- ChimeraX-users - RBVI Mailing Lists

sequence identity command
by NUR AIDA SAKINAH 18 Jul '24

18 Jul '24

Hai, I want to use the sequence identity command in ChimeraX but in the log said "Missing or invalid "src1" argument: Expected alignment-id or [alignment-id]:sequence-name-or-number". The input I gave is "sequence identity alignment-1" after open the tools>sequence>show sequence viewer and then select model e.g. #1/a and it show the ID as [ID: 1] but i got error. How to solve this problem? Hope ChimeraX teams can help. Thank you!

2 7

ChimeraX 1.8 linux download options
by Elaine Meng 16 Jul '24

16 Jul '24

Dear Charitha Shetty, Please send ChimeraX general support questions to chimerax-users(a)cgl.ucsf.edu (not chimera(a)cgl.ucsf.edu) as those of us on the commercial licensing team may not know the technical details. My recollection is that flatpak is supposed to work better in a broader set of situations than generic linux, but this is not my area of expertise so I am also forwarding this question to the chimerax-users list where linux experts may wish to correct me or add more details. When you send a message to the list in the future, be careful not to include any proprietary information, including your license key, since your message will be seen by others on the list and included in the public archive of past messages. Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > Subject: RE: Commercial Software Download and License key? > Date: July 16, 2024 at 5:04:37 PM PDT > To: Amrit Sukheja <Amrit.Sukheja(a)netascientific.com>, "'Cantero, Kimberly'" <Kimberly.Cantero(a)ucsf.edu>, Amey Kanitkar <amey.p.kanitkar(a)gsk.com>, Jim Thorpe <james.h.thorpe(a)gsk.com> > Cc: Ye Che <ye.x.che(a)gsk.com>, Chun-wa Chung <chun-wa.h.chung(a)gsk.com>, Mustapha Gbassa <Mustapha.Gbassa(a)netascientific.com>, "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu>, Andrew Verlander <Andrew.Verlander(a)netascientific.com> > > Hi Chimera Team, > > We are trying to download the latest version 1.8 for Centos 7. Do you guys have the Generic Linux 64-bit version for it, as available for 1.7 (screenshot 2)? > 1.8 version shows below option and cannot see a tar.gz as 1.7 version. Can you please provide a link from where we can download the tar.gz for the 1.8 tar.gz version. Thank you in advance! > > Screenshot 1: > > > > Screenshot 2: > https://www.rbvi.ucsf.edu/chimerax/older_releases.html <https://www.rbvi.ucsf.edu/chimerax/older_releases.html> > > > > Best Regards, > Charitha Shetty

2 1

Question about automating with ChimeraX in Visual Studio Code
by Eric Pettersen 16 Jul '24

16 Jul '24

> Begin forwarded message: > > From: chimerax-users-owner(a)cgl.ucsf.edu > From: Yue Bao <nkby(a)outlook.com <mailto:nkby@outlook.com>> > Subject: Question about automating with ChimeraX in Visual Studio Code > Date: July 15, 2024 at 11:54:25 PM PDT > To: "chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > > > Hi, > > I am using ChimeraX to visualize a list of protein structures, including hiding/showing/coloring specific chains (sometimes amino acids specific). Because I have a long list, I wanted to get it done not with the ChimeraX console but with Visual Studio Code, since you provided python APIs. > > N.B. I can do run(session, 'open 6qzp') in the Qt console in ChimeraX, as session has been loaded. It is good, just not as efficient as running in VS code. > > However, in VS code it is not working. Here are my code and error messages. Is it because I didn't setup the standalone environment correctly? If possible, could you help me with a piece of sample code and the documentation? > > best, > Yue > --- > > interpreter I used > /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11 > > I have a script basically to open a PDB structure and get some visualizations done > > from chimerax.core.session import Session > > from chimerax.core.commands import run > > > def main(): > > session = Session('chimerax') > > run(session, 'open 6qzp') > > run(session, 'hide atom') > > run(session, 'show cartoon') > > run(session, 'select #1') # select all proteins > > run(session, 'color #AAAAAA All') > > run(session, 'select #0') > > main() > > when I run it in VS code, it gives me some error > run(session, 'open 6qzp') > File > "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- > packages/chimerax/core/commands/run.py", line 49, in run > results = command.run(text, log=log, return_json=return_json) > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File > "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- > packages/chimerax/core/commands/cli.py", line 2849, in run > _compute_available_commands(session) > File > "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- > packages/chimerax/core/commands/cli.py", line 2431, in > _compute_available_commands > ts.register_available_commands(session.logger) > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > AttributeError: 'NoneType' object has no attribute > 'register_available_commands' > > > BUG: AttributeError: 'NoneType' object has no attribute > 'register_available_commands' > > File > "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- > packages/chimerax/core/commands/cli.py", line 2431, in > _compute_available_commands > ts.register_available_commands(session.logger) > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > _See log for complete Python traceback._ >

