimization to fix it. I can't seem to figure out how to select an entire (water) molecule. The select atom lets me select one atom, but I cannot chain or add more atoms. Some atoms seem to refuse to move even when I try to move one at a time using the "Move atoms" right mouse option. Any help would be appreciated as I can't find much about translating molecules (the bond rotation works perfectly!). Thanks! Eddie

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Problems with Qt6
by Hoover, David (NIH/CIT) [E] 06 Oct '22

06 Oct '22

Hi, I'm trying to create a Ubuntu 22.04 container for ChimeraX v1.4 and no matter what I do I get this error message: NOTE: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1021, in <module> exit_code = init(sys.argv) File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 573, in init from chimerax.ui import initialize_qt File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/__init__.py", line 21, in <module> from .gui import MainToolWindow, initialize_qt, menu_capitalize File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/gui.py", line 130, in <module> from Qt.QtWidgets import QApplication File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/Qt/__init__.py", line 64, in <module> from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/Qt/__init__.py", line 64, in from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION _See log for complete Python traceback._ I am attempting to install into Ubuntu 22.04 with ever Qt6 package available, but nothing seems to help. The library in question definitely exists at /usr/lib/x86_64-linux-gnu/libQt6Core.so.6, along with a multitude of other libQt6* libraries. Is there something additional that needs to be done or installed to enable ChimeraX v1.4 to run? I have tried export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH but this does not help. Any insight would be appreciated. David -- David Hoover, Ph.D. Computational Biologist High Performance Computing Services, Center for Information Technology, National Institutes of Health 12 South Dr., Rm 2N207 Bethesda, MD 20892, USA TEL: (+1) 301-435-2986 Email: hooverdm(a)hpc.nih.gov

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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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Fitmap on a subvolume?
by vincent Chaptal 27 Sep '22

27 Sep '22

Hi, I'd like to compare 2 maps, and would like to superposse them on specific portions of the map. Is there a way to do this? I was thinking to assign a pdb to each map, and apply a superposition of pdb1 onto pdb2 and have the maps follow the movement? Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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transparency
by Krishnan Raman 26 Sep '22

26 Sep '22

How to set transparency on surfaces during morphing? I start out with 95% but end up with 0%. The morphing works well though. 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.

3 2

mseries slider
by Krishnan Raman 26 Sep '22

26 Sep '22

The mseries slider appears inside chimerax main screen. Is there a command to make it appear outside the main screen(undock it automatically in a command line? 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.

3 2

Website downtime starting Tuesday, Sep 27
by Elaine Meng 26 Sep '22

26 Sep '22

Dear users, The RBVI website (Chimera, ChimeraX, etc.) and RBVI-hosted web services will be down for maintenance from Tuesday, Sep 27 9pm PDT, through Wednesday, and possibly extending to Thursday, Sep 29 5pm PDT. PDT = Pacific Daylight Time. RBVI-hosted web services called from Chimera and ChimeraX include Blast Protein, Modeller, and multiple sequence alignment with Clustal Omega or MUSCLE. Sorry for the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Combining chain #1 and residue #2: naming issue
by Dmitry Semchonok 26 Sep '22

26 Sep '22

Dear colleagues, I would like to add the residues to the secondary structure (residues come from similar structures and are aligned for the position). For that I use combine tool. When I combine the secondary structure with the residues (combine #1 #2), in the new model the residues (#2) get arbitrary names and no longer belong to each of the main chains (#1). That creates a mass. Could you please advise how to change the names of the residues so that each will belong to the corresponding main chain? (In the combined model I have chan A and residues G…ect ) I tried to use Renumber Residues tool but it did not work (renumber /A-F,I-M,X seqStart 1. 0 residues renumbered) Thanks in advance. Kind regards, Dmitry

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view saves/move commands
by Krishnan Raman 26 Sep '22

26 Sep '22

I tried to play a morph including a flyin of a ligand. It worked fine exceopt for the fly-in and out part The session file did not save the views with ligand away and ligand in the active site. Is there a way around it? How do I estimate a the move coordinates for a ligand to position it where I want it using move command? Thanks again for all the quick and timely help for all my queries. 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.

