- ChimeraX-users - RBVI Mailing Lists

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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ChimeraX tutorial pages
by Kai Cai 03 Nov '23

03 Nov '23

Hi, Just noticed that the ChimeraX tutorial pages are not accessible. Are they temporarily down or permanently removed? Thanks, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.

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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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Middle mouse click to center and move to atom
by Adrián González López 27 Oct '23

27 Oct '23

Hi, I do not know if this is possible already (I could not find it), but is there a way in ChimeraX to set the middle click mouse button (or any other button) to center and orient the atom you click? Similar to what happens on PyMOL by default. This helps so much when navigating around a structure. I know you can do it in some other way, but it takes more time and it is not so user-friendly. If there is no way to do this, could it be implemented? Many thanks! Best, Adrián 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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Cap clipped atoms or bonds
by Daniel Larsson 27 Oct '23

27 Oct '23

Is it possible to have atoms or bonds capped when they are truncated by a near clipping plane, similar to how surfaces can be capped. Currently, you can see the interior polygons when you clip the middle of a molecule. See the attached image for an example. I tried to search the mailing list and the documentations, but could not find anything. Regards, Daniel [cid:image001.png@01DA08BB.1559BC80] 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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ChimeraX for WSL: release request
by Dmitry Semchonok 27 Oct '23

27 Oct '23

Dear Elaine and Eric, Since the number of Windows WSL systems is increasing do you consider releasing the compatible version of ChimeraX? Thank you Kind regards, Dmitry

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Chimera(X) website and web services down Oct 30-31
by Elaine Meng 26 Oct '23

26 Oct '23

Dear users, Due to system upgrades, the Chimera and ChimeraX websites, associated web services hosted by the UCSF RBVI (Modeller, Blast Protein, etc.), and the ChimeraX Toolshed will be unavailable -- the estimated downtime is from Monday, Oct 30 8:00 am PDT through Tuesday, Oct 31 11:59 pm PDT. Please pardon the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: Selection with coordinates
by Tom Goddard 25 Oct '23

25 Oct '23

Hi Siyoung, The movie recording needs a "wait" command to actually render frames. If you have 300 frames in your coordinate set it would be perframe "open select_atoms.py" movie record coordset #1 wait 300 movie encode test.mp4 Also I would suggest that your python code not use "atom.hide". That is an obscure attribute for hiding backbone atoms with ribbon display. Instead use atom.display = True atom.display = False It might be possible to record the movie entirely in Python, but I've never tried it. I would not suggest trying that approach unless you want to waste a lot of time since the movie recording code was not designed to work in a Python script. Tom > On Oct 24, 2023, at 6:01 PM, Siyoung Kim <kkssy141(a)gmail.com> wrote: > > Thank you very much for the helpful information. I think I am very close to what I want to do. > > I would like to make a video of a molecular dynamics trajectory and want to show only the atoms whose x coordinates are smaller than 0. Here is what I tried. > > a) I made a python script that can be applied to each frame and named it "select_atoms.py" > --------------------------------- > from chimerax.atomic import all_atoms > atoms = all_atoms(session) > for atom in atoms: > if atom.scene_coord[0] < 0: > atom.hide = 0 > else: > atom.hide = 1 > ---------------------------------- > > b) I opened up a trajectory in ChimeraX. > > c) In ChimeraX, I executed > --------------------------------------------- > perframe "open select_atoms.py" > movie record > coordset #1 > movie encode test.mp4 > ---------------------------------------------- > > Interestingly, if I just move a frame by myself using a slider, perframe is applied well. i.e., only the atoms whose x coordinates < 0 are shown in EACH frame > However, if I record a video like the above or click a play button, perframe is not successfully applied. Only the atoms whose x coordinates < 0 in the last frame are shown in all frames. Updating a selection in each frame does not work with this approach. > I have attached the video. Would you please help me with this? Thank you. > > I would be also curious if it could be done inside a python script. In the above, I made a script that should be applied to each frame and then called this script using perframe in ChimeraX. Would there be something like RED in the below? Thank you very much! > > RECORDING A MOVIE > for s in all_atomic_structures(session): > for cs_id in s.coordset_ids: > s.active_coordset_id = cs_id > atoms = s.atoms > atoms.selecteds = atoms.scene_coords[:,0] < 0 > atoms[atoms.selecteds].hide = 0 > atoms[~atoms.selecteds].hide = 1 > SAVE THIS IMAGE > ENCODING A MOVIE > > > On Mon, Oct 23, 2023 at 11:52 AM Siyoung Kim <kkssy141(a)gmail.com <mailto:kkssy141@gmail.com>> wrote: >> Hi Eric, >> >> Thank you very much for the very helpful information! I learned a lot. >> >> Best, >> Siyoung >> >> On Fri, Oct 20, 2023 at 8:58 PM Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >>>> On Oct 17, 2023, at 1:53 PM, Siyoung Kim via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> Hi Tom, >>>> >>>> Thank you for your help. I can confirm that making a text file, select.py, that contains the below and running "run select.py" in the ChimeraX command line works. >>>> >>>> from chimerax.atomic import all_atoms >>>> for a in all_atoms(session): >>>> if a.scene_coord[0] < 0: >>>> a.selected = True >>>> >>>> I am quite interested in learning more about the chimerax.atomix library. Would there be any helpful resources about this? >>> >>> There is automatically generated documentation, but I don't recommend it because it is poorly formatted and littered with rarely used constants and functions from base classes (e.g. Structure inherits from Model and Drawing and therefore documentation for first_intercept_children() [from Drawing] is included). Instead, I'd browse through the code for atomic class definitions themselves. The Cython class definitions for Atom, Element, and Bond are here: https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/atomic_cpp… . The definitions for the other classes are here: https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/molobj… . The latter only has the base class definitions for Structure and PseudobondGroup (StructureData and PseudobondGroupData respectively). The final definitions are in structure.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/struct…> and pbgroup.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/pbgrou…> . >>> >>> Another approach is to find a bundle that does something similar to what you want to do and look at its code to see how it does it. All the ChimeraX source code is in the repository linked to above (and the Python code is included in every ChimeraX installation). >>> >>>> Would it be also possible to loop over a molecular dynamics trajectory and select wanted atoms in this way? >>> >>> Yes. A structure that is a trajectory will have multiple "coordinate sets" (sets of coordinates for the atoms). Therefore you can loop through the trajectory like so: >>> >>> from chimerax.atomic import all_atomic_structures: >>> for s in all_atomic_structures(session): >>> for cs_id in s.coordset_ids: >>> s.active_coordset_id = cs_id >>> for a in s.atoms: >>> a.selected = a.scene_coord[0] < 0 >>> >>> It may also be useful to know that the value returned by s.atoms is an "Atoms" instance (see molarray.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/molarr…>) which in many ways can be treated as a vector for efficiency, which could definitely matter when processing a trajectory. So the above code could instead be: >>> >>> from chimerax.atomic import all_atomic_structures: >>> for s in all_atomic_structures(session): >>> for cs_id in s.coordset_ids: >>> s.active_coordset_id = cs_id >>> atoms = s.atoms >>> atoms.selecteds = atoms.scene_coords[:,0] < 0 >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> >>>> >>>> Thank you. >>>> Best, >>>> Siyoung >>>> >>>> On Tue, Oct 17, 2023 at 4:06 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>>> Oops. If you put this code in a file it needs to have a ".py" suffix, so call it select.py. The ".cxc" suffix is for ChimeraX commands. >>>>> >>>>> Tom >>>>> >>>>> > On Oct 17, 2023, at 12:58 PM, Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > >>>>> > Hi Siyoung, >>>>> > >>>>> > Here is Python code to select all atoms with x < 0. >>>>> > >>>>> > from chimerax.atomic import all_atoms >>>>> > for a in all_atoms(session): >>>>> > if a.scene_coord[0] < 0: >>>>> > a.selected = True >>>>> > >>>>> > You can type this in the ChimeraX Python shell (menu Tools / General / Shell), or probably easier, put it in a text file "select.cxc" and open that in ChimeraX to run it. >>>>> > >>>>> > Tom >>>>> > >>>>> >> On Oct 17, 2023, at 9:04 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> >> >>>>> >> Hello Siyoung, >>>>> >> Sorry no, I can't think of a way to do it with a ChimeraX command. Maybe you could do it by using the initial orientation of the structure (just opening and not rotating) and veerrryyy carefully using the mouse to select a rectangle (Ctrl-click drag) but that is probably too difficult. Also you would need to know where X=0 is from just looking at the structure. >>>>> >> >>>>> >> Certainly you could do it with Python, but somebody else would have to advise on that. >>>>> >> >>>>> >> Best, >>>>> >> Elaine >>>>> >> ----- >>>>> >> Elaine C. Meng, Ph.D. >>>>> >> UCSF Chimera(X) team >>>>> >> Department of Pharmaceutical Chemistry >>>>> >> University of California, San Francisco >>>>> >> >>>>> >>> On Oct 17, 2023, at 5:33 AM, Siyoung Kim via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> >>> >>>>> >>> Hello, >>>>> >>> >>>>> >>> Would there be a selection keyword that selects atoms based on their coordinates? For instance, is there a way that I can select atoms whose x coordinates are below 0 (e.g., x < 0)? >>>>> >>> >>>>> >>> Thank you. >>>>> >>> Best, >>>>> >>> Siyoung >>>>> >> >>>>> >> >>>>> >> _______________________________________________ >>>>> >> 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/ >>>>> >> >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > 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/ >>>>> > >>>>> >>>> _______________________________________________ >>>> 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/ >>> > <test.mp4>

2 4

crop the map
by Dmitry Semchonok 25 Oct '23

25 Oct '23

Dear colleagues, Could you advise on how to crop the map to the new 3D box size and save those changes? Thank you. Sincerely, Dmitry

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Fwd: [ccpem] Help with pairing RMSD in Chimera like COOT
by JAMES MICHAEL KRIEGER 25 Oct '23

25 Oct '23

Dear Rajnandani and all, I am adding in the chimerax users list (I don't know the plain chimera one) as I think this is a better question for people there. Just to clarify, by adjust the RMSD for the map, I guess you mean scrolling the cutoff value? Best wishes James ----- Mensaje reenviado de Alfredo Jose Florez Ariza <0000b1a72b269dbc-dmarc-request(a)jiscmail.ac.uk> ----- Fecha: Tue, 24 Oct 2023 11:49:00 -0700 De: Alfredo Jose Florez Ariza <0000b1a72b269dbc-dmarc-request(a)jiscmail.ac.uk> Responder-A: Alfredo Jose Florez Ariza <alfredo.florez(a)berkeley.edu> Asunto: Re: [ccpem] Help with pairing RMSD in Chimera like COOT Para: CCPEM(a)jiscmail.ac.uk You mean you wanna show just the density corresponding to certain region of the model? If so, you can use volume zone command. It will be something like: volume zone #X near #Y/Z: aaa-bbb range 3 X and Y are the ID numbers of your map and model. Z is the chain of your model and aaa and bbb are the residues you are interested in showing the map around. The range 3 can be modified accordingly to ‘how much of your map’ you wanna show around the model region, I guess. Alfredo On Tue, Oct 24, 2023 at 10:24 AM Rajnandani Kashyap < rajnandani.kashyap(a)health.slu.edu> wrote: > Hello Everyone > > I am at a stage of preparing figures for one of my manuscripts. And I was > wondering if we could adjust the RMSD for the map file (density) in chimera > as we do it in COOT. Basically, I want to show the electron density for a > flexible N-term residues for which I do observe the density at a lower RMSD > level in chimera. > > Any help would be greatly appreciated. > > Thanks, > Rajnandani Kashyap > Postdoc Fellow > > > ------------------------------ > > To unsubscribe from the CCPEM list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 > ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 This message was issued to members of www.jiscmail.ac.uk/CCPEM, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ----- Terminar mensaje reenviado -----

2 2

ISOLDE error: Please remove “TER” card after the single residue
by Dmitry Semchonok 25 Oct '23