1 1

Coloring aligned structures by RMSD
by Chen, Daphne 16 Jul '24

16 Jul '24

Hello, I have a large ChimeraX session containing homologs of my protein of interest (~120 PDB files in one session). I’ve been able to align them using MatchMaker, but I noticed that I have to check the “Show pairwise sequence alignments” box under “Alignment” in the Matchmaker window if I want to color by RMSD in the Render by Attribute menu. Is there a way to color by RMSD without displaying all the pairwise sequence alignments? Whenever I try to open my session, there are so many pairwise alignment windows that have to be loaded that ChimeraX ends up crashing. Thanks, Daphne

2 2

How to add calcium ions into a predicted protein structure
by MARIAM ALZAABI 16 Jul '24

16 Jul '24

Dear Sir, How to add calcium ions into a predicted protein structure that I created using alpha fold colab in chimeraX Thank you.

2 1

ChimeraX generated mmCIF files not suitable for PDB deposition
by Vorländer,Matthias Kopano 15 Jul '24

15 Jul '24

Dear ChimeraX team, Structure files in .cif format that are generated by ChimeraX are unfortunately not suitable for deposition to the PDB. This is due to lack of the column _entity_poly.pdbx_strand_id in the header. The column is usually found in the header in this table and contains the chain Identifier (i.e ‘A’ for chain A): loop_ _entity_poly.entity_id _entity_poly.nstd_monomer _entity_poly.type _entity_poly.pdbx_seq_one_letter_code_can Since ChimeraX does an excellent at converting PDBs to mCIFs otherwise, would it be possible to have ChimeraX include this column in the header of mmCIF files? This would greatly help to facilitate the tiresome process of depositing models to the PDB. Many thanks in advance, Best, Matthias

2 4

AlphaFold Predicted Structures
by S.M. RAIHAN RAHMAN 15 Jul '24

15 Jul '24

Hi! Greetings. I hope you’re doing well. Recently, I did a structure prediction of a protein using the built-in AlphaFold of ChimeraX. Also, I downloaded the predicted structure of the same protein from the AF database. Surprisingly, when I superimposed these two structures, I found that they were pretty structurally different. However, the sequences are entirely similar. Could you please tell me what the reason for this is? And, is the built-in AlphaFold the AlphaFold2 or AlphaFold3? Thank you. Regards, Raihan

3 3

Re: [Chimera-users] Covalent substrate modeling and minimization
by Elaine Meng 15 Jul '24