2 1

define contour level range when molmap
by Yanhe Zhao 25 Sep '22

25 Sep '22

Dear developer, I have docked several pdb to my reference map, there are still large area of density have not assigned any models. Right now I am doing molmap onGrid of reference map, the contour range of new generated became pretty narrow and start from 0. I was wondering which option I can use to define the contour range? Thanks and best regards, Yanhe

2 2

Orientate models
by Yanhe Zhao 23 Sep '22

23 Sep '22

Dear Developer, I have aligned all my models to one reference model, What is the right way to orient all models based on reference model's xyz axis? (They have different coordinate system) Thanks and best, Yanhe

2 2

(no subject)
by Tianming Qu 23 Sep '22

23 Sep '22

Dear ChimeraX group, My name is Tianming Qu and I am currently a phd candidate in Florida State University working on MD simulation study about enzyme proteins. I am currently trying to use chimeraX to show a water density map calculated from an MD trajectory and I got the following fig as result: [cid:image001.png@01D8CD9D.17E4A690] I wonder if the ChimeraX can grab the “red region”out of the whole map, since this the “pocket region”I want. Looking forward to your reply! And it will be my great pleasure if I can have a chance to talk (maybe zoom?) to one of the developers in ChimeraX group! Thanks a lot for the help. Best, Tianming

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Website downtime starting Tuesday, Sep 27
by Elaine Meng 23 Sep '22

23 Sep '22

The RBVI website (Chimera, ChimeraX, etc.) and RBVI-hosted web services will be down for maintenance from Tue, Sep 27 9pm PDT, through Wed, possibly extending to Thu, Sep 29 5pm PDT. RBVI-hosted web services called from Chimera and ChimeraX include Blast Protein, Modeller, and multiple sequence alignment with Clustal Omega or MUSCLE. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Fixing the PDB
by Dmitry Semchonok 23 Sep '22

23 Sep '22

Dear colleagues, I tried renaming the residues. When I did so in chimeraX the file opens just fine but in pymol - it looks as a green hedgehog. I suppose that the pdb file is corrupted somehow. Is there a way to fix it? Kind regards, Dmitry

2 2

Only retrieving the first predicted model in AlphaFold?
by Yao-Chi Chen 22 Sep '22

22 Sep '22

Hi: By ChimeraX, I am using AlphaFold to predict several protein-protein complexes. These complexes totally comprised about 600-800 amino acids. To have the predicted results as soon as possible, I would like to ask: 1: Is there a way to predict only one model(the best one)? 2: what's the advantage of using the Energy-minimized structures? Could I just not use it? Thanks for your help. backy

2 1

AlphaFold July 2022 update to PAE json file - cannot open PAE file with ChimeraX.
by Brandon Payliss 21 Sep '22

21 Sep '22

Hi there, I’m having some issues loading the PAE JSON file from a recent AlphaFold multimer prediction into ChimeraX, generated using a Colab notebook. The warning message is as follows: JSON file "./predicted_aligned_error.json" is not AlphaFold predicted aligned error data, expected a dictionary with keys "residue1", "residue2" and "distance" It appears that AlphaFold reduced their JSON file size by 4X on July 28th 2022 (https://alphafold.ebi.ac.uk/faq) and it no longer uses “distances”, “residue 1” and “residue 2” keys. Just curious, will there be an update coming to ChimeraX to support the new JSON file format from AlphaFold? Thanks for your time! Best, Brandon

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fitmap command in chimerax
by Yanhe Zhao 21 Sep '22

21 Sep '22

Greeting there developer, I am using fitmap command of chimerax to fit pdb to map, the command as below: fitmap #2,3 inMap #1 seq 2 res 3.7 #2 and #3 are copy of each other and I manually placed them in different positions in map, #2 and #3 come to same position after the command running, I had shift option false, but come to same result. I remember it works in chimera. Could you please point me out? Thanks and have a nice day, Yanhe

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tips for large 180kda protein for morph
by Krishnan Raman 20 Sep '22

20 Sep '22

I morphed a 180kda protein. Trying to view it in stereo with surface. Works good but slow. Any tips/ideas to make the morph faster? 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.