25 Oct '23

Dear colleagues, I have an issue with the validation website after working with my model in ISOLDE. More detailed: When starting the simulation in ISOLDE, I am running into the error: At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parametrized. Launching the unparameterized residue widget to help sort this out. So certain ligand info is missing (MYR). Then appears the window that allows me to add the information about this ligand and proceed with the refinement. After finishing refinement in ChimeraX/ISOLDE, I loaded the model and the map on https://validate-rcsb-1.wwpdb.org/. But this website showed me the error: File upload failed. Please review the errors below and try again. Coordinates issues. ERROR: Please remove “TER” card after the single residue “MYR A 1” in line 136 and upload the file again. Some more observations: Although MYR is the first residue in the ChimeraX sequence, it is not visible. At the same time, COOT can see it. Please let me know how I can proceed with the https://validate-rcsb-1.wwpdb.org/ after refinement with ISOLDE. Please let me know if you require a model/map file for the investigation. Thank you Kind regards, Dmitry

2 4

Distinct clipping planes per model
by Dorien Pastoors 24 Oct '23

24 Oct '23

Hi, Thanks for maintaining such a nice software package! I'm still learning, and I'm currently stuck on clipping. I'm trying to clip models differently in ChimeraX. My aim is to have a global clipping plane to visualize two drugs binding to two domains (in the image in yellow/blue). Now I would like to offset the clipping plane slightly for surrounding protein (in beige). I would like to do this to increase the depth in my image and to emphasize that these domains are embedded in a bigger protein. As it is in fact a huge protein (its an alphafold predicted structure) making the entire protein transparent will still obscure the view on the compounds in their domains. As you can see, by using clip model I've been able to turn off clipping for the drugs in their binding pockets. However, with clip model I can only switch on or off the entire clipping plane , not offset it for a particular model. I've tried: clip model #2.3 front -10 clip model #2.3 offset -10 With clip model I can't specify an offset as it gives an error, I can only turn clipping off completely with "clip model #2.3 false", while "clip front -10" affects the total clipping plane, and I cannot specify a particular model for this clipping plane. (the beige protein model is #2.3) Hope this is clear enough and you have a solution! Thanks in advance! Kind regards, Dorien Pastoors

2 1

Image rendering artifacts with silhouettes and pixelSize value
by Vorländer,Matthias Kopano 24 Oct '23

24 Oct '23

Dear ChimeraX team, I am having issues when using silhouettes and saving an image while specifying the pixel size, as I get the artefacts shown in the attached image. If I don’t use silhouettes or don’t specify the pixel size things look fine. I updated to the latest daily version and uninstalled Isolde and ArtiaX, but the problem persist. I work on a MacBook Pro under Mac OS Ventura 13.5.2. Any ideas for fixes? Many thanks, Matthias [A white structure with colorful strands Description automatically generated with medium confidence]

2 2

Difference maps in chimerax?
by Francisco Murphy Pérez 23 Oct '23

23 Oct '23

When I open a map* in chimerax, how do I specify it is a difference density map? * maps are generated with `phenix.mtz2map finalpdb.pdb finalmtz.mtz` ... both files from the pdb-redo. Thanks

4 10

Morphing problem
by Raphael Bader 23 Oct '23

23 Oct '23

Dear all, I would like to ask for some information/help for a problem I am facing at the moment: I am currently working on a pentameric protein (C5 symmetric) that undergoes a big conformational change (translational & rotational movement) and would like to utilize the morph function in ChimeraX to come up with a good animation for it. For one single protomer the animation works fine – however, for the full pentamer the subunits follow both directions, clockwise and counterclockwise, during their rotational movement which obviously leads to a lot of clashes and therefore does not look very convincing. Since I tried almost all options listed as parameters for the morph (linear & corkscrew method, cartesian true and false, rates, coreFraction, etc.) and it did not affect the direction of rotation at all, I was wondering whether there are additional values I could modify or any other trick that might equalize the movement? Thank you very much in advance! Best regards, Raphael P.S.: I would be happy to provide data if it might help solving the problem.

3 2

Selection with coordinates
by Siyoung Kim 23 Oct '23

23 Oct '23

Hello, Would there be a selection keyword that selects atoms based on their coordinates? For instance, is there a way that I can select atoms whose x coordinates are below 0 (e.g., x < 0)? Thank you. Best, Siyoung

4 7

Re: [Chimera-users] How to obtain transformation matrix between protein structures
by Elaine Meng 22 Oct '23

22 Oct '23

Hi Qiancheng Xia, Please use the chimerax-users(a)cgl.ucsf.edu address (CC'd here) for ChimeraX questions so that people don't get mixed up between Chimera and ChimeraX. Chimera does not have the reportMatrix option. As for ChimeraX, you didn't show the exact command that you tried so I can only guess what went wrong. My guess is that you need to include "reportMatrix true" not just "reportMatrix" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 20, 2023, at 4:39 AM, 夏前程 via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > I want to use chimera to obtain the transformation matrix between two protein structures. I know that matchmaker can superimpose them together, but I still want to obtain the transformation matrix. I've noticed that matchmaker in chimerax (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html) offer a keyword "reportMatrix" to do that. But when I use that keyword in chimerax, "Expected a keyword" will be returned without match or a matrix. > With Regards, > > Qiancheng Xia > > National Institute of Biological Sciences > > Beijing, China > > 2023/10/20 >

2 2

Export Isolde residue paramters (xml) for phenix
by Sean Connell 21 Oct '23

21 Oct '23

Hello, Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement? Sean

2 7

Re: Movie Record/Encode with GPU?
by Tom Goddard 20 Oct '23

20 Oct '23

No. The only way to show multiple frames of a trajectory in ChimeraX is to open them as separate models. Tom > On Oct 18, 2023, at 9:37 AM, Alexander Hung Lee <Alexander.Lee(a)uga.edu> wrote: > > Oh, and I forgot to ask… Is there an option in command line to show all the hbonds in a trajectory concurrently, even if the bond shows up at a different point in time but not current frame? >

2 1

Surface calculation in ChimeraX
by Dennis Dannecker 20 Oct '23

20 Oct '23

Hello Chimera/ChimeraX team I recently asked already a question regarding the saving/exporting of vertices generated during the surface calculation in ChimeraX and the associated parameters with this surface generation. On a related note, I wanted to ask whether it is possible to also extract the surface (SESA and/or SASA) on a per atom basis. MSMS calculates not only the vertices for each atom (usually several vertices per atom) but it also calculates the SESA and SASA on a per atom basis. Now, I was wondering whether something is possible in ChimeraX too. As I was parsing through the docs, I was wondering whether ChimeraX calculates the surface no longer using MSMS. The vertices density supported by ChimeraX is considerably higher than what I can get with my standalone MSMS program (at least factor 6). So, if ChimeraX does not longer employ MSMS, what else does it use? With "MEASURE CONVEXITY" I get the surface vertex positions, normals, convexity values, and triangles. Unfortunately, the association with the corresponding residue is lost (however, can be regained with a little bit of work I guess, simply using euclidean distance). Question: Is there something similar for the SESA or SASA of the different atoms in the model/chain. In theory, this information should be available, at least the SESA. I am just wondering whether there is a way to write this out as a raw txt file in ChimeraX The closest I found in the save command is the .obj or .vtk format. However, both are semi-satisfying in that that they both do not provide the data looked for and are in somewhat special formats, at least the vtk. The .obj file is much much bigger than what MSMS or "measure convexity" generates, and not really handy for then working with the data in other programs, mainly python. As always, I very much appreciate any help and wish to thank the team for their contributions to the field. Best regards Dennis

3 5

ChimeraX Help
by Bani Kaur 20 Oct '23

20 Oct '23

Hi, I hope you are well! My name is Bani Kaur and I am a ChimeraX user. I wanted to ask you about how I can specify labels on ChimeraX, specifically with finding the names of the residues on a protein. Additionally, how does info residues work and info resattr. I would appreciate any help and guidance! Thanks! Best, Bani Kaur

2 2

ChimeraX fading?
by Elaine Meng 19 Oct '23

19 Oct '23

> On Oct 19, 2023, at 4:21 AM, Carl Johan Hagstromer <carl.johan.hagstromer(a)ki.se> wrote: > > Would love fading options, like in PyMOL > Hi Carl, We aren't Pymol users so we don't know exactly what you are referring to, but it may well be possible in ChimeraX if you could give more detail. We can put this discussion on chimerax-users(a)cgl.ucsf.edu (CC'd here) so that more folks can weigh in. ChimeraX can do: depth cueing (fading front->back), gradual fading in/out of structures and/or 2D labels by increasing or decreasing transparency over a number of image frames, and/or color modification (e.g. increasing whiteness of all current colors). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

3 2

Isolde usage in Chimera
by Dmitry Semchonok 19 Oct '23

19 Oct '23

Dear colleagues, How to drag the structure, preserving the secondary structure (alpha-helix and beta-sheet) geometry in Isolde? Can I set up certain restraints to keep the correct geometry of the structure while dragging it? Many thanks! Kind regards, Dmitry

2 1

Uncaught bounce notification
by postmaster＠cgl.ucsf.edu 18 Oct '23

18 Oct '23

From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> Subject: command for moving atomic models in ChimeraX Date: October 18, 2023 at 5:51:07 PM PDT Dear All, I have a set of 8 proteins forming a mega complex that we are working on. The density map of the mega complex has a resolution of 2.7Ang. The atomic structures of the proteins were determined. Out of the 8, proteins 3 have C5 symmetry. I am trying to generate potential models using the atomic structures where these pentameric proteins can be expanded out (kindly see the schematic diagram S1 to S2). Is there a command (move command ??) to do so? Thanks Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

1 0

Movie Record/Encode with GPU?
by Alexander Hung Lee 18 Oct '23

18 Oct '23

Hi everyone, I have another question about scripting. I decided to use the morph command over a trajectory with 200 frames (imported as separate pdb's) to make a really smooth movie. Currently, my .cxc has matchmaker #2-200 to #1; morph #1-200 frames 8 same true play false; close #1-200 (< 5 mins) hbonds #201:UNL restrict :UNL :< 5 reveal true interModel false cacheDa true coordsets true (< 5 mins) movie record supersample 4; perframe "~label; label hbondatoms" ; coordset #201 1,1593; wait 1593; ~perframe; movie encode output movie.mp4 bitrate 6000 framerate 25 (> 1 hr) The output is buttery smooth, and the hbond calculation only takes 3-4 mins even with 1600 frames. However, I have a problem with the speed of recording/emcpdomg... it's more than an hour. I found it strange since if I played the trajectory from morph using coordset/slider, it barely takes any time and is very smooth. I was wondering if there was a way to make this recording/encoding faster or to switch from cpu to gpu if that was possible (and if it would help any)? On another note, I'm experimenting with smooth_md.py script but with trajectory files instead of pdb's. I'll see which one looks better/is faster Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

2 2

Open small molecule cif
by Jaremko, Matt Joseph 18 Oct '23

18 Oct '23

Hello, How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: [cid:image001.png@01DA0026.3D6BC080] Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko(a)merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

3 8

memory questions
by Tintos-hernandez, Alonso A 17 Oct '23

17 Oct '23

Hi i was trying to do some modeling using the alfafold colab but it says that i need to buy more memory to run more modeling, hos should i do that ? Jesus Tintos Childrens Hospital of Philadelphia Senior scientist II

3 2

model becomes invisible behind the map when color with hexadecimal color codes
by Kai Cai 17 Oct '23

17 Oct '23

Hi, I've got this weird bug that hope you can help me with. When I try to color a selected protein model with nonmajor hexadecimal color codes (e.g. #f17d21cc), the selected model will become invisible behind the map it was fit with. The map is set as transparent surface. Once it becomes invisible, it won't come back no matter how I change the color. This appears to be a recent issue. Not sure if it's a bug caused by recent macOS update. I am running the most recent ChimeraX daily update on a macOS 14.0. Here is an example if you would like to test it: open 25428 fromDatabase emdb open 7sth transparency 50 select #2 color sel #f17d21cc Thanks, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 2