15 Jul '24

Hi Kelvin, First make sure of which program you are using. You sent this to the chimera-users mailing list which is for the program Chimera. However, the commands that you mention are for ChimeraX, so you must really be using chimeraX instead. In the future, please use chimerax-users(a)cgl.ucsf.edu for ChimeraX questions (CC'd here). I included both since the answer may involve both. Everything below is for ChimeraX unless stated otherwise: (1) Is this substrate included in the experimental structure? If the experiment was not done with the substrate bound, there is no reason to expect the density map to include density for it. 4kqo does not have a density map in EDS, so I guess you meant 4kq0. 4kq0 has plenty of density near the ligand residue MED, if that's what you meant by "substrate." You just need to use the slider in the Volume Viewer to change the isosurface level of the density ("volume" command below "level" option, but for interactive use, it is easier to use the slider in the GUI). To make it easier to view you can also limit the density to a zone near that ligand with the command "volume zone" open 1kq0 open 1kq0 from eds view ligand volume #2 level 0.01339 volume zone #2 near :MED The isosurface level in the example above is lower than what is shown initially when you open the map. However, I have no opinion as to what value exactly you should use. See help for "volume" and "Volume Viewer" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> (2) if you use "Join Models" section of "Build Structure" to create the bond (before combining) it will move one model to use your specified input bond distance and angles, and automatically combine the models. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> If you combine first and then add a bond, it won't move the atoms and the bond distance and angles may be poor, but it depends on your situation as to which approach is better, i.e. I'm not saying the way you did it was wrong. You may also be interested in using the other sections in Build Structure (see link above): Adjust Bonds, Adjust Torsions You can also measure and change angles with "angle" and "torsion" commands. You can also rotate bonds manually using the "rotate bond" mousemode. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> (3) there isn't a simple minimization tool that handles nonstandard residues in ChimeraX yet. You could save a PDB file of the result from the above and use Chimera instead, which has a Minimize Structure tool. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 12, 2024, at 3:26 AM, Kelvin Chung via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Good day > I am a researcher studying antibiotic interaction and trying to make a model with a substrate covalently bound to the active site. > There is a homolog with a crystal structure (PDB: 4KQO), and I am going to add the bound substrate in this pdb file to my target protein where the mode was generated by alphafold server. > > Although the workflow shall be simple, I still have some problems, could you kindly help? > > 1. Firstly, I would like to check whether the model of 4KQO is good enough for modeling, by examining the electron density map (open 4KQO, open 4KQO from eds). However, I found that it is a bit different from the tutorial (https://www.cgl.ucsf.edu/chimerax/docs/quickstart/index.html, pdb:1a0m) that the electron density of 4KQO did not cover the substrate molecule. I am totally ignorant in crystallography, so, how could I visualize the electron density of the substrate? by any symmetry operation / command so that I could check whether there is "electron density in the substrate" ? > > 2. I aligned 4KQO with the alphafold generated model, and I deleted the protein from 4KQO, and combined the two model, make a bond between the active residue with the substrate, however, I am not sure how to (1) check the bond length and angle is appropriately assigned, and (2) do energy minimization to reorientate side change to eliminate the crash with the substrate. > > Thank you very much for your help in advance > > Have a nice weekend

4 6

Modify a pdb structure
by GAETANI, LUCIA (PGR) 15 Jul '24

15 Jul '24

Hi, I am a PhD student at the University of Warwick (UK). I am contacting you to know if I can modify a pdb structure in ChimeraX. I would need to create a covalent bond between the epsilon -NH2 group of a Lys residue and the hydroxyl group of fructose to make a bond like R-CH2-NH-R'. Is this modification possible in Chimera X? If so, how can I do this? Best wishes, Lucia

2 1

stereo
by Krishnan Raman 12 Jul '24

12 Jul '24

Hi guys, How to reverse the sequential stereo in chimerax using camera command? Thanks Krish 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 3

3d glasses free monitors from acer....
by Krishnan Raman 12 Jul '24

12 Jul '24

https://www.acer.com/ee-en/spatiallabs maybe we can see chimerax😊 in 3d in these… they do have a plugin for unity.. Iam trying get one of these to try things out. 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

