- ChimeraX-users - RBVI Mailing Lists

Re: [ccpem] Making thioester bond in Chimera/ChimeraX
by Elaine Meng 13 Nov '23

13 Nov '23

Hi Firdous, No trick, it is an option of cartoon (on by default) to prevent showing backbone atoms at the same time. Glycine only has backbone atoms (no sidechain). If you really want to show cartoon and backbone atoms at the same, use cartoon suppress false This is explained in the "cartoon" or "ribbon" command help. Just type command "help cartoon" to see your downloaded copy of the help page, or see the copy on our website here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> The full name of the option is "suppressBackboneDisplay" but you can shorten all options in commands as long as there is no other option that starts with the same letters. Actually Chimera ribbon also hides backbone atoms by default, although you can allow showing both at the same time with the Chimera "ribbackbone" command. The best address to use for ChimeraX questions is the chimerax-users one that I CC'd on this message, unless you are including data that must be kept private. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 13, 2023, at 2:59 PM, Firdous Tarique <kahkashantarique(a)gmail.com> wrote: > > Hi Elaine > > Now I know where the problem is. In ChimeraX I am not able to show Gly simultaneously as a stick and cartoon. If I am trying to show Gly as a stick then the cartoon line breaks up at this position. And this is for any structure if you see. By showing a cartoon and stick together, the sticks for all amino acids show up except for Gly where it remains in the cartoon (you can try that). However this is not the case in Pymol and Chimera. Do you know any tricks to fix that in ChimeraX? > > Best > > Firdous > > On Thu, Nov 9, 2023 at 6:11 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hello Firdous, > Probably the problem is that mol A and mol B are two different models. You can't add a bond in Chimera or ChimeraX until after combining them into one model first. > > ChimeraX combine command: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> > > ChimeraX bond command or Build Structure tool, Adjust Bonds section: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> > > For the best chance of getting an answer to a question about ChimeraX, please use the chimerax-users(a)cgl.ucsf.edu address: > <https://rbvi.ucsf.edu/chimerax/docs/contact.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > From: Collaborative Computational Project in Electron cryo-Microscopy <CCPEM(a)JISCMAIL.AC.UK> on behalf of Firdous Tarique <kahkashantarique(a)GMAIL.COM> > > Date: Thursday, November 9, 2023 at 12:27 PM > > To: CCPEM(a)JISCMAIL.AC.UK <CCPEM(a)JISCMAIL.AC.UK> > > Subject: [ccpem] Making thioester bond in Chimera/ChimeraX > > > > Hi > > > > Does anybody know how to make thioester bonds in Chimera or ChimeraX ? > > > > I am unable to make a bond between Cys321 in mol A with Gly1 in mol B (S-glycyl-L-cysteine) using Chimera or ChimeraX. > > > > I tried Isolde in ChimeraX and Build Structure in Chimera to make a bond between selected atoms but so far have been unsuccessful. I don't know if I am missing something. > > > > Any help would be appreciated. > > > > Thanks > > > > Firdous > > > > To unsubscribe from the CCPEM list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 > > >

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projecting full model from monomer
by Dmitry Semchonok 13 Nov '23

13 Nov '23

Dear colleagues, I have a monomer with biomt information that describes the full model. To see the full model, I use the command sym when opening the monomer in Chimera. Could you please prompt the correspondent command in ChimeraX to project the complete model in ChimeraX based on the information stored in the monomer? Thank you Kind regards, Dmitry

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ChimeraX trial license
by Jang,Chang Woon,US-St. Louis 12 Nov '23

12 Nov '23

Dera UCSF ChimeraX Team, My name is Chang Woon Jang working for Nestle Purina. I am interested in ChimeraX for a molecular modeling project. Could I use a trial license for a month before buying the commercial license? Thanks, Chang Woon Jang

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updating ChimeraX for rc/daily build with Isolde
by Dmitry Semchonok 11 Nov '23

11 Nov '23

Dear colleagues, I would like to update ChimeraX to rc version or daily build. Trying to install Isolde / Clipper delivered me the following error (either via the command line within ChimeraX, or via the ChimeraX update button) Clipper toolshed install C:/Users/Dmitry/Downloads/ChimeraX_Clipper-0.22.1-cp311-cp311-win_amd64.whl ERROR: Could not find a version that satisfies the requirement ChimeraX-Core<1.8,>=1.7.dev202306142048 (from chimerax-clipper) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core<1.8,>=1.7.dev202306142048 ISOLDE toolshed install C:/Users/Dmitry/Downloads/ChimeraX_ISOLDE-1.7.dev0-cp311-cp311-win_amd64.whl ERROR: Could not find a version that satisfies the requirement ChimeraX-Core<1.8,>=1.7.dev202306142048 (from chimerax-isolde) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core<1.8,>=1.7.dev202306142048 Is it possible to install Isolde/clipper with rc/daily version? If yes, how to fix the error? Thank you. Kind regards, Dmitry