3 2

comparison of 2 similar models
by Dmitry A. Semchonok 18 Sep '22

18 Sep '22

2 1

clickable commands
by Krishnan Raman 16 Sep '22

16 Sep '22

How do I make an html file for chimerax with clickable(executable) commands? 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.

2 2

Feature request: combine while keeping chain IDs
by mailman-bounces＠cgl.ucsf.edu 15 Sep '22

15 Sep '22

From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Subject: Feature request: combine while keeping chain IDs Date: September 14, 2022 at 9:10:48 AM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Dear ChimeraX team, With the addition of Isolde, ChimeraX is now such a powerful modelling tool that I would like to suggest a new option for the “combine” command. It would be great if it were possible to specify that chain IDs are kept rather than being renumbered if both input models have the same chain ID (ideally this would only work if there were no overlapping residue numbers). This is very helpful if separately refined domains of proteins are put together in one PDB. Thanks a lot in advance, Matthias

2 1

save symmetry information to cif header
by Pranav Shah 15 Sep '22

15 Sep '22

Hi Team, Is it possible to insert BIOMT like fields into the asymmetric unit of a symmetric molecule when saving the coordinates as a cif file? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Why is this happening
by Noriega, Heather 15 Sep '22

15 Sep '22

Hello, Hi Elaine and Tom. I appreciate your help on the inner volume from before both methods with blob and shape, I think I have been able to tailor it for my usage. I also have been using the icosahedron surface in Chimera, and have not had any issues until this capsid, why is it not forming inside the capsid? Did I do something? Thanks in advance. icos_why.py <https://drive.google.com/file/d/1AozCkS-zpp1M9h3ZtXIxNZUhN420WeJB/view?usp=…> Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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cuboid eraser?
by Walton, Travis Steven 14 Sep '22

14 Sep '22

Greetings everyone, I was wondering if there is a way to change the shape of the eraser tool for manually deleting map densities. By default, it is a circle, but a flat surface could be really useful in many circumstances. Thanks, Travis

3 2

closest to playing animation chimer to chimerax
by Krishnan Raman 14 Sep '22

14 Sep '22

What is best way to play a series of frames(images)with changing representation/colors, zooming in on regions of interest etc. in chimerax? In chimera I used to create them as individual frames and play them using the animation tool/player. I do not want to encode a movie as I want them to be in stereo3d to play them within the chimerax . All suggestions welcome... 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.

2 2

Multi-sampling in ChimeraX
by Chen, Zhen 14 Sep '22

14 Sep '22

Hi all, May I ask is there a super-sampling option in ChimeraX to turn on so that the edges of maps are smoother? Somethiing equivalent to Tools - Viewing Controls - Effects, there is a Graphics quality, you can choose subdivision and whether to turn on multisample. Thanks! Best, Zhen

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Recall the color code from a previously defined color
by HONG ZHAN 14 Sep '22

14 Sep '22

Dear all, I checked through old archive mails, I may iterate this question again about the color code. Is there a command/option to retrieve the color codes in the Reply log from previously used in the ChimeraX session? I saved my session when I defined the Grey scale for one of my surface model in the palette GUI… When I clicked on the other structure I want to know what color I previously used, the RGB code changed to grey as well… Would be a way to retrieve the color code in the Log I defined previously? Thanks, Hong

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Re: [chimerax-users] 2D plots and graphs for protein-ligand interactions
by Tom Goddard 13 Sep '22