Re: Same residues look different
by Guillaume Gaullier 12 Jul '24

12 Jul '24

Hi Adinda, You will get answers faster if you send your questions to the list, so keep it in CC. 😊 I also observe this difference in coloring when using the button or your command. Note that the log reports a slightly different command when using the toolbar button. But I don't know why these two commands produce such different results. Try reading the documentation (the command "help coulombic" will open the relevant page). Regarding your second question, this is explained in the documentation (and in physical chemistry textbooks): "Coulombic electrostatic potential is calculated from atomic partial charges and coordinates according to Coulomb's law: φ = Σ [qi / (εdi)] φ is the potential (which varies in space), q are the atomic partial charges, d are the distances from the atoms, and ε is the dielectric, representing screening by the medium. The resulting potential is in units of kcal/(mol·e) at 298 K. A distance-dependent dielectric is sometimes used to approximate screening by implicit solvent. By default, distDep true and dielectric 4.0 are used" What is represented on the surface of the protein as a red-blue gradient are the values of this electrostatic potential, which is continuous in space. So, your example aromatic residue appears blue because there must be a positively charged residue sufficiently close in space (look around, you should find it). This is not too surprising: lysine and arginine often make cation-pi interactions with aromatic residues. See https://en.wikipedia.org/wiki/Cation%E2%80%93%CF%80_interaction for more info. I hope this helps, Guillaume ________________________________ From: ADINDA <adinda.fitri.falinka(a)gmail.com> Sent: Friday, July 12, 2024 9:27:12 AM To: Guillaume Gaullier Subject: Re: [chimerax-users] Same residues look different Dear Dr Guillaume, Thank you for your prompt response. I have another question. * How does the ESP colouring work? When you click on molecular display and click "electrostatic" after that, it shows you the charges on the surface protein display (blue for positive, red for negative). But if you run the command "coulombic protein surfaces #sample", you'll get a different view, with the positive and negative parts becoming more pronounced. <https://preview.redd.it/need-help-with-chimerax-v0-loexjv50glbd1.png?width=…> [r/labrats - this is the view I get when I just click electrostatic in the molecular display bar (PDB: 2j1a)] this is the view I get when I just click electrostatic in the molecular display bar (PDB: 2j1a) <https://preview.redd.it/need-help-with-chimerax-v0-vmusn036glbd1.png?width=…> [r/labrats - this is what I get when I run the command "coulombic protein surfaces" (PDB: 2j1a)] this is what I get when I run the command "coulombic protein surfaces" (PDB: 2j1a) * Why is tryptophan/phenylalanine (actually any hydrophobic a.a for that matter) "positively charged" when I turn on ESP? (it's coloured blue when it should be white) <https://preview.redd.it/need-help-with-chimerax-v0-3fmfb2rjglbd1.png?width=…> [r/labrats - my mouse is hovering at the light blue area next to phenylalanine label] my mouse is hovering at the light blue area next to phenylalanine label Best, Adinda On Fri, Jul 12, 2024 at 2:50 PM Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se<mailto:guillaume.gaullier@kemi.uu.se>> wrote: Hello Adinda, These two lysines look different because one displays the hydrogen atoms while the other one doesn’t. The one that doesn’t show them probably doesn’t have them in the coordinate file (omitting them is a common practice when doing model building), but you can add them with the command "addh". Once they are added, or with a coordinate file that already had them, you can hide them from the display with the commande "hide H". The other reason these two lysines look different is because they have different rotamer conformations. As far as I can tell, they seem to be from different structures, so this is normal. These conformations depend on the underlying experimental data that were used to build these atomic models (an electron density map from a crystallographic dataset, or a cryoEM map). If you display the map overlayed on the atomic model, you can determine how well these rotamers are supported by the data. But lysines exposed at the surface, like these ones, often show poor density (because they are flexible), so the rotamer modeled in the atomic model is unlikely to fully account for the real conformations. I hope this helps, Guillaume On 12 Jul 2024, at 06:35, ADINDA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear developers, I have a few questions about how residues are visualised on your software. <image.png> <image.png> They're both lysine but look different. What can I do to solve this? Best, Adinda VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.

2 1

Same residues look different
by ADINDA 11 Jul '24

11 Jul '24

Dear developers, I have a few questions about how residues are visualised on your software. [image: image.png] [image: image.png] They're both lysine but look different. What can I do to solve this? Best, Adinda

2 1

Generating long fibrils
by Binh Nguyen 11 Jul '24

11 Jul '24

Dear all, Is there a way in chimeraX that I can use to generate a long fibril, say 20 chains, from a single chain with a twist angle of -1.4 degree and the rise (distance between layers) of 4.75 Angstrom. Some thing like this: [cid:4fb0d318-2ddd-4570-99a9-99846b9ee27c] I normally used Coot and manually add a single layer into density. Thanks, B ________________________________ UT Southwestern Medical Center The future of medicine, today.

4 9

Install ChimeraX on Linux without sudo
by Roden Deng Luo 10 Jul '24

10 Jul '24

Dear ChimeraX Team, The install notes for all the current distributions for the Linx system require sudo. I wonder is it possible without sudo? On Rocky Linux VERSION 9.4 (Blue Onyx), I tried the following. $ flatpak --user install ChimeraX-1.8.flatpak error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/23.08 which was not found $ rpm -ivh ucsf-chimerax-1.8-1.el9.x86_64.rpm error: Failed dependencies: fftw-libs-single is needed by ucsf-chimerax-1.8-1.el9.x86_64 mesa-libOSMesa is needed by ucsf-chimerax-1.8-1.el9.x86_64 sqlite is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-cursor is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-image is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-keysyms is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-renderutil is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-wm is needed by ucsf-chimerax-1.8-1.el9.x86_64 Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 6