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Zooming in and out in ChimeraX
by Dale Calleja 09 Nov '23

09 Nov '23

Hello, I am currently learning to use ChimeraX (v1.6.1) and I am having issues with my scroll wheel. I notice when I first open the software using the scroll wheel on my mouse will zoom in and out of the structure but, after some time it simply stops working and the scroll wheel does nothing. Is this a button I am accidentally pressing or have I discovered a bug? It doesn’t seem to have any pattern, I am just clicking around changing the display of my protein. Thanks! Dale. Dale Calleja PhD Student, Komander Lab Ubiquitin Signalling Division WEHI 1G Royal Parade Parkville VIC 3052 Australia Email calleja.d(a)wehi.edu.au<mailto:calleja.d@wehi.edu.au> [WEHI Logo] Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville Victoria 3052 Australia www.wehi.edu.au<https://wehi.edu.au> Twitter<https://twitter.com/WEHI_research> | Facebook<https://www.facebook.com/WEHIresearch/> | Instagram<https://www.instagram.com/wehi_research> | Youtube<https://www.youtube.com/user/WEHImovies> | LinkedIn<https://www.linkedin.com/company/wehi_research> WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. Private and confidential The content of this e-mail and any attachments may be private and confidential, intended only for use of the individual or entity named. If you are not the intended recipient of this message you must not read, forward, print, copy, disclose, use or store in any way the information this e-mail or any attachment contains. If you are not the intended recipient, please notify the sender immediately and delete or destroy all copies of this e-mail and any attachment.

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ui mousemode right when in ISOLDE
by Alexis Rohou 09 Nov '23

09 Nov '23

Hi there, Wondering if anyone else gets this behavior: When ISOLDE is running, setting the right mouse click to translate selected atoms does NOT associate shift-right-click with rotating selected atoms; instead, shift-right click does a zoom. In addition, if I try to force it by issuing the two commands below, the shift right click still isn't a rotate selected atom; instead, it does a translate selected atoms. ui mousemode right "translate selected atoms" ui mousemode shift right "rotate selected atoms" My workaround is to use alt-right for rotating instead. That does work: ui mousemode right "translate selected atoms" ui mousemode alt right "rotate selected atoms" This is with ChimeraX 1.6.1, but I'm pretty sure I noticed this behavior in earlier versions also. Tristan recently posted a screen capture where it's clear he doesn't have this problem, but he's on Windows and I'm on Mac, so I wonder whether that might have something to do with it. Any ideas? Cheers, Alexis

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how to build N-linked glycans
by Alexis Rohou 09 Nov '23

09 Nov '23

Hi there, How would you recommend I go about building an N-linked glycan chain off of an ASN in an existing model using ChimeraX or ISOLDE? Is there documentation on this somewhere? Cheers, Alexis

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Custom calculation of forcefields for ligands in Isolde
by Paul Sauer 09 Nov '23

09 Nov '23

Dear ChimeraX and Isolde experts, I am trying to parameterize a ligand in Isolde 1.6 in order to fit it into my density. The ligand conforms to the requirements that are outlined in the manual (not covalently bound, only consists of certain elements, etc). However, parameterizing the residue using the inbuilt ANTECHAMBER/AMBER utility times out unfortunately, with an error saying that convergence in SCF cannot be reached. Upon investigating the issue I learned that it could be possible to avoid this error with adjusted command line parameters for AMBER in order to let it run longer for correct values. My question is: Is it possible to pass custom flags or command line arguments from Isolde to AMBER in ChimeraX? And if yes, how? The default command ‘Isolde parameterize residue’ does not seem to have any AMBER specific options. For example, how can I add 'adding ndiis_attempts=700’ (or other modifications) to my input sqm file? Thank you in advance, Paul

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How to refine a symmetric model with ISOLDE
by Guillaume Gaullier 09 Nov '23

09 Nov '23

Hello, A question for Tristan, since I know you read this list. :-) I have a cryoEM map that was produced with C7 symmetry enforced. I can fit the alphafold prediction of one protomer, and am pretty confident in this initial rigid fit because the map is good. Now with Tom's help I know how to generate the C7 symmetric assembly and store the symmetry info in a cif file with a single protomer, so I can regenerate the heptamer as needed (and this seems like the correct way to deposit the end result). But this model still needs proper refinement: the rigid fit shows that the conformation predicted by alphafold deviates from the map at several locations. What is a sensible refinement strategy for something like this? Because symmetry was enforced for the map, I am inclined to refine only a single protomer and add the correct symmetry info that will regenerate the heptamer. But don't I need the neighboring protomers during refinement, for the interface residues to behave correctly during MDFF? I would think so. Not sure what to do, some advice would be very helpful. Thank you in advance, Guillaume 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