Opening series of pdb's in incorrect sequential order
by Alexander Hung Lee 13 Oct '23

13 Oct '23

I have a series of pdb's in a folder numbered 1 - 500 (so 1.pdb ... 500.pdb). I'm opening them in ChimeraX using *.pdb. I'm expecting 1.pdb to have ID1 and 2.pdb to to be ID2, but it appears ChimeraX is only looking at the first digit and not the whole number. Is there a way around this? For now, my work around is to use 001, 002 ... 500 instead [cid:d19d2d17-71bb-430f-8a09-65921a0ca962] Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

2 1

Gaussian surface visualization of a subset of residues
by Stefano Pellegrini 13 Oct '23

13 Oct '23

To whom it may concern, I am a PhD student at the Biomedical Genomics Lab at the Institute of Biomedicine of Barcelona. I am using ChimeraX to produce figures for the publication of an in-house recently developed tool for cancer driver gene discovery. I am new to using ChimeraX, so I am sorry if my question might seem very naive to you. Anyway, I can't find this information anywhere else. My problem is simple: I want to show the surface (or volume) occupied by the atoms of a selected number of residues within a chain. I can easily achieve this by using the Gaussian surface (GS) by adding the parameter "resolution" to the "surface" command as "surface :10-20 resolution 6" The problem is that the surface visualized in this way has "gaps" where it overlaps with other atoms that are not from the selected residues. As expected, these gaps get larger when using a greater resolution. Now, I would like to show the complete surface around these residues, without gaps. Could you please provide any suggestions? Thank you in advance, and best regards, Stefano Pellegrini -- *Stefano Pellegrini, **PhD student* Barcelona Biomedical Genomics Lab Institute for Research in Biomedicine (IRB) Carrer de Baldiri Reixac 10, 08028, Barcelona, Spain http://bbglab.irbbarcelona.org

2 1

About saving alphafold2 predictions
by Luz Cristina Vallejo Garcia 12 Oct '23

12 Oct '23

Hi there! I have a problem using ChimeraX. I tried to use the aphafold2 tool to predict a large protein structure. The process to predict the structure of my protein was successfully completed, but the downloading of my results failed. I observed that the folder for the prediction was created but is empty. So my questions are: Why did the program fail to download my results? Is there a possibility to obtain my results without to re-run the process? Thanks in advance Cris Vallejo IBt, UNAM, México <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus.www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

saving alignment in ESP format using chimerax
by Ferreira Ramos, Ana Sofia 11 Oct '23

11 Oct '23

Hi, I would like to save a sequence alignment in ESP format but in my chimerax the option "Save EPS" is not present in the menu of the sequence viewer. The menu is only show if I right click inside the sequence viewer and I do not have all options there: [cid:55913c6a-a21d-45c9-b616-c60bdb4a6b4a] Please, could you let me know how can I save the alignment in the ESP format? Is there a way to do it through the command line? Thank you very much for your attention. Kind regards, Ana

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Re: [Chimera-users] ChimeraX Redistribution Policy Question
by Tom Goddard 10 Oct '23

10 Oct '23

Hi Pat, The ChimeraX license does not allow redistribution. But we have sometimes given permission for that, for example the Structural Biology Grid Consortium (SBGrid). The main issue is our project is funded almost entirely by grants and we have to document how widely the program is used to continue to get funding. Could you explain more details about your distribution? In what way does it use ChimeraX? Can ChimeraX visualization use desktop graphics rendering accelerated by the graphics card within in a Docker image? In general we recommend using ChimeraX on laptop/desktop computers, not containerized, not remotely displayed, because the interactive 3D rendering is often slow or broken in virtualized setups. Let's continue this discussion on the ChimeraX mailing list, not the Chimera mailing list. Tom > On Oct 8, 2023, at 5:53 PM, Patrick Rynkiewicz (RIT Student) via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello! > > I am a co-developer on a molecular dynamics software package that relies on UCSF ChimeraX, and am looking to package this software in a docker container. It's unclear to me from the licensing process what the policy is for ChimeraX redistribution, such as including the .deb package in a docker build. Can you please clarify if I would be able to cite and redistribute ChimeraX 1.6, Ubuntu 22.04 to non-commercial users in my software package, or does each individual user need to accept the non-commercial license agreement separately? > > Thanks! > > Pat Rynkiewicz > _______________________________________________ > 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/

2 2

ChimeraX- protein protein interaction parameter
by Elaine Meng 05 Oct '23

05 Oct '23

Hi Ali, My colleague shared your question with me and I will try to answer it here. For the future, please send your ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here so you don't need to do anything this time) so that other users can benefit, unless you are including data that needs to be kept private. Sorry, ChimeraX does not calculate binding affinities (binding free energy) or predict their changes when you mutate the protein. You can only get a an approximate, first-order impression of whether they appear to improve or disrupt favorable interactions by measuring things like the surface area in the interface or the number of hydrogen bonds or clashes (bad packing) between the binding partners. See command "measure buriedarea" and the tools "Hbonds" "Contacts" and "Clashes" : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> The picture that you get from these tools might still be incorrect if any of the 3D structures are predicted inaccurately (wrong sidechain conformations, wrong binding interface, wrong fold, etc.). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > From: Ali Aljasser <aljassera(a)cua.edu> > Subject: ChimeraX- protein protein interaction parameter > Date: October 5, 2023 at 5:12:46 PM PDT > > I am part of Dr. Choy's group at the Catholic University of America. I work on studying the protein-protein interaction for two kinetochore proteins. Based on alpha fold prediction, we utilized Chimerax to predict the strength of the interaction of these two proteins. We also added some mutations that are known to influence the interaction. However, I still struggling with how to find parameters such as delta G that would help me to predict the strength of the interaction and whether the mutations affect the interaction. > > Please let me know if you can assist me in this regard. Thank you for your time and I am looking forward to hearing from you soon. > Regards, > Ali

1 0

Saving Looking Glass shots and movies
by tolung.bio＠gmail.com 05 Oct '23

05 Oct '23

Hi, Once I open a structure, create a scene and adjust the depth in the Looking Glass display, is there way to save that in a format that can then be imported into the Looking Glass Studio to be displayed in the stand-alone mode of the display? It is possible to do the same thing with animation, such as a 360 rotation or rocking? Thanks, Gökhan

2 1

Surface representation - Dots
by Dennis Dannecker 04 Oct '23

04 Oct '23

Hello, I would like to ask a question regarding the surface representation of protein molecules in ChimeraX. I remember from Chimera that one could very customize the surface representation in terms of probe size, vertices density, and dot size used in the dot surface representation. While ChimeraX also allows to show dot surface representation, does it also allow for setting these attributes? But the more important question of mine is, can one export/extract the coordinates (spherical or cartesian) of the dots generated during dot surface representation. I would be interested in a file that holds the coordinates of these dots/particles around the molecule. In principal that should be possible, but as always, how amenable is that data? Thank you very much. Cheers Dennis

2 2

Showing CAVER channels and tunnels
by Tom Goddard 03 Oct '23

03 Oct '23

I wrote a brief tutorial on how to show channels and tunnels computed by CAVER using ChimeraX. https://rbvi.github.io/chimerax-recipes/caver/caver.html Tom

1 0

worm plots?
by Gabriel Lander 03 Oct '23

03 Oct '23

Is it by any chance possible to do b-factor worm plots in ChimeraX yet? I recall this was going to take a lot of effort since the code for ribbon depiction would have to be overhauled, but hoping maybe there's been some progress. If not I'll keep exporting from Chimera. thanks, -gabe

2 1

Speeding up commands from cxc
by Alexander Hung Lee 02 Oct '23

02 Oct '23

Hello everyone, I'm working to automate making movies from 10,000 frame trajectories. Currently, my cxc contains the following commands windowsize 1920 1080 set bgColor white view zalign ligand inFrontOf #1 sel protein surface; surface color salmon; transparency protein 60 target s sel :UNL color sel dark slate gray; color sel byhetero sel :SIA color sel dim gray; color sel byhetero sel :UNL hbonds :UNL reveal true surface zone #1 nearAtoms ligand distance 15 select zone ligand 15; select add ligand select ~sel ~cartoon sel delete sel ~sel view ligand movie record supersample 4 perframe "~label; label hbondatoms" ; coordset #1 1,10000,50; wait 200; ~perframe movie encode output hbond.mp4 bitrate 6000 framerate 4 The above takes ~ 30 mins, and it's something I would like to do for whole libraries I'm screening. I think the longest process is "hbonds :UNL reveal true" while second longest is movie record and perframe. Is there a way to speed this up? Is there a way to take advantage of multi-threading if it isn't already enabled? If multi-threading is already being used, what can I change to be more efficient? I deleted the parts that I didn't need "delete sel" since they're not involved in the binding site, and I thought it would help speed up surface calculations while recording. Regards, Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

2 7

Bright light while using fly command
by Haselbach,David 02 Oct '23

02 Oct '23

Hi, I am trying to make a fly movie in which I move from one rotation state of the molecule to the next. Unfortunately, the lighting during the flight is not nice. The light goes very bright while moving and in the end jumps back to normal. However, if I do the turn life with mouse the light is fine. I am using soft lighting. Find attached an example movie. What could I do? Can anyone help? Best, David

3 2

ChimeraX Alphafold Question
by Vincent Candela 02 Oct '23

02 Oct '23

Hello, I am an undergraduate researcher at McGill University using the Alphafold feature of ChimeraX to study the role of tau on microtubule dimers, and I was wondering if you could point me to detailed documentation on the energy-minimization feature of Alphafold. I’ve been looking at the ChimeraX documentation and couldn’t find an in-depth documentation on what it does. Thank you so much, Vincent Candela

3 2

Color info
by Margulies, David (NIH/NIAID) [E] 29 Sep '23

29 Sep '23

If I color, say, “bychain” how do I get the info on what the displayed color is. Is there an info color command? 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.

2 2

wildcard used within SAVE command
by 洪冉 28 Sep '23

28 Sep '23

Hi all, I have been trying to produce some high-resolution pictures recently using ChimeraX. And "save C:/xxxx/xxxx/test.png" was used to produce the pic, then I had to change the context "test" into each structure name manually. e.g. save C:/xxxx/xxxx/benzene.png or save C:/xxxx/xxxx/methanol.png Actually, the structure loaded into chimeras was with the right name. Hence, I want to ask for help if is there a wildcard that could be used in the "save" command for saving the picture with the name of the structure. e.g. save C:/xxxx/xxxx/${nameofstruc}.png Of course, it does not work. I just want to give this as an example to suggest my opinions. Thanks in advance. Yours, Ran

2 2

How to activate the Extract button in Segment Map function?
by Bo Chen 25 Sep '23

25 Sep '23

Dear ChimeraX, I tried to use Segment Map to remove some portions of the cryoEM map, and extract the selected portion, but the extract button remains shaded. The only tab in the "other tools" row that appears to be activated is "Fit". I have the most recent version of ChimeraX installaed(Sept 19). Could you give me some hints how to activate the extract in "Other tools" under the "Shortcut options" in "Segment Map"? Thanks! Bo

3 2

Changing mesh size to save as STL file
by Arthur Melo 25 Sep '23

25 Sep '23

Dear colleagues, Is there a way to refine or decimate a mesh of a map to save as an STL file? All the best, Arthur

2 2

symmetrizing the model
by Dmitry Semchonok 22 Sep '23

22 Sep '23

Dear colleagues, A very quick question - what is the command to apply the symmetry to the 3D model? (please provide a usage example if possible). Will the soft generate the symmetrized model after this command application? I found the one for Chimera but not for ChimeraX. Many thanks. Sincerely, Dmitry

3 4

Equivalents to sop split & mask?
by Oliver Clarke 21 Sep '23

21 Sep '23

Hi, Is there a direct equivalent to the command “sop split” in ChimeraX? In the documentation for the “surface” command, I can see that there is an option to split by color, but not to split into individually selectable blobs. We use this a lot in Chimera, as a quick way to make a starting point for a mask to use in refinement, so it would be great to have in ChimeraX too. Also, is there an equivalent to the “mask” command from Chimera? I can’t seem to find it but perhaps it has a different name? Cheers Oli

