- ChimeraX-users - RBVI Mailing Lists

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.

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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

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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

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(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

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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

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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.

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

18 Sep '22

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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.

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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

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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

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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.

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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> >

2 3

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. > > >

2 1

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

morphed model
by Krishnan Raman 09 Sep '22

09 Sep '22

How do we get the morph player after reopening the saved session with a prexisting morphed model ? thanks Krishnan Raman 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.

5 7

2D plots and graphs for protein-ligand interactions
by Enrico Martinez 09 Sep '22

09 Sep '22

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/ Many thanks in advance! Cheers Enrico

3 9

Create Complete Oligomers
by Samuel Kyobe 09 Sep '22

09 Sep '22

Dear ChimeraX We have a protein NLRX1 which functions as a trimer, however only the terminal component of this trimer has been experimentally resolved (3UN9) and in alpha fold the complete monomer of NLRX1 has been predicted (Q86UT6). Is it possible to build a complete trimer of NLRX1 starting with the partial X-ray resolved structure as a reference using ChimeraX and the alphafold model. We would like to use the complete structure for MD studies. Thank you Samuel

2 1

Visualization of the carbon - Cl bond in a small molecule
by Enrico Martinez 09 Sep '22

09 Sep '22

Dear ChimeraX users! I have an issue with the visualization of the small molecule obtained from the tleap module of the amber tools. First of all in vmd and pymol everything looks OK. In the ChimeraX there is no bond between atom CL of the ligand and the aromatic C atom. I've tried to change atom type for the CL: setattr :lig@CL1 atoms idatm_type CL show :lig@* but the bond is still absent. Would it be possible to rebuild it manually? Cheers, Enrico

3 11

How to update the bonding status in a molecular trajectory?
by 洪冉 08 Sep '22

08 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

1 0

image
by 洪冉 08 Sep '22

08 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

1 0

Moving one map in a session while keeping the other/s inactive
by mailman-bounces＠cgl.ucsf.edu 08 Sep '22

08 Sep '22

Dear All, This question might have been answered before but could you let me know how to move 1 map from one position to another without disturbing the other map/s (as we inactivate the maps in Chimera). Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

2 1

Re: [chimerax-users] [Chimera-users] How to caluculate buried surface area
by Elaine Meng 07 Sep '22

07 Sep '22

Hi Kenji, You are using ChimeraX? I CC'd the ChimeraX address chimerax-users(a)cgl.ucsf.edu (different than chimera-users(a)cgl.ucsf.edu) The "measure buriedArea" command does not require picking any blobs. You just specify the parts that you want in the command line. <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> So, maybe something like command: measure buriedarea protein with ligand ...but maybe "ligand" doesn't get your ligand. You would have to use whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead: measure buriedarea protein with :UNK You sent a Pymol session... I don't use Pymol so I can't open that file, sorry. 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 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera > > I am sorry to interrupt your busy schedule. > > My name is Matsui, and I am a second-year master's student at a Japanese university. > Thank you for taking time out of your busy schedule to respond to my question the other day. > > We are investigating the buried surface area to see the magnitude of the interaction between protein and ligand. > > For this purpose, I calculated the solvent accessible area of the ligand. However, the value is 9955, which shows the entire surface area of the protein. > > What should I do? I am not in a hurry for answers , so I would appreciate a reply when you have the time. > > In this case, the ligand was in the binding pocket of the protein, so I would like to calculate the ligand's solvent contact area = buried surface area. > > I tried to check and tried , but it did not work. > > 1.See https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html > > 2.Try to use measure blob using chimera X. > Reference: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea > > However, I didn't know how to solve this command. > Command ;ui mousemode right "pick blobs > > Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html > --------------------------------------------------------------------------- > Kenji Matsui > Graduate School of Tokyo University of Agriculture and Technology　M2 > 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan > > <Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove LXRβ_1P8D).pse>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

2 3

Structure editing
by Niklas Laenger 06 Sep '22

06 Sep '22

Good afternoon, Here is Niklas Laenger. I am a graduate Student at Saint Joseph University. I am trying to modulate conformational changes due to mutation in a protein. In a YouTube tutorial I watched, they used a “minimize structure” tool under the structural editing menu. I could not find this tool, is this not there anymore? With good wishes, Niklas Link to video: https://www.youtube.com/watch?v=eJkrvr-xeXY&t=221s

