- ChimeraX-users - RBVI Mailing Lists

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.

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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.

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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 16 Sep '22

16 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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