3 3

Labels of selected residues even with their model name
by svle＠tiscali.it 21 Sep '23

21 Sep '23

Hi, I have used matchmaker with four loaded models to compare the side chains orientation of some selected residues. It is possible to label the selected residues even with the information of the model name they belong to? Thanks. Saverio

3 3

Open and play volume series in ChimeraX
by Wout Oosterheert 20 Sep '23

20 Sep '23

Dear ChimeraX team, I’m currently trying to open a volume and play a volume series in ChimeraX. According to the website (https://www.cgl.ucsf.edu/chimerax/docs/user/trajectories.html) opening a volume series should work like this: “Volume data can be opened as a series with open, employing filename wildcard symbols or globbing as needed to specify multiple files in a single command”. This seems simple enough, I indeed can open the volumes as a group. However, when I then try to play the series using: vseries play #1 direction oscillate loop true, I get the error: no volume series specified. Could you explain to me how I can get my group of volumes recognized as a volume series? The vseries page (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/vseries.html) is very elaborate, but I cannot find alternative options of opening my volumes as a series. I know how to do things in regular Chimera, but would prefer to stick with ChimeraX because I make all my other figures with it. Thank you very much in advance!! Best, Wout Wout Oosterheert, PhD Humboldt Postdoctoral Fellow Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany Phone +49-(0)231-133-2357 Email: wout.oosterheert(a)mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de>

2 2

seq_rmsd and align command
by dng26＠mrc-mbu.cam.ac.uk 19 Sep '23

19 Sep '23

Hello, I have two PDB models I am comparing, but I am having some issues generating the seq_rmsd attribute across all of the chains in the superposition that I want. My current models (same protein, but different states and slightly altered built sequences) have chains A/B/C/D/E/F separated over two domains of A/B/C and D/E/F, for example. My problem is that domain D/E/F is much larger than the former and when I run a matchmaker command such as this: matchmaker #1/A/B/C/D/E/F to #2/A/B/C/D/E/F pairing ss show true I get the resulting superposition favoring the /D/E/F domain (larger RMSD values on A/B/C). This would be fine, however, I want to investigate RMSD variation in D/E/F relative to a fixed position of A/B/C. If I run the following command I only get pairwise RMSDs (seq_rmsd header) for the specified chains but lack those of the larger D/E/F domain as they are not included. matchmaker #1/A/B/C to #2/A/B/C pairing ss show true I look to Calculate the RMSD between paired residues of chains /A/B/C/D/E/F without moving the current structures (after ‘mmaker’ alignment to A/B/C) with the ‘align’ command but the ‘move’ option set to nothing: align #1/A/B/C/D/E/F toAtoms #2/A/B/C/D/E/F move nothing matchNumbering (or matchAtomNames also tested) true I believe the above is what I want with regards to superposition for the RMSD calculations, but the ‘align’ job does not appear to give a seq_rmsd header attribute once run, even though the log seems to suggest it does a pairwise residue alignment to calculate the RMSDs. (Possibly because it does not just look at the CA like matchmaker does?) Is there a way to generate seq_rmsd attributes from the ‘align’ command, or is there a way to have an equivalent ‘move nothing’ in ‘mmaker’? I am looking to use seq_rmsd information to color the model and I am using v1.6.1. Any help is much appreciated! Dan.

2 2

Chimerax
by François Ferron 15 Sep '23

15 Sep '23

Hi I am making a figure using a pdb and a density map in chimeraX1.6.1. each time I do that I have coloured arrows representing an axis that is in the middle. how do I get rid of them. I am sure it is trivial but I just could not find the answers in the manual. thanks François -- François Ferron, Ph.D. francois.ferron(a)univ-amu.fr @F2erron@fediscience.org Laboratoire CNRS - UMR 7257 (AFMB) AFMB - POLYTECH Case 925 163, Av de Luminy 13288 Marseille Cedex 09 France & European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany ######################################### Success is not final, failure is not fatal; it's the courage to continue that counts.

2 2

Request to Resolve the Issue of Modifying Surface Dot Size in ChimeraX
by 18802001045＠163.com 14 Sep '23

14 Sep '23

Dear ChimeraX Maintenance Team, I hope this email finds you well. I am writing to seek assistance regarding an issue I have encountered while working with protein models in ChimeraX. After performing MPL calculations on protein models, I have found that I am unable to modify the dot size of the resulting surface representation. In Chimera, this task was easily accomplished through the "Model Panel" by adjusting the "MSMS Model Attributes". However, I have not been able to find a similar option or command in ChimeraX. I would greatly appreciate it if you could provide guidance or suggest a solution to address this matter. Being able to adjust the dot size of the surface representation is crucial for my current research project, and I rely heavily on the functionalities provided by ChimeraX. Thank you very much for your attention to this matter. I look forward to your kind assistance and prompt response. Best regards, Zhuangwei Zhang, Ph.D. State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Centre of Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University E-mail: dg21240166(a)smail.nju.edu.cn

5 4

Monitor distance angle and torsion angles along trajectoty
by CUNIASSE Philippe 14 Sep '23

14 Sep '23

Dear all, I am wondering if there is a mean in ChimeraX to monitor distances, angles and torsion angles along a MD trajectory. The ideal would be to export a vector containing the frame id (a number) and the value measured for the distance or torsion angle. At the moment I can only built a distance histogram (which is already very usefull) after having created a pseudobond. But doing this, you lose the time evolution along the trajectory. Thanks in advance for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:philippe.cuniasse@cea.fr> Web: http://biodev.cea.fr/rasmot3d/ [signature_575242473][signature_2653780937][signature_3407707164] -----------------------------------------------

2 2

Setting default volume step and rms level
by Samuel Haysom 13 Sep '23

13 Sep '23

Hello, Is it possible to change the default step and level that ChimeraX uses when it opens maps? My data (cryoEM) mostly opens at step 2 with the level set too low for useful viewing, necessitating adjusting these settings for every map I open. Is there a global setting that I can change (for instance by specifying it in a startup script) to change this behaviour so my maps always open at step 1 and at a specified level (say rmsLevel 8)? KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

4 5

Advice on handling cofactor-protein electrostatic interactions
by Boaz Shaanan 12 Sep '23

12 Sep '23

Hi, I would like to present effects of mutations around cofactors (TDP derivatives) on the protein - cofactors electrostatic interactions. I use APBS and chimerax to display the electrostatic surface potential of the protein, but since PDB2PQR eliminates the cofactor from the pqr file I need a tool for the cofactor surface potential. I'm wondering what tool I should use for this. Is it Antechamber+chimerax or something else? Is there by chance a demo for such scenario? I'd appreciate your advice. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

2 7

ChimeraX "Fly" Command
by Kayla Deuter 12 Sep '23

12 Sep '23

Good afternoon, I am emailing you to try and troubleshoot the ChimeraX software I am currently using. I just recently downloaded ChimeraX 1.1.1 and I am operating on a Macbook Pro with High Sierra 10.13.6 software. I am currently teaching myself the program by watching tutorials and referencing the User Guide. Everything seems to work fine except for the "fly" command. I am trying to record movies for practice and examples but every command works except for the "fly" command. I went into the user guide, I've tried researching the issue, and I've done about all I can do to try resolving this issue on my own. After I create my view points, I attempt to create transitions by typing "fly view 1 view 2" but every time I try typing fly it always says command unknown and gives me error messages. When I try to further investigate the error code, it is useless and I get no answers. If there is anything I can do to fix this, please let me know. The fly command is crucial for creating a smooth animation. Best, Kayla Deuter

2 1

Re: Trouble installing plugin
by Eric Pettersen 11 Sep '23

11 Sep '23

Hi Barry, We continue to work on this issue, but have not yet succeeded in getting installation as a source dependency to work. We hope to get it resolved soon, but it's hard to say exactly how long it will take, so in the interest of allowing you to make progress I suggest using an alternate approach -- include mdtraj as an additional package in your bundle. In your bundle_info.xml you would use an AdditionalPackages tag with a child tag of "Package" which has a "name" attribute of "mdtraj" and a "folder" attribute of wherever mdtraj got installed. Since mdtraj is not pure Python, you would also have to use a "platform" attribute of mac/linux/windows. If you also built mdtraj on other platforms you could copy it over to the machine you're building the bundle on and include additional Package tags with different platform/folder values. You also have to have a DataFiles tag with a "package" attribute of "mdtraj" and an appropriate "platform" attribute, with child DataDir/DataFile tags enumerating what to copy from the installation. One thing to keep in mind is that the installation has to be compatible with the version of Python ChimeraX is using, which is Python 3.9 for ChimeraX 1.6.1 and Python 3.11 for the daily build. So you would want to include the corresponding dependency on ChimeraX-Core. Also, a binary version of mdtraj is available for Mac (Python 3.9) so you could conceivably include that directly as a dependency (i.e. in a Dependency tag rather than a Package tag) with a "mac" platform attribute and a ChimeraX-Core dependency of ==1.6.1. For reference, SEQCROW uses the AdditionalPackages tag in its bundle_info.xml, which you can see here. <https://github.com/QChASM/SEQCROW/blob/master/bundle_info.xml> --Eric Eric Pettersen UCSF Computer Graphics Lab > OK. So, we decided to wipe some computers and start fresh to install our plugin. And using the daily build from a couple days ago and a daily build from 7-15 and always on a freshly built linux 20.04 system we are unable to install my plugin. However, it somehow installed in the past on my coworker's system (using 7-15 chimerax) and my system (using 6-6 chimerax). He and I can both repeatedly install and uninstall my plugin. But any clean system will not "devel install" the plugin. Below is the latest log output using the daily build from 7-15 (because we have one user successfully using it). I am at a real loss as to what is going on. FWIW the clean systems do also have python 2.7. I know recently you fixed a problem of installing a plugin on a system that has python 2.7 on it. Please let me know what I can do. Our plugin is alpha ready and if I can't get it easily installable then our project is at a standstill.

1 1

Lock model(s) to rotation/translation?
by Oliver Clarke 08 Sep '23

08 Sep '23

Hi, I know that in ChimeraX the preferred way to manipulate models with respect to one another is using the mouse modes. This works, but is still (in my experience) less precise/ergonomic than deactivating selected models in Chimera and freely manipulating the remaining active models using the trackpad/mouse. Is there any possibility in the future (or present) of adding the capacity to “lock" selected models to rotation/translation, to allow free manipulation of the remainder? Cheers Oli

2 14

Add model number to pop up balloon?
by Oliver Clarke 08 Sep '23

08 Sep '23

Hi, Currently the info in the pop up balloon that appears when one hovers over a residue is of the following format: res-name res-num.chain atom-name. Would it be possible to add the model number at the start? The model number is in the pop up balloon for maps, but not atomic models, and it would be convenient to have it to avoid having to bring up the model panel when typing commands. Cheers Oli