13 Sep '22

So the chimerax-daily command is installed in a separate location from the production releases. So if you install both, you will have a /usr/bin/chimerax and a /usr/bin/chimerax-daily. The bug in the installation process was in the post-install script, so the command is already there. That particular bug has to with with integrating ChimeraX in the system menus and no effect on starting ChimeraX from a terminal. You might see a similar error when installing the next chimerax-daily -- that will not have that bug :-). -- Greg On 9/9/2022 10:41 AM, Tom Goddard wrote: > Greg Couch our Linux expert would have to answer that question. > > Tom > >> On Sep 9, 2022, at 1:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> P.S. Are there other possibilities to install chimera-daily in a distinct directory from the chimerax stable release not to overlap between the both ? >> >> Il giorno ven 9 set 2022 alle ore 10:07 Enrico Martinez <jmsstarlight(a)gmail.com <mailto:jmsstarlight@gmail.com>> ha scritto: >> Thank you Tom! >> Actually I faced the problem with the installation of the chimerax-daily on the ubuntu-20.04 >> (currently I am using the 1.4 version realized in june 2022). Here is the error of the installation: >> >> root@Perfetto-7920-Tower:/home/enrico/Downloads# dpkg -i ./chimerax-daily.deb >> (Reading database ... 322925 files and directories currently installed.) >> Preparing to unpack ./chimerax-daily.deb ... >> Deregister desktop menu and associated mime types >> Remove Python cache files >> Unpacking ucsf-chimerax-daily (2022.09.08ubuntu20.04) over (2022.09.08ubuntu20.04) ... >> Setting up ucsf-chimerax-daily (2022.09.08ubuntu20.04) ... >> Install desktop menu and associated mime types >> Traceback (most recent call last): >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py", line 724, in init >> run(sess, cmd) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38, in run >> results = command.run(text, log=log, return_json=return_json) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run >> result = ci.function(session, **kw_args) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/cmd.py", line 23, in linux_xdg_install >> install(session, verbose=verbose, system=system) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py", line 428, in install >> generate(session, info, system, verbose) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py", line 421, in generate >> from chimerax.core import localized_app_name >> ImportError: cannot import name 'localized_app_name' from 'chimerax.core' (/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__init__.py) >> dpkg: error processing package ucsf-chimerax-daily (--install): >> installed ucsf-chimerax-daily package post-installation script subprocess returned error exit status 70 >> Processing triggers for man-db (2.9.1-1) ... >> Errors were encountered while processing: >> ucsf-chimerax-daily >> >> >> Il giorno ven 9 set 2022 alle ore 00:07 Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> ha scritto: >> Hi Enrico, >> >> As Elaine says, ChimeraX isn't a plotting package, so it doesn't let you set colors, sizes, scales, ..., of plots. You could save the plot ChimeraX makes with Python, but I don't think it is very useful to do in an automated way because the aspect ratio of the plot will probably be poor and you cannot control it in a script. At any rate, for reference here is Python that would save the image >> >> from chimerax.core.commands import run >> plot = run(session, 'crosslinks histo #1.1') >> plot.save_plot('histogram.png') >> >> This will need a September 9, 2022 or newer daily build because I just made the "crosslinks histogram" command return the plot, before it did not return it. >> >> The figures in the paper were made interactively in ChimeraX on a high resolution display and just a screen capture was used to save an image. Although as Elaine notes the right-click context menu on those plot windows has a "Save Plot As..." menu entry that will save at 300 dots per inch resolution. >> >> Tom >> >> Example histogram of hydrogen bond lengths for pdb 7qfc saved with the context menu entry "Save Plot As..." >> >> <histogram.png> >> >>> On Sep 8, 2022, at 9:10 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello, >>> The main advantage of these plots inside ChimeraX is that they are interactive with the 3D structure (e.g. you click something on the plot, it does something in the 3D window). They weren't meant for making figures for hundreds of molecules in scripts. >>> >>> So, there are no options to customize plot appearance, and the only way to save the histogram currently is by interactively using the context menu on that window, as mentioned in the help: >>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram>> >>> >>> If you wanted to make your own plots with everything about the appearance customized, currently you would have to write python scripts to dump the data and then use your own favorite plotting program to generate images. >>> Best, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>>> On Sep 8, 2022, at 1:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> Thanks a lot, Elaine! >>>> Actually crosslink hist #1 works very well! >>>> Could you please specify would it be possible to plot the histogram >>>> (using batch chimera-x execution) or alternatively add it directly to >>>> the produced png image? >>>> I did not find any possibility to save the plot or to customize its >>>> appearance (color of the bars etc). >>>> Cheers >>>> Enrico >>>> >>>> Il giorno mer 7 set 2022 alle ore 17:52 Elaine Meng >>>> <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> ha scritto: >>>>> >>>>> Hello! >>>>> The chain contacts diagram shown in Fig 4b is made with the "interfaces" command. Then you can use context menu on that contacts diagram to make the interface-residue plot in Fig 4d. Please see the "interfaces" help for details on both of those. >>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>> >>>>> >>>>> The histogram plot in Fig 5b is made with the command "crosslinks histogram" but first you have to have some crosslinks, or other pseudobonds such as from finding H-bonds or contacts. Then in the "crosslinks histogram" command you specify the pseudobond model to plot their distances. See "crosslinks histogram" help: >>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram>> >>>>> >>>>> Also for a more detailed example see the "Interactive H-bond Histogram" feature highlight, which includes a script (.cxc file): >>>>> <https://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram <https://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram>> >>>>> >>>>> I hope this helps, >>>>> Elaine >>>>> ----- >>>>> Elaine C. Meng, Ph.D. >>>>> UCSF Chimera(X) team >>>>> Department of Pharmaceutical Chemistry >>>>> University of California, San Francisco >>>>> >>>>> >>>>>> On Sep 7, 2022, at 2:18 AM, Enrico Martinez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>>> >>>>>> Dear ChimeraX users! >>>>>> I am dealing with the analysis of protein-ligand interactions in a >>>>>> single PDB structure. I am looking for any tools implemented in >>>>>> Chimera-X, which could be used to analyse the interactions (besides >>>>>> the hbond and contact tools giving info in the log files). >>>>>> I wonder to know which commands and corresponded ChimeraX tools could >>>>>> be used to produce the 2D contact diagrams shown on the Fig.4 as well >>>>>> as python graphs demonstrated on the Fig.5 in the Chimera-X article: >>>>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/> >>>>>> >>>>>> Many thanks in advance! >>>>>> Cheers >>>>>> Enrico >>> >>> >>> _______________________________________________ >>> 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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Saving obj files
by Daniel VillanuevaAvalos 12 Sep '22

