- ChimeraX-users - RBVI Mailing Lists

Doubt about volume cropping
by Leyre Marin Arraiza 29 Jul '24

29 Jul '24

Dear UCSF ChimeraX, I have a practical question regarding 3D volume visualization and cropping in ChimeraX. I have a big 3D density map which includes the densities for several models of different proteins. To facilitate visualization and model building, I would like to crop the density map, so that it includes only two of the models. Is it possible to crop my density map around those models, to make it a bit smaller and more focused on the areas of interest? 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…>

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ChimeraX adjacent question about ConSurf
by David S. Fay 26 Jul '24

26 Jul '24

Hi, I’m curious if anyone else is having trouble getting results from ConSurf? The site appears to be up, which maybe wasn’t the case a while back. But trying various kinds of inputs doesn’t lead to any results. Rather, it just seems to just get hung up. (It’s also possible I’m doing something incorrectly.) Thanks in advance! David David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming davidfay(a)uwyo.edu

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Question about Creating/Displaying Vectors
by John Watters 25 Jul '24

25 Jul '24

Hi All, I was wondering if anyone had any advice on how to make figures where vectors show the difference in the RMSD of the alpha carbons like in A/C here in ChimeraX: [https://iiif.elifesciences.org/lax/51898%2Felife-51898-fig3-v2.tif/full/617…] From this paper: https://elifesciences.org/articles/51898 [https://elifesciences.org/assets/images/social/icon-600x600@1.52e87ee6.png]<https://elifesciences.org/articles/51898> Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon–anticodon pairing<https://elifesciences.org/articles/51898> Chemical modifications near the tRNA anticodon and specific mRNA–tRNA pairs combine to control the ribosomal three-nucleotide mRNA reading frame, essential for the sequential addition of amino acids into polypeptide chains. elifesciences.org

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Re: combining and splitting chains
by Elaine Meng 25 Jul '24

25 Jul '24

Hi Dmitry, You can do the combining into one model with "combine" and the splitting into multiple models with "split", see links in my previous message. The "split" command can use residue ranges (not just chain IDs) so you can split it however you want even if it is one chain. However, I don't know if it makes sense to make it all one chain, but I think Eric already explained that part in his reply. The "changechains" command can change the chain ID, and "rename" can change the model name and ID: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html> I hope this helps, Elaine > On Jul 25, 2024, at 9:05 AM, Dmitry Semchonok <semchonok(a)gmail.com> wrote: > > Dear Elaine, > Thank you for your answer. > You were right. I meant to combine chains inside 1 model so that there would be only 1 model with 1 chain (instead of multiple). > Can we rename all of them to 1? > And vice versa — when there is one model, and one wants to split it into domains (chains)? > Any ideas? > Thank you. > Kind regards, > Dmitry > > Ps. Sorry, I can not send the emails with illustrations to ChimeraX somehow.From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: 22 July 2024 18:10 > To: Dmitry Semchonok <semchonok(a)gmail.com> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] combining and splitting chains > Hi Dmitry, > I thought you meant combining multiple chains into a single chain. However, if you instead meant combining chains that are in different models into a single model (still with multiple chains), see command "combine": > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> > > Then if these chains have different chain IDs, it is easy to split that single model into multiple models again, one for each chain, with "split": > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> > > Regards, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jul 20, 2024, at 3:50 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hello Eric, > > Thank you for your answer. > > Following up combining and splitting chains topic I would like to specify more details. > > My question is connected to modelangelo output where one gets the separate chains. I would like to combine those chains in one structure. > > But maybe later I may need to divide the complete structure on chains again. > > Kind regards, > > DmitryFrom: Eric Pettersen <pett(a)cgl.ucsf.edu> > > Sent: 17 July 2024 19:26 > > To: Dmitry Semchonok <semchonok(a)gmail.com> > > Cc: ChimeraX <chimerax-users(a)cgl.ucsf.edu> > > Subject: Re: [chimerax-users] combining and splitting chains > > > > Hi Dmitry, > > You don't say why you want to combine/split these chains, so there might be more direct way to accomplish whatever your ultimate goal is than my answers below, if we knew what your goal was. > > You combine chains by using the 'bond' command (or Build Structure tool) to form the C→N bond (or O3'→P bond for nucleic acids) between the chains. ChimeraX will combine them into a single chain. > > Splitting chains is uglier because ChimeraX knows that the residues in a chain form a chain even if you delete connecting bonds or even entire residues. The recipe would be to open multiple copies of your model. In the first copy, in the chain you want to split delete everything but the first "segment" you want split off. In the second copy delete everything but the second segment (and all other chains if there are any). So on and so forth. Then use the "combine" command to combine the models into one. > > > > --Eric > > > > Eric Pettersen > > UCSF Computer Graphics Lab > > > >> On Jul 17, 2024, at 9:33 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > >> > >> Dear colleagues, > >> I have a lot of chains that I want to combine just in 1. > >> How to do that? > >> And vice versa – I have 1 chain, and I want to split it into several. > >> Thank you in advance, > >> Kind regards, > >> Dmitry