2 2

Re: Trouble installing plugin
by Zach Pearson 07 Sep '23

07 Sep '23

Per https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8927 which broke on the same dependency (mdtraj), dealing with recursive pip was such a nightmare that ChimeraX’s pip command searches for the python executable _next to_ ChimeraX.exe and uses that instead of ChimeraX; toolshed_utils will have to do the same to fix this error. — Zach > On Aug 30, 2023, at 14:40, Tom Goddard <goddard(a)sonic.net> wrote: > > Hopefully Zach or Greg can help you with this pip install error. > > Tom > > >> On Aug 30, 2023, at 2:19 PM, BARRY E DEZONIA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> OK, so we have now installed chimerax-daily on another system that already had it on there. We were getting similar errors as detailed in my earlier email. After carefully cleaning the system and removing and reinstalling the July 14 daily build we are still getting install errors for my plugin. Instead of the python 3.9 complaints they are now python3.11 complaints. So that part of the earlier problem was fixed by my cleanups. But it is still broken. We still have pip running problems. Even with upgrading chimerax's python's pip and making sure that the chimerax's pip's bin dir is in the path. The error message is basically "AssertionError: Cannot run __pip-runner__.py as a non-main module". I will post the (lengthy) log output of my plugin install process below. Please let us know what might be causing this. We were just going to install a new daily build but your website has been down today. >> >> ==================================================== >> >> UCSF ChimeraX version: 1.7.dev202307150241 (2023-07-15) >> © 2016-2023 Regents of the University of California. All rights reserved. >> How to cite UCSF ChimeraX >> devel install /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qtrunning build >> running build_py >> running bdist_wheel >> installing to build/bdist.linux-x86_64/wheel >> running install >> running install_lib >> creating build/bdist.linux-x86_64/wheel >> creating build/bdist.linux-x86_64/wheel/chimerax >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt >> copying build/lib/chimerax/tut_tool_qt/tool.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt >> copying build/lib/chimerax/tut_tool_qt/__init__.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/zncc.sh -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/zncc.jar -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/simCC.com <http://simcc.com/> -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/simNC.com <http://simnc.com/> -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable >> copying build/lib/chimerax/tut_tool_qt/Installable/install_traj2nmr.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/README.md -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/setup.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/session.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/ucsf.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/__init__.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/resonance.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/shifts.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/utils.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/LICENSE -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> running install_egg_info >> running egg_info >> writing ChimeraX_BphonTool.egg-info/PKG-INFO >> writing dependency_links to ChimeraX_BphonTool.egg-info/dependency_links.txt >> writing requirements to ChimeraX_BphonTool.egg-info/requires.txt >> writing top-level names to ChimeraX_BphonTool.egg-info/top_level.txt >> reading manifest file 'ChimeraX_BphonTool.egg-info/SOURCES.txt' >> writing manifest file 'ChimeraX_BphonTool.egg-info/SOURCES.txt' >> Copying ChimeraX_BphonTool.egg-info to build/bdist.linux-x86_64/wheel/ChimeraX_BphonTool-0.4-py3.11.egg-info >> running install_scripts >> creating build/bdist.linux-x86_64/wheel/ChimeraX_BphonTool-0.4.dist-info/WHEEL >> creating 'dist/ChimeraX_BphonTool-0.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it >> adding 'chimerax/tut_tool_qt/__init__.py' >> adding 'chimerax/tut_tool_qt/tool.py' >> adding 'chimerax/tut_tool_qt/Installable/install_traj2nmr.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/LICENSE' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/README.md' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/setup.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/__init__.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/resonance.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/session.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/shifts.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/ucsf.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/utils.py' >> adding 'chimerax/tut_tool_qt/Runnable/simCC.com <http://simcc.com/>' >> adding 'chimerax/tut_tool_qt/Runnable/simNC.com <http://simnc.com/>' >> adding 'chimerax/tut_tool_qt/Runnable/zncc.jar' >> adding 'chimerax/tut_tool_qt/Runnable/zncc.sh' >> adding 'ChimeraX_BphonTool-0.4.dist-info/METADATA' >> adding 'ChimeraX_BphonTool-0.4.dist-info/WHEEL' >> adding 'ChimeraX_BphonTool-0.4.dist-info/top_level.txt' >> adding 'ChimeraX_BphonTool-0.4.dist-info/RECORD' >> removing build/bdist.linux-x86_64/wheel >> Distribution is in /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> [toolshed install](help:user/commands/toolshed.html#install) >> /home/crow/bphon/bphon/chimerax- >> plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> >> [toolshed install /home/crow/bphon/bphon/chimerax- >> plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none- >> any.whl](cxcmd:toolshed install /home/crow/bphon/bphon/chimerax- >> plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl) >> >> Traceback (most recent call last): >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 517, in _pip_install >> results = _run_logged_pip(command, logger) >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 583, in _run_logged_pip >> raise RuntimeError(s) >> RuntimeError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ >> Processing /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> Requirement already satisfied: ChimeraX-Core~=1.1 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.7.dev202307150241) >> Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.30.2) >> Collecting mdtraj (from ChimeraX-BphonTool==0.4) >> Using cached mdtraj-1.9.9.tar.gz (2.2 MB) >> Installing build dependencies: started >> Installing build dependencies: finished with status 'error' >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> [22 lines of output] >> ERROR: >> Traceback (most recent call last): >> File "<frozen runpy>", line 198, in _run_module_as_main >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 1044, in <module> >> exit_code = init(sys.argv) >> ^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 801, in init >> runpy.run_path(opts.run_path) >> File "<frozen runpy>", line 291, in run_path >> File "<frozen runpy>", line 98, in _run_module_code >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/pip/__pip- >> runner__.py", line 49, in <module> >> assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main >> module" >> ^^^^^^^^^^^^^^^^^^^^^^ >> AssertionError: Cannot run __pip-runner__.py as a non-main module >> >> >> [end of output] >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> See above for output. >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> >> >> During handling of the above exception, another exception occurred: >> >> Traceback (most recent call last): >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/devel.py", line 174, in _run >> unbound_method(bb, *args, **kw) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder.py", line 154, in make_install >> run(session, cmd) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 38, in run >> results = command.run(text, log=log, return_json=return_json) >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897, in run >> result = ci.function(session, **kw_args) >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/toolshed.py", line 301, in toolshed_install >> ts.install_bundle(bundles, logger, **kw) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 916, in install_bundle >> _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 252, in _install_bundle >> results = _pip_install( >> ^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 520, in _pip_install >> raise UserError(str(e)) >> chimerax.core.errors.UserError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ >> Processing /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> Requirement already satisfied: ChimeraX-Core~=1.1 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.7.dev202307150241) >> Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.30.2) >> Collecting mdtraj (from ChimeraX-BphonTool==0.4) >> Using cached mdtraj-1.9.9.tar.gz (2.2 MB) >> Installing build dependencies: started >> Installing build dependencies: finished with status 'error' >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> [22 lines of output] >> ERROR: >> Traceback (most recent call last): >> File "<frozen runpy>", line 198, in _run_module_as_main >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 1044, in <module> >> exit_code = init(sys.argv) >> ^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 801, in init >> runpy.run_path(opts.run_path) >> File "<frozen runpy>", line 291, in run_path >> File "<frozen runpy>", line 98, in _run_module_code >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/pip/__pip- >> runner__.py", line 49, in <module> >> assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main >> module" >> ^^^^^^^^^^^^^^^^^^^^^^ >> AssertionError: Cannot run __pip-runner__.py as a non-main module >> >> >> [end of output] >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> See above for output. >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> >> From: Tom Goddard <goddard(a)sonic.net> >> Sent: Thursday, August 24, 2023 9:49 PM >> To: BARRY E DEZONIA <barry.dezonia(a)wisc.edu> >> Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> >> Subject: Re: [chimerax-users] Trouble installing plugin >> >> The ChimeraX daily build is using Python 3.11 and your error message includes paths to Python 3.9. It will probably cause havoc if you have both in your same ChimeraX installation. >> >> ChimeraX developers Greg or Zach who know more about Linux would have to comment on whether it is even possible to install ChimeraX over another ChimeraX without the original copy being deleted. And they also work on the "devel install" command. >> >> Tom >> >> >>> On Aug 24, 2023, at 12:08 PM, BARRY E DEZONIA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> It is possible that on my home machine I installed the latest daily build over an earlier daily build. >>> From: BARRY E DEZONIA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> >>> Sent: Thursday, August 24, 2023 6:33 AM >>> To: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> >>> Subject: [chimerax-users] Trouble installing plugin >>> >>> I am having trouble installing a plugin I am developing. It works on one system I am using at work and fails on my system at home. The home system has the latest daily build on it. The work system has an earlier daily build on it. >>> >>> This is what I try to do inside chimerax: >>> >>> devel install ~/dev/bphon/chimerax-plugin/tut_tool_qt >>> >>> And this is the installation error: >>> >>> open /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.pyTraceback (most recent call last): >>> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py", line 49, in <module> >>> assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main module" >>> AssertionError: Cannot run __pip-runner__.py as a non-main module >>> >>> Error opening python file /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py >>> >>> Any idea what is happening? I may have run into this problem some time ago on the work computer and fixed it but I honestly don't know. >>> >>> Please forward this to the bugs email list of it should go there instead. Thanks. >>> >>> Sorry for yet another question. You guy seems very busy with mail recently. >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >> _______________________________________________ >> 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/ >

3 3

Coloring of trajectory using mpl command
by Alexander Hung Lee 07 Sep '23

07 Sep '23

Hello everyone, I'm sorry for bothering all of you so often these past few days... but I ran into another issue. I opened a pdb and corresponding trajectory .nc file, and I ran "mlp #1 key true". Lipophilicity coloring showed up, but when I played the trajectory, the mpl colors went away and the default colors came back. I noticed the same happened for "coulombic" command. For now, I'm making due with a custom attribute file and "color byattribute name palette lipophilicity" from this tutorial https://www.cgl.ucsf.edu/chimerax/docs/user/formats/defattr.html#examples. It does stay throughout the trajectory but doesn't look as good, and the colors aren't blended. I have also tried doing "mlp map true" and "color sample #1 map #2" with #1 being the pdb with trajectory and #2 the resulting map from mlp. It looked really bad. The protein is now one color. "mlp map true" command [cid:41c39c60-61c8-47ff-b996-f063b013d319] [cid:d2f10dad-4f81-40e6-99cc-407b2d96a17f] [cid:ec390e08-8756-45ce-af0d-8e8a03992457] Alex

2 1

Selection syntax for atomic models vs surfaces/volumes?
by Oliver Clarke 06 Sep '23

06 Sep '23

Hi, Is there anything in the ChimeraX selection syntax to select by model type? For example, I would like to select only atomic models, excluding surfaces and volumes, and do something to them in a script or an alias - is there an efficient way of doing that? Right now, I can do this using "sel @*”, which selects everything is an atom, but I have the feeling that this is not so efficient (it is quite slow for large models). Cheers Oli

3 12

inquiry
by Talha Shafi 06 Sep '23

06 Sep '23

hi I am using chimerax for model visualization. i wanted to inquire how can drag and rotate a selected model to manually overlap with my density may. in chimera1.13 version in model panel i could just uncheck the action option and perform my task. i can not figure this in chimerax to move my model over the density. fit in map is not able to align the models. may be manually aligning them and then perform fit to map works better. looking forward to hearing from you talha -- Talha Shafi Postdoc Scholar York Structure Biology Laboratory. University of York United Kingdom

2 1

Dealing with artefact bonds
by Enrico Martinez 06 Sep '23

06 Sep '23

Dear Chimera-X users ! I am performing visualisation of the protein-protein complex obtained from md trajectory. The issue is that the pbd lacks the TER record between two different chains so Chimera-X recognises it as a bound complex and consequently adds a long unusual bond (>30A) between C term of one unit and N term on the another. Are there any commands that could be useful to omit such an artifact (e.g. to hide all bounds > 5 A etc) ? I found only a solution to hide several residues from the both units that will remove the long bond automatically. Many thanks in advance Enrico

3 3

Aligning residue/ligand to foreground
by Alexander Hung Lee 05 Sep '23

05 Sep '23

Hello everyone, In old Chimera, I was able to center the ligand to the foreground of view using "align ligand ~ligand" no matter the orientation, if the ligand is in view or not. Is there a comparable way in ChimeraX? The same command gives "expected a keyword" and using "view ligand" or "view sel-residues zalign sel" does not bring it to foreground if it's behind something else. Thanks, Alex

4 3

Predict a large protein structure with Alphafold2 and Chimerax
by Sara Qubisi 05 Sep '23

05 Sep '23

Hello Chimerax team. I am a postdoc at SICKKIDS hospital, and I am currently working on a project that involves large protein (~5400 aa). I am new to Alphafold and Chimerax and I want to perform a structure comparison between the wild type protein and a set of frameshift mutation (result in protein truncation) versions of the protein. I learned online and from your YouTube videos that I cannot enter more than 1200aa per assay request. Is there a way to overcome this where I can use the full protein sequence. Regards, Sara Qubisi. ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