12 Sep '22

Hello, I am exporting molecules in the backbone view from chimera x as obj files, but only the points are saving and not the faces. When I import the file to another 3D software, only points show up. How can I save the faces too? Thank you, Daniel.

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Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)
by Tom Goddard 12 Sep '22

12 Sep '22

Hi Asmahan, Ok, probably you used ChimeraX 1.3 since 1.4 was not released in December 2021. So of course Model_1_multimer_pae.json goes with Model_1_multimer_unrelaxed.pdb. And Model_5_multimer_relaxed.pdb is the energy minimized version of Model_5_multimer_unrelaxed.pdb and in that older ChimeraX it only energy minimized the best scoring model so model 5 is the best scoring one. The best_model.pdb file is a copy of Model_5_multimer_relaxed.pdb. Tom > On Sep 12, 2022, at 1:07 PM, Asmahan Alghamdi <Asmahan.Alghamdi(a)nottingham.ac.uk> wrote: > > Hi Tom, > Thank you very much for your time and help. > > I used ChimeraX 1.4 December 2021 on my laptop. The type of files I have got are as follows: > > Best model file , then three files for each model except model 5 in this particular prediction > > Model_1_multimer_pae.json > Model_1_multimer score > Model_1_multimer_unrelaxed > > The same for model2,3,4 > > But 5 with extra file that is: model_5_relaxed > > After that, a list of sequence files > > Best regards > Asmahan > > Get Outlook for iOS <https://aka.ms/o0ukef> > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, September 12, 2022 8:03:22 PM > To: Asmahan Alghamdi <stxamalg(a)exmail.nottingham.ac.uk> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?) > > Hi Asmahan, > > I'm not sure how you ran your AlphaFold prediction. Currently ChimeraX AlphaFold predictions creates JSON PAE files that match the 5 predicted models > > af111_unrelaxed_rank_1_model_4.pdb > af111_unrelaxed_rank_1_model_4_scores.json > af111_unrelaxed_rank_2_model_5.pdb > af111_unrelaxed_rank_2_model_5_scores.json > af111_unrelaxed_rank_3_model_3.pdb > af111_unrelaxed_rank_3_model_3_scores.json > af111_unrelaxed_rank_4_model_2.pdb > af111_unrelaxed_rank_4_model_2_scores.json > af111_unrelaxed_rank_5_model_1.pdb > af111_unrelaxed_rank_5_model_1_scores.json > > The file names have both the scoring order (rank 1 best, rank 5 worst). If you ran AlphaFold on your local machine it might put out > > relaxed_model_1_multimer.pdb > relaxed_model_2_multimer.pdb > relaxed_model_3_multimer.pdb > relaxed_model_4_multimer.pdb > relaxed_model_5_multimer.pdb > result_model_1_multimer.pkl > result_model_2_multimer.pkl > result_model_3_multimer.pkl > result_model_4_multimer.pkl > result_model_5_multimer.pkl > > where the .pkl files contain the PAE data. These are not in score ranked order but you can find the score ranked order from another file AlphaFold writes > > ranking_debug.json > > There are other ways to run AlphaFold that give different output files. You'd have to show your list of output files to advise further. > > Tom > > >> On Sep 12, 2022, at 2:37 AM, Asmahan Alghamdi via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> >> Dear ChimeraX users support, >> Thanks for making AlphaFold such accessible and user friendly tool that has added a great deal to my protein-protein investigations. >> >> I have modelled a number of protein complexes a long while ago effortlessly. However, i need to get the PAE for the best model only, so I managed to know which model is the best because from file name but the pae.json file does not. >> >> Just I am wondering if there is a way to know which json file is associated with the best model? >> >> Thanks a lot. >> Asmahan >> >> Get Outlook for iOS <https://aka.ms/o0ukef> >> From: Asmahan Alghamdi <stxamalg(a)exmail.nottingham.ac.uk <mailto:stxamalg@exmail.nottingham.ac.uk>> >> Sent: Thursday, June 23, 2022 9:39:46 AM >> To: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>; ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>; Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?) >> >> Thank you very much, I will try that and see how it goes. >> >> your help is much appreciated. >> Asmahan Alghamdi >> >> >> Get Outlook for iOS <https://aka.ms/o0ukef> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Thursday, June 23, 2022 12:52:50 AM >> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>; Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> >> Cc: Asmahan Alghamdi <stxamalg(a)exmail.nottingham.ac.uk <mailto:stxamalg@exmail.nottingham.ac.uk>> >> Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?) >> >> Hi Asmahan, >> >> I added an outputFile option to the "alphafold contacts" command so the pairs of close residues and their PAE value can be written to a file. This will be in tomorrow's ChimeraX daily build. >> >> alphafold contacts /B to /C output contact_pae.txt >> >> and the output_pae.txt file looks like >> >> /B:24 /C:30 4.30 >> /B:56 /C:9 9.84 >> /B:68 /C:32 1.48 >> ... >> >> with chain identifier and residue number for both residues and their PAE value. >> >> Elaine is right that the PAE values are in a file produced by AlphaFold. For ChimeraX AlphaFold predictions using Google Colab the file is JSON format (text) like >> >> ~/Downloads/ChimeraX/AlphaFold/prediction_20/best_model_pae.json >> >> If you run your own installation of AlphaFold with multimer or monomer_ptm presets the PAE data is in Python pkl format (binary) like >> >> alphafold_output/result_model_1_multimer_v2_pred_0.pkl >> >> Each of these files have a matrix of all residue by all residue PAE values. It is not too convenient to get the values for specific residues out of such a file unless you write some code. That is why I made ChimeraX do it for you. >> >> Tom >> >> > On Jun 22, 2022, at 1:43 PM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Dear Asmahan Alghamdi , >> > I am guessing you are talking about the AlphaFold PAE values. These are output by the AlphaFold calculation into a file. What you see as a plot using ChimeraX was already read from that file. So you don't need to export it, you just need to find the file that already exists. >> > >> > I am not sure where this file is stored, or whether it is in some "temp" location. We will get back to you on that. >> > >> > I should also clarify that a PAE value by itself is not a measure of how likely the residues are in contact. It is the predicted error in the relationship between the two residues in the Alphafold-predicted structure, where some pairs of residues are close together like a contact, but many more are far apart and not in contact. Although the "alphafold contacts" command does draw lines between residues that are close together based on a cutoff value, the presence of a line does not mean a contact is predicted with high confidence unless its coloring also shows a favorable PAE value. >> > >> > I hope this helps, >> > Elaine >> > ----- >> > Elaine C. Meng, Ph.D. >> > UCSF Chimera(X) team >> > Department of Pharmaceutical Chemistry >> > University of California, San Francisco >> > >> > >> >> On Jun 22, 2022, at 1:21 PM, Asmahan Alghamdi via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> >> >> Dear Chimerax team, >> >> >> >> Thanks a lot for the extremely useful software that has been helping a great deal in improving my protein complex investigations. >> >> >> >> Recently I succeeded in using version 1.5 to determine contacts and the correlated confidence but exporting that list of contact not clear to me yet although searched within software guide and tutorials available online. >> >> >> >> Your help would be much appreciated in this respect. >> >> >> >> Thanks in advance >> >> Asmahan Alghamdi >> >> The university of Nottingham >> > >> > >> > _______________________________________________ >> > 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> >> > >> >> This message and any attachment are intended solely for the addressee >> and may contain confidential information. If you have received this >> message in error, please contact the sender and delete the email and >> attachment. >> >> Any views or opinions expressed by the author of this email do not >> necessarily reflect the views of the University of Nottingham. Email >> communications with the University of Nottingham may be monitored >> where permitted by law. >> >> >> >> _______________________________________________ >> 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 > > > This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this > message in error, please contact the sender and delete the email and > attachment. > > Any views or opinions expressed by the author of this email do not > necessarily reflect the views of the University of Nottingham. Email > communications with the University of Nottingham may be monitored > where permitted by law. > > >