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Re: ChimeraX-SASA mismatch with contiguous sequences
by Elaine Meng 24 Jul '24

24 Jul '24

Dear Suhas, I hope your week is great as well, and we're glad you like ChimeraX! We recommend sending ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) unless they include private data. That way others can also answer, or benefit from the answers. In this case, it is explained in the "measure sasa" help. Please see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> The command measures the surface area *enclosing* the specified atoms. That is different than the surface area of those atoms in the context of the larger structure. So when you give two commands measuring two parts you also get more surface that goes around the ends of those parts. If you wanted the SASA in the context of the whole protein or whole chain, you would have to do it differently. As explained in the help link above, if you want to measure the SASA of those parts in the context of the whole protein chain's surface, it would instead be something like measure sasa /A sum /A:1-10 measure sasa /A sum /A:11-20 measure sasa /A sum /A:1-20 The Log gives: measure sasa /A sum /A:1-10Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:1-10 (66 atoms) of /A (2615 atoms) = 1143 measure sasa /A sum /A:11-20Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:11-20 (80 atoms) of /A (2615 atoms) = 427.09 measure sasa /A sum /A:1-20Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:1-20 (146 atoms) of /A (2615 atoms) = 1570.1 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 23, 2024, at 11:59 PM, Suhas Srinivasan <suhas.srinivasan(a)stanford.edu> wrote: > > Dear Dr. Meng, > > Hope you are having a great week! > > Thank you for developing and maintaining ChimeraX as an essential analytical software for the community. > > We had a query since we noticed a discrepancy in the way SASA is reported. > If you were to consider the AlphaFold database structure for PCBP1 (Q15365) and perform the below SASA measurements, we noticed that: > SASA(1 to 10) + SASA(11 to 20) ≠ SASA(1 to 20) > > measure sasa /A:1-10 > Solvent accessible area for /A:1-10 (66 atoms) = 1385.3 > measure sasa /A:11-20 > Solvent accessible area for /A:11-20 (80 atoms) = 1632.6 > measure sasa /A:1-20 > Solvent accessible area for /A:1-20 (146 atoms) = 2850.8 > > There is a difference of ~167 sq. A. > It would be very helpful to understand why such a large difference exists when considering contiguous sequences of atoms/residues. > > ChimeraX-1.8 > macOS-14.5 (Intel) > > Thank you for your consideration. > > Kind regards, > Suhas Srinivasan

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Re: [Chimera-users] column selection: chimera vs chimeraX
by Eric Pettersen 23 Jul '24

23 Jul '24

Hi Mike, There wasn’t, but I just added code to do it. In tomorrow’s daily build (well, the next daily build that works :-) ) the alignment viewer’s context menu will have an “Expand Selection to Columns” entry that will do this. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Jul 22, 2024, at 9:01 AM, 7mkf via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi there, > > I'm an avid user of chimera and have begun transitioning to chimeraX. A feature I find very useful in chimera is expand selection to columns within the multialignviewer. Is there a way to do this in ucsf chimeraX? > > Many thanks, > Mike > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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saving modifications
by Claudio Andres Aguilar Pena 23 Jul '24