2 1

[AMBER] Converted PSF file (prmtop > psf) failed to open in ChimeraX but did in old Chimera
by Alexander Hung Lee 05 Sep '23

05 Sep '23

Hello, I converted prmtop to psf to use with ChimeraX by just editing the suffix as suggested http://archive.ambermd.org/201902/0118.html and also converted it a second way with ParmEd. ChimeraX couldn't read either version and gave me the error "list index is out of range." I successfully opened the original prmtop and the two psf versions in the old Chimera with trajectory .nc file. What do I need to do? Alex

2 2

save "side view" settings
by vincent Chaptal 05 Sep '23

05 Sep '23

Hi, I opened the side view dialog window and adjusted the view planes for a nice figure. I would like to save the parameters so I can go back and modify the figure at a later stage, but the setting are not stored in the "view matrix" command. Could you tell me which command can save these settings? (I'm using chimeraX 1.5). Thank you. Best 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/

5 13

Zone map around center of rotation?
by Oliver Clarke 01 Sep '23

01 Sep '23

Hi, Surface zone allows one to carve the map in a sphere around a selected atom (with “nearAtoms”). When navigating around the map, it would be convenient to be able to use the center of rotation as a reference point instead. Would it be possible at some point to add a “nearCofR” option to surface zone to facilitate this? In Chimera, I had kind of a hack-y way to do this, by placing a marker atom at the center of rotation and using that as the reference, but this option is not yet available in ChimeraX. Cheers Oli

3 4

Set defaults for molecule display?
by Oliver Clarke 01 Sep '23

01 Sep '23

Hi, Is there anyway to set default preferences for molecule display? Currently it seems to vary (I think?) based on the number of atoms in the model - so relatively small proteins will load as ribbons, while larger ones will load in sphere representation. I would rather set a default such that all molecules load as ribbons, rainbow colored by chain. Is this possible? Cheers Oli

3 4

morph for non-protein atoms?
by Alexis Rohou 01 Sep '23

01 Sep '23

Hello, The documentation for morph reads very protein-centric, and testing it with default options certainly makes it look like ligands are removed. Is there a way to have ligands included in a morph (assuming the same atoms are present in both models)? Cheers, Alexis

2 3

getting HEX code from molecule
by Matzov Donna 01 Sep '23

01 Sep '23

Hello, I was wondering if there's a command that would give me the HEX code of a particular atomspec. Using the "pick from screen" option in the color editor is somewhat helpful samples the colors that are the results of shadows so I can't really the exact color. Thanks, Donna Matzov, PhD Department of Structural Biology Weizmann Institute of Science The Shalev-Benami Lab<https://www.weizmann.ac.il/Structural_Biology/Shalev-Benami/home>

3 4

Structure Comparison->Morph conformations
by Revan Katte 01 Sep '23

01 Sep '23

Hello, For morphing my structures, I'm using ChimeraX 1.6.1, but I cannot find structure comparison and morph conformations in the tool menu. Could you please assist me with this? Thank you! Revan -- Revan Katte, Ph.D. Postdoctoral Research Associate, Prof. Maolin Lu Laboratory, Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, Texas 75708, USA. E-mail: *Revansiddha.Katte(a)uthct.edu <Revansiddha.Katte(a)uthct.edu>* Professional Website: Google Scholar <https://scholar.google.com.tw/citations?user=phuOXjgAAAAJ&hl=en> LinkedIn <https://www.linkedin.com/in/dr-revan-katte-3b53a788/>

2 2

More shades in color byattribute
by Enrico Martinez 01 Sep '23

01 Sep '23

Dear Chimera-X users ! I am using ChimeraX to color pdb file according to its structural flexibility determined in the b-factor column color byattribute bfactor palette rainbow range 2,100 This info is taken directly from the rmsf calculations of short MD trajectory and stored in a single pdb structure in the b-factor column. Technically It works very well, however in the case of flexible systems, the most of the structures is colored in "red". I enclose a screenshot of an example image along with the corresponded rmsf chart. Would it be possible to define the gradient of the coloring in more accurate fashion in order that the red zones could have more shades ? I believe this could be fine-tuned via the "range 2, 100 " attribute and / or switching to other palettes e.g. 'Paired-12' , which naturally has more shades compared to 'rainbow' .. I would be grateful for any further suggestions ! Yours with thanks, Enrico

2 4

Render by attribute - custom rmsd
by Dominik Sordyl 31 Aug '23

31 Aug '23

Hi, I am developing the custom plugin for sequence alignment and structure superposition, that will have it's own sequence viewer. I would like to use 'Render by attribute" feature of ChimeraX 1.16. But without using 'matchmaker ... show True' I do not have such option. Is there a way to pass the rmsd values for superimposed structures' residues to be available for 'render by attribute'? While looking through the ChimeraX source code, I have noticed that it uses Sequence Viewer headers to store rmsd, but I can not figure out how can I add such thing to my plugin. Best, Dominik

2 1

Trouble installing plugin
by BARRY E DEZONIA 30 Aug '23

30 Aug '23

I am having trouble installing a plugin I am developing. It works on one system I am using at work and fails on my system at home. The home system has the latest daily build on it. The work system has an earlier daily build on it. This is what I try to do inside chimerax: devel install ~/dev/bphon/chimerax-plugin/tut_tool_qt And this is the installation error: open /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.pyTraceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py", line 49, in <module> assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main module" AssertionError: Cannot run __pip-runner__.py as a non-main module Error opening python file /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py Any idea what is happening? I may have run into this problem some time ago on the work computer and fixed it but I honestly don't know. Please forward this to the bugs email list of it should go there instead. Thanks. Sorry for yet another question. You guy seems very busy with mail recently.

2 3

Coloring by Ca-RMSD
by Abhilash Padvannil 30 Aug '23

30 Aug '23

Hello, I am working with a multi-subunit protein. I aligned current structure with a previously determined structure using mm command. I am trying to color my protein using RMSD. Chimerax is however, coloring only one-subunit by RMSD, the other chains have default colors. Is there a way to color the whole molecule with RMSD attribute. Thanks Abhilash.

3 3

Camera Viewfinder
by Vytautas Raškevičius 29 Aug '23

29 Aug '23

Hi It would be nice to have camera viewfinder to make images. Like here: https://expertphotography.b-cdn.net/wp-content/uploads/2021/02/Viewfinder-v… So it would be much easier to put something in center exactly and so. VR

2 1

How to reduce subdivision of the mesh?
by HL F 29 Aug '23

29 Aug '23

Dear ChimeraX Development Team, I hope this email finds you well. First and foremost, I would like to express my heartfelt gratitude for developing such a powerful and invaluable tool like ChimeraX. Your dedication to providing the scientific community with a free and versatile platform is truly remarkable. I am writing to inquire about a technical aspect related to exporting 3D models in ChimeraX. I'm using ChimeraX-1.1.1 to export protein meshes(surface model) into Blender. I've got a problem that the mesh is too smooth which means it has too many vertices. And that makes my Blender run very slow. Is there a way to reduce the subdivision(resolution/vertex number) of the mesh in ChimeraX? Thank you very much! Looking forward to your reply. Regards, Hualing [image: image.png]

2 2

updating session with new version of model
by Alexis Rohou 28 Aug '23

28 Aug '23

Hi there, I have a nice figure saved as a .cxs session file. But I've since had to change the PDB file to refine the model. I think myself and others have asked this in the past, and there isn't a way to substitute one PDB file for another in a ChimeraX session file. Please correct me if I'm wrong. Failing that, I have to recreate the same display style (colors, ribbon vs sticks vs balls, etc) with the new PDB file. What I was thinking of doing is to save a series of files containing attributes' values from the original model (with option ModelId set to false), and then open these files back and read the attribute values into the new model. Things like display, draw_mode, color, ribbon_display, ribbon_color, etc. In principle, do you think this approach should work? One stumbling block: I can't seem to save the display attribute. Specifically, the following command: > save browse format defattr attrName a:display models #1 modelId false Gives the following output in the log: > One or more attribute values aren't integer, floating-point, string or > None (e.g. False); skipping those > Saved attribute 'display' of 0 atoms using match mode: 1-to-1 to > <filename_redacted> This is with version 1.6.1 (2023-05-09). I have tried with other attributes (e.g. draw_mode), and they seemed to work. What is the correct way to save the atom display attribute to file? Cheers, Alexis

5 5

How allow a plugin to save a startup setting
by BARRY E DEZONIA 28 Aug '23

28 Aug '23

Hello, I am developing a plugin. One attribute my plugin has is an output directory. I want to save that value somewhere so that if you exit chimerax, come back in, and reload my plugin the output directory value will default to what it was during the last run, I've read a bit about session data and preference data and I don't think they get at what I want. I might be able to make my app save a data file in the installed plugin directory (and read it on startup) but maybe there will be things like permissions issues trying to do something like this. Any suggestions on how to do what I want to do?

2 1

Re: [Chimera-users] Atlocs
by Elaine Meng 28 Aug '23

28 Aug '23

Hi Hernando, ChimeraX has an Altloc Explorer tool (also implemented as "altlocs" command) that lists all the residues with alt locs and allows switching which ones are used: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/altlocexplorer.html> The rules that ChimeraX uses for deciding which ones to show initially are described in that link, namely: "For each contiguous (through-bond) set of atoms with alternate locations, the location used initially is that with the highest average atomic occupancy, then as a tie-breaker, the lowest average atomic B-factor, and if a tie-breaker is still needed, by alphabetical order of the alternate location ID." We found that altloc A is not always the most occupied! So yes, this is a new feature of ChimeraX, but we also added the tool to make it easy to switch if you want to use a different altloc than what is shown initially. By the way: You may be interested that there is a chimerax-users(a)cgl.ucsf.edu list (CC'd here) specifically for asking questions about ChimeraX. Since ChimeraX and Chimera are two different programs with different behaviors, we try to somewhat separate the questions so that people won't get too confused! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 28, 2023, at 12:38 PM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear ChimeraX, > > I have an atomic model with several chains that have residues with alternate locations A and B. I noticed that > while Chimera by default displays alternate locations A. ChimeraX for some chains display alternate locations A and for other chains alternate locations B. Why is this behavior different in Chimera and ChimeraX? Is this a novel feature of ChimeraX? I this is the case how ChimeraX decides which of the two alternate locations A or B to display? > > Thanks > > Hernando

1 0

consult
by UehkVt 27 Aug '23

27 Aug '23

Hi, I am using ChimeraX on Linux OS.I think ChimeraX only has a single-line command window which isn't convenient for complex script. I want to know there are other ways to type multiple-line command and display protein structure whin ChimeraX at real time. could Jupyter notebook combine with ChimeraX? When we type command in Jupyter notebook, ChimeraX could display the result of the command.Could you tell me the method that can solve the above issue? Thanks! Sincerely!

2 1

General developer questions
by BARRY E DEZONIA 25 Aug '23

25 Aug '23

Hello, I have been writing a plugin for ChimeraX. One feature it does now is read a PDB file, parse some info, and act on that data internally. I'd like to change it so that it can use information about a loaded PDB in ChimeraX. To this I have a couple questions: 1. Are there some basic docs on how someone could access a protein that is memory resident that was loaded from a PDB (i.e. just what data structures can I access programmatically related to a protein loaded with open(<pdbname>)). 1. How do I find the data structure(s) for the currently viewed or selected or ??? protein? I'd like someone to be viewing a protein and then launch my plugin which will use that protein and its data for the plugin's internal calculations. I'm sorry if this is noise. If there are good developer docs for these topics please feel free to point me in the right direction. Thanks.