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How to write biological assembly info in PDB or mmCIF?
by Guillaume Gaullier 08 Nov '23

08 Nov '23

Hello, I have a cryoEM map that was generated with C7 symmetry enforced, with its symmetry axis parallel to the z axis in ChimeraX. I fetched a prediction from AlphaFoldDB and docked it in the map. So far, so good. I can generate the other protomers with a command like this: sym #1 C7 axis z center cofr (assuming #1 is the single protomer from AlphaFoldDB, and the cofr is correctly lying on the symmetry axis, which I get sufficiently close if I center the view on the map) Now, because symmetry was enforced for the map, it makes no sense to model, refine and store the entire heptamer. I should be able to do everything with a single protomer, and store relevant info as "biological assembly" so the heptamer can be regenerated from the protomer. At least if I am understanding this correctly. I tried the above command, or this variant: sym #1 C7 axis z center cofr addMmcifAssembly true And subsequently saving in PDB or mmCIF format, but none of this produces what I want, which is a file containing the single protomer + assembly info. I either get a file with the single protomer or a file with the heptamer, in both cases without any biological assembly info. I looked up the options of the save command for PDB and mmCIF format, but found nothing that seemed relevant to this problem. Is there a way to do this? Or am I misunderstanding something? Related question: it might make sense to use the whole heptamer for refinement, so all interfaces between protomers "see" each other (probably important when using ISOLDE). What is the best way to deal with this? Build and refine the whole heptamer and save only a single protomer + assembly info at the very end? Or have the symmetry enforced from the beginning, throughout the whole refinement process, and really ever refine a single protomer? (7 times less work, so probably the preferred option). Thank you in advance, Guillaume 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

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Modeller down
by Dominik Dekleva 08 Nov '23

08 Nov '23

Hi My name is Dominik Dekleva, phd student at the University of Ljubljana. I'm attempting to use the Modeller feature in ChimeraX but doesn't seem to be working. Is the webservice down? Best regards, Dominik Dekleva

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Alphafold2_multimer on chimeraX
by Margulies, David (NIH/NIAID) [E] 08 Nov '23

08 Nov '23

Beginning yesterday, I have had repeated failure of alphafold2_multimer running through chimerax to generate models of two protein complexes (Ab H cand L chains, for instance). Individual chains work fine. The error from Colab AI says: The error is due to a bug in the ColabFold library. The kabsch function in the colabfold.py file is using the linalg.svd function to calculate the singular value decomposition of a matrix. However, the linalg.svd function is not guaranteed to converge, and in some cases it can fail to converge. This can cause the kabsch function to fail, and in turn cause the plot_protein_backbone function to fail. The bug has been fixed in the latest version of the ColabFold library, which is available on GitHub. To fix the error, you can upgrade to the latest version of the library. You can do this by running the following command in the Colab notebook: content_copy !pip install colabfold --upgrade Use code with caution<https://g.co/legal/generative-code> Once you have upgraded to the latest version of the library, you can run the code again and the error should be fixed. Can you advise? Thanks for your help. D David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892 Email: dmargulies(a)niaid.nih.gov<mailto:dmargulies@niaid.nih.gov>, dhm(a)nih.gov<mailto:dhm@nih.gov> Ph: 301-496-6429 Fax: 301-480-7352 Web: https://www.niaid.nih.gov/research/david-margulies-md-phd “Public service is a public trust, requiring employees to place loyalty to the Constitution, the laws, and ethical principles above private gain.” – executive order 12674, https://www.federalregister.gov/documents/2016/02/17/2016-03214/standards-o…<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.federalregister.go…> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender’s own and not expressly made on behalf of the NIAID by one of its representatives.

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Zone interaction in rRNA
by tim smith 07 Nov '23

07 Nov '23

How do we select a zone in ribosomal RNA (nucleotide residues of rRNA) to visualize all its interaction interfaces with ribosomal proteins/H2O/ions using ChimeraX? Thank you for your support. Thank you. Best Tim

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Dynamic bonds
by Michael Patzschke 06 Nov '23

06 Nov '23

Dear colleagues, I have a trajectory from an ab initio MD run. The output is in the form of concatenated .xyz information. I can open and visualise this in ChimeraX, but the bond topology is determined from the first step. As the simulation progresses, bonds are stretched and the broken bond in my example just gets drawn, although the distance of the involved atoms gets larger then 7 Å by the end of the simulation. Is there a way to use dynamic bonds in ChimeraX? By this I mean that the bonds are only drawn when the distance of the involved atoms is below a certain threshold. I would appreciate any help in the matter. Kind regards, Michael Patzschke