2 1

AlphaFold prediction template structures
by Tom Goddard 06 Sep '22

06 Sep '22

Hi Hernando, When you run an AlphaFold prediction using the sequence of a structure you have open in ChimeraX, for instance, it shows "Sequence #1/A" to use the sequence of model #1 chain A, it only uses the sequence. It does not use the atomic coordinates in any way. AlphaFold can use structure templates but it is rather inflexible and finds them itself from the Protein Data Bank. If you get a ChimeraX daily build and press the Options button in the AlphaFold panel it will show a checkbutton "Use PDB templates when predicting structures" (default false). This checkbutton is not in ChimeraX 1.4. You can turn that on an AlphaFold will find up to 4 templates from the Protein Data Bank. AlphaFold does a really horrible job finding templates and it does not even report the templates it used. Also in my tests trying to get AlphaFold two different structure conformations by running it with different template structures, it always found just one conformation. It seems that the sequence alignment has much more influence on the final prediction than a template structure. Still if you want to try forcing AlphaFold to use your templates, the ColabFold notebook web server (not in ChimeraX) has an option to use custom templates. https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/Alph… ChimeraX uses this same improved method (called ColabFold) of running AlphaFold but does not offer all of the options that the web server does. Tom > On Sep 4, 2022, at 7:45 PM, Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> wrote: > > Hi Tom, > > Not sure is I've been accepted yet in the ucsf-chimeraX list but perhaps I can ask you another Alphafold related question:. > > When specifying the sequences to predict structures they van be pasted into the input sequence window, but they can also be taken from the structures/models already opened in chimera. In this second case does these 3D structures are used as templates or in any way (other than the sequence) in the Alphafold prediction? > > Thanks > > Hernando > > ___________________________________ > Hernando Sosa > Dept. of Biochemistry > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > emai: hernando.sosa@einsteinmed. <mailto:hernando.sosa@einsteinmed.org>edu > ___________________________________ > > > From: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> > Sent: Sunday, September 4, 2022 10:59 AM > To: Tom Goddard <goddard(a)sonic.net> > Subject: Re: [chimerax-users] AlphaFold > > By the way I find a bit disconcerting the way ChimeraX arranges the windows. For example, when the new window with the Alphafold run is hovered a bit over the ChimeraX window, ChimeraX grabs it and all windows inside ChimeraX gets rearranged. It takes a while to put things back the way they were. Is there a button to reset the windows display ? Perhaps like other programs that have a view menu ? > > Thanks again > > Best > > Hernando > > ___________________________________ > Hernando Sosa > Dept. of Biochemistry > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > emai: hernando.sosa@einsteinmed. <mailto:hernando.sosa@einsteinmed.org>edu > ___________________________________ > > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Friday, September 2, 2022 5:17 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] AlphaFold > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > Hi Hernando, > > I have not seen that problem. Does that always happen when you run an AlphaFold prediction? What operating system are you on? Mac? I have seen Mac ask for permission to download from a web site the first time you download from that site. It may be that the browser in ChimeraX showing the Alphafold run does not know how to ask. But it doesn't make much sense because I do not observe this. Another idea -- if your machine is sleeping when the job finishes maybe Google Colab gives up trying to download the results to your machine. If it is sleeping you might want to set your machine not to sleep during the run. This can also be important to avoid Google Colab dropping your job entirely due to inactivity. I guess another possibility is that it could be a firewall problem where your network firewall blocks the download. Since the download seems to succeed for most users, there seems to be something specific about your computer setup that causes the problem. > > At any rate, to get the results you should be able to click on Files in the left column of the AlphaFold google colab panel and among the files you should see results.zip which is what ChimeraX downloads when the job finishes. There should be a vertical "..." if hover over that file that pops up a menu that allows you to download the file. Try that. ChimeraX is receiving the download and putting it in ~/Downloads/ChimeraX/AlphaFold/prediction_N. It may also hang if there is some issue that prevents the downloads. Possibly you could connect to Google Colab through a standard web browser and try downloading the results.zip file and maybe you would at least get an error that would help diagnose the problem. > > Tom > > >> On Sep 2, 2022, at 1:26 PM, Hernando J Sosa via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Dear Chimera/ChimeraX, >> >> I've been running Alphafold through UCSF ChimeraX and sometimes the procedure gets stuck indefinitely at the last step, downloading the results files (see screenshot). Is this a known issue? is there a workaround ? >> >> Thanks >> >> Hernando >> >> <image.png> >> _______________________________________________ >> 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://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.…>

2 1