2 6

How to use ColorBrewer palette?
by Tianyang Liu (Staff) 25 Aug '23

25 Aug '23

Hello, I would like to colour my structure with the ColorBrewer palette using ChimeraX. But I can't seem to get it to work. I used the command: color bychain cartoons;palette Pastel1-9. The error message displayed is "Unknown command: palette Pastel1-9." Could you help me with this please? Many thanks, Tian

2 1

Does getcrd return coordinates in pixels or in angstroms?
by Samuel Haysom 25 Aug '23

25 Aug '23

Hello, I am trying to determine the coordinates of a point on a volume for use in cryoSPARC (as described here for Chimera: Job: Local Refinement (Legacy) - CryoSPARC Guide<https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/loca…>). I was wondering if the getcrd command returns coordinates in angstroms (as it did in Chimera) or whether they are in pixels? This was not specified on the getcrd documentation page as far as I could see (Command: getcrd (ucsf.edu)<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/getcrd.html>). KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

2 4

Changing Colors and Unable to Save as pdb File
by Natalia Tegenfeldt 25 Aug '23

25 Aug '23

I have been using chimerax to visualize the proteins I'm working with, and have been highlighting sections of the sequence and changing the color to highlight those sections, but when I try to save it as a pdb, it gets rid of the colors. Is there a different way to be able to keep a section highlighted/different color when I save it as a pdb file? Thanks!

3 2

Question on Chemistry StackExchange regarding ChimeraX Python Log.
by nikolic＠uwm.edu 24 Aug '23

24 Aug '23

Hello, I'm developing a series of commands and presets for ChimeraX and run into the following trouble in self-support: https://chemistry.stackexchange.com/q/175802/136866 Thank you! Nickolas Nikolic

2 1

Play a volume morph
by James Kizziah 24 Aug '23

24 Aug '23

Hi, I need to record a movie of a modified volume morph focused on a small part of much larger structure. Is it possible to just play an existing morph with a command? I can generate the morph, volume zone to a reference atomic model, and make it transparent to visualize the features I'm interested in, but how can I record the movie after accomplishing these steps? Incorporating the volume morph command in a movie-making script regenerates the original morph without zoning our transparency. Thanks! James

2 1

ViewDockX Options
by Ute Roehrig 24 Aug '23

24 Aug '23

Dear ChimeraX Developers, thank you very much for developing and providing ChimeraX! I was wondering if you could make the ViewDockX command more user friendly, especially providing the following features: 1. When opening a docking results file (format SwissDock/Dock/Vina/Glide), launch the ViewDockX tool automatically 2. In the ViewDockX table, provide the possibility to select several poses by Shift+clicking on several lines in the table (the way it was working in Chimera) 3. Let the user automatize/customize the columns he wants to see by default (provide columns as option in the command line?) Thank you very much for considering these points, Ute -- Ute Roehrig SIB | Swiss Institute of Bioinformatics Unil, Quartier Sorge, bâtiment Amphipôle, 1015 Lausanne t: +41 21 692 40 86 - f: +41 21 692 40 65 Ute.Roehrig(a)sib.swiss<mailto:Ute.Roehrig@sib.swiss> - http://www.sib.swiss

2 2

Re: Help with ChimeraX and dual extruder 3D printing
by Tom Goddard 24 Aug '23

24 Aug '23

Hi Billy, ChimeraX writes out the STL files using the coordinates in the ChimeraX scene, so the STL files contain aligned coordinates. The problem is your 3D printer software is changing the alignment. Here's an example of ChimeraX commands open 1eqz surf enclose protein surf enclose nucleic save histones.stl models #1.3 save dna.stl models #1.4 If you open these two STL files in ChimeraX you will see that they are aligned. The STL files only contain x,y,z coordinates and the format does not support any positioning transformations. So the 3D printer software cannot interpret the file in a different way. So your problem is to tell the printer software not to change the alignment given in the two files. Perhaps when you specify the origin in the printer software that origin is relative to the center of the surface bounding box, so it will center the two STL files differently. Tom > On Aug 23, 2023, at 9:40 AM, Dye, Billy via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > I have been using ChimeraX to generate STL files for 3D printing models of a variety of protein structures that I use in my biology classes. I recently acquired a dual extrusion printer which should allow me to print models in two different colors. For example, I am currently trying to print a nucleosome from RCSB model 7PFX such that the DNA is printed blue from one extruder and the histones white from the second extruder. I am exporting two different STL files from ChimeraX, one with the DNA and one with the histones, and I am attempting to slice with FlashPrint 5 software for a FlashForge Creator Pro 2 printer. However, when I import the two STL files into the slicing software, they are not aligned. Even if I position both at 0,0,0 coordinates, it is obvious that the DNA and histones are not lining up properly. Is there a way to export the two STL files from ChimeraX such that they have a common reference point or origin and will thus align with one another when both are placed into the slicing software? > > Many thanks for your consideration and advice, > Billy Dye > > <PastedGraphic-2.png> > > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

1 0

Change default step size for volumes?
by Oliver Clarke 24 Aug '23

24 Aug '23

Hi, Is there any way in ChimeraX to change the default step size for volumes? There are volume commands (e.g. volume limitVoxelCount false) that look like they ought to do the trick but these only seem to apply to already opened volumes - is there a way to make it a persistent preference for newly opened volumes? In Chimera this was a setting in the Volume Viewer, but I can’t find an equivalent yet in ChimeraX in either the global settings or the docs for the volume command. Cheers Oli

3 5

Saving the resolution of structure to a file
by Prathvi Singh 24 Aug '23

24 Aug '23

Hi Elaine, Is there a way to save the resolution of a protein structure to a file using command line, either in chimeraX or chimera? Thanks -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

3 4

Equivalent to "ac ri" in ChimeraX?
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, In Chimera, the accelerator “ri” selects intervening residues. This is convenient because one can select two residues (let’s say at the start and end of a domain) and then select all the residues between them without having to explicitly specify a residue range (I have this bound to the alias “selbetween”) in Chimera. Is there any equivalent accelerator in ChimeraX? Cheers OIi

2 1

Help with ChimeraX and dual extruder 3D printing
by Dye, Billy 23 Aug '23

23 Aug '23

I have been using ChimeraX to generate STL files for 3D printing models of a variety of protein structures that I use in my biology classes. I recently acquired a dual extrusion printer which should allow me to print models in two different colors. For example, I am currently trying to print a nucleosome from RCSB model 7PFX such that the DNA is printed blue from one extruder and the histones white from the second extruder. I am exporting two different STL files from ChimeraX, one with the DNA and one with the histones, and I am attempting to slice with FlashPrint 5 software for a FlashForge Creator Pro 2 printer. However, when I import the two STL files into the slicing software, they are not aligned. Even if I position both at 0,0,0 coordinates, it is obvious that the DNA and histones are not lining up properly. Is there a way to export the two STL files from ChimeraX such that they have a common reference point or origin and will thus align with one another when both are placed into the slicing software? Many thanks for your consideration and advice, Billy Dye [PastedGraphic-2.png]

2 1

Trackpad modifier to translate in z?
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, In Chimera, I have shift-two-finger-drag set to translate the view in Z. This is very useful for precisely navigating around large structures without reorienting the camera, particularly when the cofr is bound to the center of view. Is there any way to replicate this behavior in ChimeraX? Cheers Oli

4 10

Add shortcuts to Model panel, log and Volume viewer to toolbar?
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, I love the ability to customize the home tab of the toolbar, but there are some other things that I would like to add there and I don’t see how. Is there any way to add shortcuts/icons for the model panel, the log and the volume viewer? The use case is that I prefer to keep all panels undocked, in order to maximize screen real estate when working on a laptop - having shortcuts to bring these up would be convenient. It would also be great to have a shortcut for either a specific alias, or a dropdown menu of aliases, for custom lighting/visualization modes defined in the startup commands. Cheers Oli

4 6

W-9 Request, Belharra Therapeutics | For Chimera
by Belharra Therapeutics Purchasing 23 Aug '23

23 Aug '23

Hello, I've recently tried to reach out regarding Chimera. All of my emails have been returned as undeliverable. Can I please get you assistance with the following information for Chimera? * A copy of your W-9 (or W-8, W-8BEN, W-8BENE for International) * Contact for your accounting department * Our account number for us to reference on our PO's, or if we are to refer to our company name. * Sales or email address to submit PO's Thank you, Heath Jarred Earle Belharra Therapeutics, Inc.. - Purchasing belharra(a)iabuyer.com<mailto:belharra@iabuyer.com> Innovative Advancement, LLC Brand & Vendor Specialist Ph: 425-686-9566 Ext. 703 www.innovativeadvancement.com<http://www.innovativeadvancement.com/> [cid:image001.gif@01D9D5BC.E5247540] <https://www.facebook.com/Innovativeadvancement/> [cid:image002.gif@01D9D5BC.E5247540] <http://twitter.com/innoadvance> [cid:image003.jpg@01D9D5BC.E5247540] CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential information and may be legally protected from disclosure. If you are not the intended recipient of this message, or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited

2 1

Regarding use of attribute assignment files and difference between ChimeraX and ChimeraX daily build
by SUHANI BHATTACHARYYA 23 Aug '23

23 Aug '23

Dear Team Chimera, I am a second-year undergraduate student at IISER, Pune. I have been using ChimeraX for some time. Earlier I have also used some older Chimera versions. They had the kdHydrophobicity under Render by Attribute for residues. However, ChimeraX does not. On reporting a problem, I was told to use attribute assignment files for kdHydrophobicity. I downloaded the file as .txt file with .defattr suffix. Then, following the instructions in the user guide, I tried to use the open command to start using the attribute file. But I was shown an error that no such file existed. I even changed the file location and checked with multiple directories, including where ChimeraX files are stored on my PC to try to open the file, but nothing has worked. Kindly provide clearer instructions on where to save and open the attribute assignment files. Thank you. Regards, Suhani Bhattacharyya

2 2

Fwd: Help with ChimeraX and 3D printing
by Elaine Meng 23 Aug '23

23 Aug '23

Dear Billy, Please use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list to ask ChimeraX questions (CC'd here so you don't need to re-send) -- I am not sure of the answer, and others on the list have more expertise in this area. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: "Dye, Billy" <Billy.Dye(a)volstate.edu> > Subject: Help with ChimeraX and 3D printing > Date: August 23, 2023 at 8:31:21 AM PDT > To: "meng(a)cgl.ucsf.edu" <meng(a)cgl.ucsf.edu> > > Hello > > I hope you might give some advice on using ChimeraX with dual extrusion 3D printing. > > I have been using ChimeraX to generate STL files for 3D printing models of a variety of protein structures that I use in my biology classes. I recently acquired a dual extrusion printer which should allow me to print models in two different colors. For example, I am currently trying to print a nucleosome from RCSB model 7PFX such that the DNA is printed blue from one extruder and the histones white from the second extruder. I am exporting two different STL files from ChimeraX, one with the DNA and one with the histones, and I am attempting to slice with FlashPrint 5 software for a FlashForge Creator Pro 2 printer. However, when I import the two STL files into the slicing software, they are not aligned. Even if I position both at 0,0,0 coordinates, it is obvious that the DNA and histones are not lining up properly. Is there a way to export the two STL files from ChimeraX such that they have a common reference point or origin and will thus align with one another when both are placed into the slicing software? > > Many thanks for your consideration and advice, > Billy Dye > > > >

1 0

Regarding probeRadius
by Sakiat　Hossain 23 Aug '23

23 Aug '23

Dear Sir/Madam, Greetings. I am a nanomaterial chemist, and I would like to measure solvent accessible surface area (sasa) of my metal nanocluster using its single crystal x-ray diffraction structure. Specifically, I want to calculate H+ accessible surface area. I would appreciate it if you kindly let me know how to change probeRadius for calculating sasa in ChimeraX. I look forward to your kind help. Best, Sakia Hossain Tokyo University of Science, Japan Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

2 1

Trackpad rotation
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, The trackpad zoom/rotation settings in ChimeraX seem very different from “old” Chimera. Is there any way to replicate the behavior from Chimera? Specifically, when I pinch to zoom in ChimeraX, I often find the view rotating a lot, unless I am very careful, which does not happen in Chimera. I have tried playing around with the trackpad twist sensitivity, but so far have been unable to find settings similar to the default in Chimera. Cheers Oli