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Change default colour cycle for EM maps
by James Hooker 06 Nov '23

06 Nov '23

Hello all, I am looking for a way to change the qualitative colour cycle in ChimeraX from the default (grey, yellow, blue, purple, pink, …). I have flicked through the online documentation, but have not yet found a solution. Many people must have desired to do this at some point, right? Any advice is welcome! Best, James

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commandline to hide a map region or set a transparency in chimeraX
by Rayees Mattoo 06 Nov '23

06 Nov '23

Hi, I was wondering if there is a command line in chimeraX to hide a region of the map. To be more specific if I have to hide map around a model #1 chain A, how could I do that? Also, using the same case how do I set a transparency of 50% for the map around the chainA model #1? Actually, I want to make a movie of the vseries where I need to hide/delete/transparent some portion of the map to show the internal details of the map while playing the vseries. Any suggestions are welcome. Best

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problem with color by conservation option
by elzbieta.wator＠doctoral.uj.edu.pl 06 Nov '23

06 Nov '23

Hi, I am trying to color my protein structure by conservation. I prepared alignement file i fasta format and when I upload it to the ChimeraX and use command: color byattribute seq_conservation palette cyanmaroon not the whole structure of my proteins get coloured. Namely despite no mismatch in the PDB file and sequence which is first in aln file there are several residues which stays in the previously selected colour. I've already made sure that the sequence is correct and I have no further ideas how to solve this problems. I will be very grateful for your tips. Best, Ela Wator

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color by conservation problem
by Elżbieta Wątor 05 Nov '23

05 Nov '23

Hi, I am trying to color my protein structure by conservation. I prepared alignement file i fasta format and when I upload it to the ChimeraX and use command: color byattribute seq_conservation palette cyanmaroon not the whole structure of my proteins get coloured. Namely despite no mismatch in the PDB file and sequence which is first in aln file there are several residues which stays in the previously selected colour. I've already made sure that the sequence is correct and I have no further ideas how to solve this problems. I will be very grateful for your tips. Best, Ela Wator [cid:e1499547-d8cf-48a6-89cb-b2ea6e696097]

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Select truncated residues in PDB
by Vorländer,Matthias Kopano 05 Nov '23

05 Nov '23

Dear ChimeraX team, Is it possible to select all residues in a model that have been truncated to backbones rather build as a complete sidechain? Many thanks, Matthias

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installing plugin
by Dmitry Semchonok 04 Nov '23

04 Nov '23

Dear colleagues, Is anything happened with the website https://cxtoolshed.rbvi.ucsf.edu/ It seems to be still down. Kind regards, Dmitry

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mseries oscillate/loop ?
by vincent Chaptal 04 Nov '23

04 Nov '23

Hi again, it is possible to use vseries play #1 loop true, but the same command with mseries doesn't work. Same with oscillate or similar commands. I've also tried mseries #1.1-20-1 or mseries #1.20-1 but these 2 commands don't work. Is there a way to make the movement go back to the origin? 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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ISOLDE and heparin
by Xuewu Zhang 04 Nov '23

04 Nov '23

Dear Tristan, Can ISOLDE handle heparin molecules now? I tried to simulate a heparin chain, it says one residue is not properly parametrized. I am using ISOLDE in Chimerax 1.6. Thanks, Xuewu

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UCSF Chimera 1.17.1
by hj_bowles＠sky.com 03 Nov '23

03 Nov '23

Good Evening, I need to download UCSF Chimera 1.17.1 for a examination, however due to the downtime on your website i am unable to do so. is there any way you can send me a link to download of get around this issue for me? I would be very grateful. Kind regards,Heather.

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fly command
by Sean Connell 03 Nov '23

03 Nov '23

Hello, I have a question about the fly command. I am trying to iterate over a series of saved views (p1-p6) using the fly command. The views are close-up views of residues because I am trying to make a movie similar to that made with resfit. The issue is that the cutting plans don't seem to update as it moves from view to view. Do you have a hint that could let me know what I am doing wrong? Thanks for any tips you have

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Show models from the same file, one by one into a movie
by vincent Chaptal 03 Nov '23

03 Nov '23

Hi, I have a PDB file with 20 models inside(#1.1 to #1.20)that I color as a rainbow. I would like to show them sequentially and make a movie showing one model at a time, back and forth (show #1.1, hide #1.1 and show #1.2, etc...). I've played with the morphing command but it is not what I want, and then with the Coordset command thinking it would be like a trajectory but I can't make it to work. I would appreciate a pointer to get me to the right direction. Thanks a lot. 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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