Morphing of different surfaces
by Leonardo Talachia Rosa 10 Jul '24

10 Jul '24

Dear ChimeraX community, I hope you are well. I have a set of models for which I want to show the exposure of specific regions as protein changes conformation through morphing. I can do a morphing between atoms or ribbons, and that looks ok, but the presentation would benefit from a morphing between surface representation coloured by electrostatic potential of each state. I scavenged the youtube tutorials and chimeraX documentation but could not find a way to do it. Would anyone know how to produce this? All models have identical sequence and I calculated the surface for all of them. Thank you for your time, Kind wishes, Leonardo -- ************************* Leonardo TALACHIA ROSA, PhD Associated professor Department of Biochemistry and Tissue Biology (DBBT) Biology Institute Universidade Estadual de Campinas - UNICAMP Rua Monteiro Lobato, 255 - Campinas - SP - Brasil - CEP 13083-862 **************************

2 3

Re: ChimeraX Coloring Single Residues
by Elaine Meng 09 Jul '24

09 Jul '24

Hi Colorado (CC'ing the chimerax-users list), This page in the User Guide covers how to specify models, chains, residues, etc. in commands: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> Besides commands ("color" "show" "style" etc.) you can use the menu and other graphical interfaces. E.g. Select menu or drawing boxes in the Sequence Viewer to select atoms/residues and then the Actions menu to act on the selection. All these commands and tools have help pages in the User Guide. <https://www.rbvi.ucsf.edu/chimerax/docs/user/index.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/selection.html> You may also want to look at the tutorials, e.g, "protein-ligand binding sites" for general structure analysis <https://www.rbvi.ucsf.edu/chimerax/tutorials.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> ...and many example images on our website with links to the command scripts (.cxc files) to generate them, <https://www.rbvi.ucsf.edu/chimerax/gallery.html> <https://www.rbvi.ucsf.edu/chimerax/features.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 9, 2024, at 11:07 AM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > Hi Colorado, > Happy to hear you like ChimeraX images! In general it would be best to send these kind of general usage questions (that don't include proprietary information) to the chimerax-users list (chimerax-users(a)cgl.ucsf.edu) ChimeraX is developed by a team of people with varying roles, so some questions may best be answered by one team member whereas other questions might better be answered by another. The answer to a question might also benefit other users this way. > To actually answer your question :-), you add :residue-number to the specifier, so if it was residue 53 then "#1/T:53". Also, you only need to include the model number if you have multiple models open. This is all documented of course. To find that documentation you could type "help color", which would bring up the color help page. That page shows the syntax of the command, including "spec", which is a link to another page that explains command-line specifiers in detail. > > --Eric > >> On Jul 9, 2024, at 9:33 AM, Colorado Wilson <colorado(a)neurosnap.ai> wrote: >> >> Hello Dr. Petterson, >> >> Our company has recently swapped from PyMol to ChimeraX for creating images as ChimeraX provides some beautiful image generation scenes. However, for the life of me and a number of colleagues we cannot figure out how to color a single residue in a chain / structure. >> >> I am able to color a chain like so: >> >> color #1/T#ffffff (color hexcode) >> >> Would you be able to provide any guidance? Thank you for your time and the tool you've made! >

1 0

Alter method of distance calculated for "closest" command
by Alexander Lee 09 Jul '24

09 Jul '24

Currently, I have these commands to calculate the closest 5 :SIA out of 45 to a binding site each frame parm ../2_md/CPLX_Neut_Sol.parm7 trajin ../2_md/10.1.produ.nc rms :1-1469 first # align receptor closest 5 :132-134 solventmask :SIA closestout SIA2ChainA_Binding_sites.dat name SIA run exit The output file contains Frame Molecule Distance FirstAtom# which to my understanding, the distance is from the :SIA atom closest to the center of mass of the residues :132-134. 1. Is there some way to do the distance from center of mass :SIA to center of mass residues instead? * ex: [distance of closest :SIA atom to residues] > [distance of :SIA center of mass to residues] 2. Is there a way to do RMSD calculation of those selected closest ligands to a pdb reference? I was thinking along the lines of "for FRAME in" maybe? Thank you, Alex