23 Jul '24

Dear ChimeraX team, First of all, many thanks for the app, it’s really wonderful!. I have a question regarding one feature I would like to have and maybe it’s possible to do but I just don’t know how. I have a PDB of the structure of an enzyme that has 5 different domains: I can select the aa of each domain and give each domain a color. This is very useful for me when comparing structure predictions of the enzyme and see what happens when making mutations in the primary structure. My problem is that I cannot save the PDB with the colors for each domain, so I have to select and assign the colors every time, or leave the app and the PDB permanently open, which is not very convenient. Is there a way to save the PDB with the modifications I made? Many thanks for your help. Best, Claudio Dr. Claudio Aguilar, PhD Virologisches Institut Universität Zürich Vetsuisse Fakultät Winterthurerstrasse 266a CH-8057 Zürich Switzerland phone: +41446358712 Fax: +41446358911

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chimerax-0.1.71 python API: failed imports in module
by ishaanawasthi05＠gmail.com 22 Jul '24

22 Jul '24

Dear ChimeraX Team, I'm trying to use the ChimeraX API in python to automate some analysis. My code is not executing due to some missing/failed imports inside the ChimeraX module. File "/opt/anaconda3/lib/python3.11/site-packages/chimerax/core/models.py", line 54, in <module> from chimerax.graphics import Drawing, Pick, PickedTriangle ModuleNotFoundError: No module named 'chimerax.graphics' In the same file (models.py) there are also problems with this: "from .state import State" Together they are being used in the following class definition: class Model(State, Drawing): """ A Model is a :class:`.Drawing` together with an id number that allows it to be referenced in a typed command. .... """ I haven't been able to find any information on what these imports are, why they are missing, or how to resolve this issue. I also don't know if there are more missing imports, as it keeps failing here. I would appreciate your support in getting the Chimerax API to work — if this is the wrong place to ask, please do point me toward the right forum for ChimeraX. Thanks so much for the help!

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combining and splitting chains
by Dmitry Semchonok 22 Jul '24

22 Jul '24

Dear colleagues, I have a lot of chains that I want to combine just in 1. How to do that? And vice versa – I have 1 chain, and I want to split it into several. Thank you in advance, Kind regards, Dmitry

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ChimeraX journal-quality figures script !
by Gupta, Arun 22 Jul '24

22 Jul '24

Dear ChimeraX team, Recently, I came across this review article “Front. Microbiol.13, 2022, 891610” and I am quite fascinated by the visually appealing figures made in the above-mentioned review article. Since the figures were created with UCSF ChimeraX in the review article. I was just wondering can somebody advice or suggest what should be the specific ChimeraX command scripts for making similar journal-quality figures. Find attached one of the example figures from the review article for the reference. Thanks! Arun

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Chimerax on Fedora 40
by Vito Calderone 19 Jul '24

19 Jul '24

I have installed ucsf-chimerax-1.8-1.el9.x86_64.rpm on a fedora 40 pc. Installation was fine. When I launch 'chimerax' I get the following error: $ chimerax Fatal Python error: Segmentation fault Current thread 0x00001500f588ab80 (most recent call first): File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed File "<frozen importlib._bootstrap_external>", line 1233 in create_module File "<frozen importlib._bootstrap>", line 573 in module_from_spec File "<frozen importlib._bootstrap>", line 676 in _load_unlocked File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 1176 in _find_and_load File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/Qt/QtWebEngineWidgets.py", line 4 in <module> File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed File "<frozen importlib._bootstrap_external>", line 940 in exec_module File "<frozen importlib._bootstrap>", line 690 in _load_unlocked File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 1176 in _find_and_load File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed File "<frozen importlib._bootstrap>", line 1232 in _handle_fromlist File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/Qt/__init__.py", line 112 in qt_have_web_engine File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 108 in __init__ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 653 in init File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in <module> File "<frozen runpy>", line 88 in _run_code File "<frozen runpy>", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._p cg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets (total: 18) Segmentation fault (core dumped) Any hint? Thanks Vito -- Dr. Vito Calderone Ph.D. Associate Professor of Inorganic Chemistry CERM and Department of Chemistry University of Florence Via Luigi Sacconi, 6 50019 Sesto Fiorentino (FI) Italy tel: +39 055 457 4276

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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!

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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

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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._ >

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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

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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.

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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

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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

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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

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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

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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.

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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.

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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.

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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

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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.

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