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Export list of contacts
by Asmahan Alghamdi 12 Sep '22

12 Sep '22

Dear Chimerax team, Thanks a lot for the extremely useful software that has been helping a great deal in improving my protein complex investigations. Recently I succeeded in using version 1.5 to determine contacts and the correlated confidence but exporting that list of contact not clear to me yet although searched within software guide and tutorials available online. Your help would be much appreciated in this respect. Thanks in advance Asmahan Alghamdi The university of Nottingham Get Outlook for iOS<https://aka.ms/o0ukef> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

3 5

inquiry about label the residues of pseudo bonds
by Jiaqiao Zhou 12 Sep '22

12 Sep '22

Dear Chimerax users, I am trying to analyze the results of AF2 predictions. I used the "alphafold contacts" command to the interfacing residues, then several pseudobonds are displayed. "label sel pseudobonds" shows the length of the bonds, but I want to show the residue name the number that makes the pseudobonds. Actually, I found that in the label mode of right mouse, it shows the residue name and the number. However, I have to do it one by one. So I am wondering if there are any easier ways. Another question is about the "alphafold contacts" command itself, I want to know the definition of "distance of residues". Is it the distance of the centroid, the average distance of heavy atoms of the residues. or some other ways of determining the distance between two residues? Thanks in advance.

2 1

How to update the bonding status in a molecular trajectory?
by 洪冉 12 Sep '22

12 Sep '22

Dear ChimeraX developers and users, I tried to use ChimeraX to visualize my MD trajectory and I found some bonds were stretched very long and weird, see below In VMD, I could fix this phenomenon using updatebond features, could anybody tell me how to enable this feature in ChimeraX? Many thanks in advance. Ran hong hongran(a)ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000

2 2

Failure in installing daily build version
by jq 10 Sep '22

10 Sep '22

2 1