3 2

Label “check_interface” residues in ChimeraX
by Gupta, Arun 09 Jul '24

09 Jul '24

Hello ChimeraX team, I came to know this fabulous ChimeraX custom “check_interface” command to instantly identify interface residues between chains A and B of protein complex model #1. It works nicely with any number of protein complex models for e.g. #1, 2, 3, 4 with chains A and B However, when I am trying to “label” the identified interface residues using the below mentioned ChimeraX command for the various protein complex models #1, 2, 3, 4. It doesn’t seem to work. I am interested to identify and label the interface residues for the related set of various protein complex models #1, 2, 3,4. label sel text "{0.label_one_letter_code}{0.number}" Can somebody suggest what I am doing wrong with the ChimeraX “label” command ?? Thanks a lot ! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

2 1

ChimeraX for mobile platforms
by Schäfer, Christian 05 Jul '24

05 Jul '24

Hello I was wondering if you are planning to release a ChimeraX version for mobile platforms such as iOS for iPad? Best, Christian

2 1

markers radius
by Yanhe Zhao 05 Jul '24

05 Jul '24

Dear ChimeraX community, I thought the radius of marker is in angostrom, right? And is that possible to set the transparency of the marker? Thanks and cheers, Yanhe

2 2

Announcing chimerax-emacs
by Zach Pearson 05 Jul '24

05 Jul '24

Hi ChimeraX Users, Over the holiday, I wrote a package that will let you use the command line from Emacs, leveraging ChimeraX’s rest server. https://github.com/zjp/chimerax-emacs This should be helpful if you use Emacs as your main editor and you want to debug your bundles without leaving your editors. Contributions from other emacs users welcome. — Zach

2 2

Doubt about sequence visualization after real.space.refinement in phenix
by Leyre Marin Arraiza 04 Jul '24

04 Jul '24

Dear UCSF ChimeraX, I have a practical question regarding model sequence visualization after real.space.refinement in phenix. After I worked on my model in ISOLDE and Coot, I deleted some residues that were out of the map density. Then, a dashed line appeared in my model, connecting the gap between the remaining residues (example, ALA97------GLN110). When I visualize the model sequence in ChimeraX, the deleted residues appear boxed with a rectangle, to indicate they are missing in the structure. Once I get the results back from the phenix real.space.refinement, and I visualize the model sequence in ChimeraX again, the deleted residues do not appear boxed anymore, but they are gone instead from the visualized sequence, keeping their corresponding numbers but not showing a boxed gap (in the example I mentioned they jump from 97 to 110 directly). I would like to keep the deleted residues boxed in the sequence when I visualize it. Is that possible? Hope I am explaining myself. Thanks and best regards, Leyre Leyre Marin Arraiza PhD fellow University of Copenhagen Novo Nordisk Foundation Center for Protein Research Taylor Group Blegdamsvej 3B, Building 6, 6-1-10 2200 København N leyre.arraiza(a)cpr.ku.dk<mailto:leyre.arraiza@cpr.ku.dk> [CvwfJbQuv4S75bEAAAAASUVORK5CYII=] How we protect personal data<https://informationssikkerhed.ku.dk/english/protection-of-information-priva…>

2 1

show 5% or 10% Z-axis of a fibril density
by Binh Nguyen 03 Jul '24

03 Jul '24

Dear all, Is there a way to display say 10% on the Z-axis of a fibril density map? Or maybe save 1 or 2 layers of the map? [cid:11c579f0-867a-4136-b817-27e4c071e57e] I know 2 ways to do it but they both take a long time, and I wonder if we have an easier way to do it. 1. Use volume eraser with a big diameter sphere 2. Build a rough backbone carbon model in 1 layer, and do zone selection. Thanks, B ________________________________ UT Southwestern Medical Center The future of medicine, today.

3 3

Doubt about chimera
by DIEGO ANGOSTO BAZARRA 03 Jul '24

03 Jul '24

Hello, My name is Diego. I’m a beginner user of ChimeraX (1.8) and I was wondering if there is an option to check the % of similarity between two structures after making the matchmaker. I mean, I make a matchmaker with two structures, can I see the % of similarity between these two structures? Not between the sequences, but between the structures. Thank you very much for your time and attention. Best regards Dr. Diego Angosto Bazarra Molecular inflammation and experimental surgery group. IMIB. University Hospital Virgen de la Arrixaca

3 3