2 8

ChimeraX registration
by Rouzer, Carol A 21 Aug '23

21 Aug '23

To Anyone who can help: I recently downloaded ChimeraX after many years of using Chimera. I keep getting the following warning message: Registration file '/Users/carol/Library/Application Support/ChimeraX/registration' has expired I assume this means I should re-register, but I can’t find any mechanism to do that. Sorry for my stupidity, but I do want to be using the software legitimately. Please instruct. Thanks, Carol Carol A. Rouzer, Ph.D., M.D. Senior Editor/Writer A.B. Hancock Memorial Laboratory for Cancer Research Basic Sciences, School of Medicine Vanderbilt University Nashville, TN 37232-0146 c.rouzer(a)vanderbilt.edu<mailto:c.rouzer@vanderbilt.edu>

2 2

Installation of chimera failing
by Royan, Santana (Manufacturing, Clayton) 20 Aug '23

20 Aug '23

Hi there, I'm having trouble installing chimera on my work windows laptop for the IUCR2023 Phenix workshop. The installation keeps failing due to being unable to create the directory in the C drive (see screenshot). [cid:image003.jpg@01D9D3B7.892B9130] My organisation does restrict administrator rights on this laptop and requires me to apply for it for a limited period of time, but I have enabled these before starting the installation. I note that the installer didn't ask for admin access when installing here on this computer before the License Agreement, but it did on my personal laptop which proceeded with the installation just fine. Am I missing something with the installation package? This is happening for both the daily build executable and the 1.6.1 build. Regards, Santana Santana Royan CERC Fellow in Optimising Biodegradation of Plastics MCM Manufacturing | CSIRO santana.royan(a)csiro.au<mailto:santana.royan@csiro.au> | 03 9662 7107 Building 201 Level 2, Research Way, Clayton VIC 3128 CSIRO acknowledges the Traditional Owners of the land, sea and waters, of the area that we live and work on across Australia. We acknowledge their continuing connection to their culture and we pay our respects to their Elders past and present. CSIRO Australia's National Science Agency | csiro.au<www.csiro.au>

2 2

Difficulty docking proteins
by Weidenbach, Megan 18 Aug '23

18 Aug '23

Hi there, My name is Megan Weidenbach and I am a user of the ChimeraX software. We have been trying to dock built organic molecules to coagulant factor proteins. So far, we have had no luck with the AutoDock Vina feature. This has been tested on the mac and microsoft versions of the software. I was wondering if your team might be able to point us in the direction of some resources that could help dock the proteins and identify their binding sites? Thank you! Megan L. Weidenbach B.A. Biology & Pre-Veterinary Studies meganweidenbach(a)myunt.edu University of North Texas [cid:c8b6bc7f-58c7-4404-8b08-46a6fb60aca9]

2 1

Plugin development questions
by BARRY E DEZONIA 18 Aug '23

18 Aug '23

Hello, I have been developing a plugin in bits and pieces for a while. I am now hoping to build a bundle (or whatever) to make installation pretty seamless. My program is a bit unconventional so I have a few questions on how to proceed. My plugin templating copies one of the examples (maybe the Tool example). My plugin uses a couple of python packages/modules: * mdtraj (https://mdtraj.org/1.9.3/installation.html) * traj2nmr (https://github.com/weberdak/traj2nmr) It also will have some shell scripts I want to include and also a java program. So far we have been getting by installing things like this: * in chimerax using the command prompt entering "pip install mdtraj" or similar * from an OS terminal invoking chimerax's version of python to run traj2nmr's setup.py program so that it goes into chimerax's python's installed packages * including our shell scripts in a Runnable directory under the plugin installation directory (during development) and copying them in a similar directory under the ~/.local/share/....chimerax-path-stuf.../the-plugins-Runnable-dir. Maybe the plugin installation process does this for me already but it is often not showing the latest changes even after plenty of "dev installs" in the chimerax command prompt line. * I am just starting to want to place the java app and the shell script that launches it somewhere. Hopefully in that same Runnable directory. Right now, I am trying to learn what is the best approach to bundle this all together and have a simple installation process. Can someone advise a bit? Thanks.

4 9

Is there a python module to access ChimeraX from outside with Python?
by Jonathan David Karl Krahl 17 Aug '23

17 Aug '23

Good morning, my name is Yona and I am working at the chair of Computational BioEngineering at the Technical University in Dortmund, Germany. I was wondering, if there is a possibility to access ChimeraX from outside with Python; the module "pychimera" provides an API for Python and Chimera, but not ChimeraX, as far as I know. Do you know an alternative or a way to do it? Thanks for your help :) Yona

2 1

info retrieval
by Eduardo Mauricio Martin 17 Aug '23

17 Aug '23

To whom it may concern: According to the documentation sequences infor from a model can be retrieved by the following command: info polymers #1 saveFile "C:\Users\faits\Documents\test8.txt" Though the console keeps throwing the following error attached as image. [cid:image002.png@01D9D083.452CFE10] I just need to retrieve the residue number for each subunit to run a Python script that removes sasa values from hetatm which are not in the protein per se. If there is a work around to acquiere this inforation in a file please let me know. Kind regards, Eduardo M Martin PhD Candidate Information systems Department Autonomous University of Aguascalientes. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

2 1

re error with Movie recorder utility
by Anna Lohning 16 Aug '23

16 Aug '23

Hi I have the freeware version installed and trying to make a movie using the Tools/Utilities/Movie recorder window. At this stage, I seem to only have the command line available for commands one at a time. Anyway, under the Tools/Utilities, the only options there currently are Register Updates Be grateful for some clarification as I cant seem to find anyone having this issue. Many thanks Kind regards Anna Dr Anna Elizabeth Lohning Associate Professor - Biochemistry Faculty of Health Science & Medicine Bond University ROBINA 4229 (07) 5595 4779 alohning(a)bond.edu.au<mailto:alohning@bond.edu.au>

2 1

Getting number of residues from a PDB contain only a fragment
by huybk81＠gmail.com 16 Aug '23

16 Aug '23

Hi, I used this Python code to get the number of residues: model = run(session, 'open %s' % input_model)[0] print(model.chains[0].num_residues) It works when the input_model is a complete pdb file. However, when the input_model only contain part of the structure of the full pdb but retains the full sequence information, the code above always return the num_residues of the full structure, not the input_model only. Is there any way to get this done? Best, Huy

2 2

colouring by entity
by Manon Demulder 15 Aug '23

15 Aug '23

Hi I have a model that consists of a sheet made out of repeats of a dimer. Currently I have a .mmcif file with the monomers in each dimer being labelled either 1 or 2. I would like to give monomer 1 and 2 a different color in my sheet. Is it possible in ChimeraX to recolour the different monomers by their entity 'name'? Thanks in advance! Best Manon ------------------------------------------------------------ Manon DEMULDER PhD | Post-doctoral researcher University of Basel | Biozentrum | Ben ENGEL lab Spitalstrasse 41 | 4056 Basel | Switzerland manon.demulder(a)unibas.ch | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch>

2 1

AreaSAS Function in ChimeraX
by Andy Nguy 14 Aug '23

14 Aug '23

Hello, I was wondering if there is a AreaSAS function for ChimeraX. To my knowledge, there was such a function in Chimera under "Render by Attribute". If not, is there a way to identify all solvent-accessible residues for a protein of interest? Thanks! -- Andy.

2 1

Problem with saving files through command line
by Vorländer,Matthias Kopano 14 Aug '23

14 Aug '23

Dear Developers, I have found a strange behavior when saving files through the chimeraX command line. Essentially, file naming does not seem to be properly sensitive to capitalization. For example, when I am trying to save a file called “chain_A.pdb” and then another file called “chain_a.pdb”, “chain_A.pdb” will be overwritten with the contents of “chain_a.pdb”. It also does not matter if I am saving a pdb file or a log file. If “chain_A.pdb” does not exist, then “chain_a.pdb” will be correctly saved with as a lowercase a. Details: version 1.6.1 (2023-05-09) OS: MacOS Catalina Version 10.15.7 Would be great if this could be fixed : ) Many thanks in advance, Matthias

2 1

Library Missing in Debian v-12
by Stephen P. Molnar 14 Aug '23

14 Aug '23

I have just downloaded ucsf-chimerax_1.6.1ubuntu22.04_amd64.deb for installation on my Debian-12 platform. Unfortunately, the missing dependency libffi7 is not part of the distributiojn. Please Advise. Thanks in advance. ucsf-chimeax-- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

3 2

Opacity of atoms
by Haaris Ahsan Safdari 13 Aug '23

13 Aug '23

Hi ChimeraX team, I am working on a protein that clashes with RNA. Hence, to show those, I selected atoms of proteins (sphere representation) which are less or equal to 3.5Å from RNA and then colored them red. Through this criteria, some atoms of protein which do not clash with RNA, I keep them as lime colour. All of this works fine. Now, I wanted to show the clash more clearly since RNA segments pierces through many atoms of protein, so I wanted to make protein atoms (which is now a combination of red for clashing atoms and lime for non-clashing atoms) transparent. However, as soon as I make my protein more transparent (by changing opacity), all atoms of my protein turn red and I lose the green ones which I dont want. I just wanted to know if there is any workaround for this (to retain green while making everything more transparent) or if it is just a bug? Best regards, Haaris Ahsan Safdari

2 1

Fwd: how to fix this.... it is windows machine.
by Eric Pettersen 11 Aug '23

11 Aug '23

> Begin forwarded message: > > From: Krishnan Raman <RKrishnan(a)BIOCRYST.com> > Subject: how to fix this.... it is windows machine. > Date: August 11, 2023 at 12:20:16 PM PDT > To: "chimerax-users-owner(a)cgl.ucsf.edu" <chimerax-users-owner(a)cgl.ucsf.edu> > > > > 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. >

5 5

Regarding Volume Morph Issue
by Chen, Shin-Fu 11 Aug '23

11 Aug '23

Hello, I hope this message finds you well. I am currently working on creating a movie using the "volume morph" command based on ten sets of mrc files. I have encountered an issue that I would appreciate your assistance with. Prior to applying the "volume morph" command, I have utilized the "color near atoms" option to assign colors to the visualization. However, after executing the "volume morph" command, the previously assigned colors are reset to a default single color. I am reaching out to seek guidance on resolving this issue. Your insights and advice would be greatly appreciated. Thank you for your attention to this matter, and I eagerly await your response. Best regards, Shin-Fu Shin-Fu Chen, Ph.D. Postdoctoral Fellow Department of Biochemistry and Molecular Biology McGovern Medical School University of Texas Health Science Center Houston 6431 Fannin St | MSB 6.326 | Houston, Texas 77030

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Re: [Chimera-users] making composite map using vop maximum command
by Elaine Meng 10 Aug '23

10 Aug '23

Hi, In ChimeraX it is documented as "volume maximum" (even though I believe that "vop maximum" like in the older program Chimera could be used). Also if you want to ask about ChimeraX specifically, there is a different email address, chimerax-users(a)cgl.ucsf.edu -- I CC'd it here so you don't need to do anything this time. Here is the ChimeraX "volume maximum" help link: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#maximum> For example, if your maps are #2 and #3, you can create a new map containing the maxima of their two values with ChimeraX command: vol max #2,3 ... but there are many additional options that could also be included in that command, so you should check the help link above to see if you want to use any of them. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 7, 2023, at 2:20 PM, ytakagi--- via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi > I want to make a composite map using two locally refined maps. I tried Phenix but did not work well. So, I like to do it by Chimera. Apparently, a composite map can be made using Chimera's vop maximum command. But I could not find the instruction of how to do it. Can you tell me how to do it? > Thanks

2 5

Spherical mask
by Grundmann,Lorenz Emanuel 10 Aug '23

10 Aug '23

Dear chimerax-team, I am looking into a possibility to generate a spherical volume in chimerax that I can then use as a spherical mask for focused 3D classifications and signal subtractions. For my specific need, a sphere would be the ideal shape. So far I managed to generate a surface model using the ‘shape sphere’ command, to place it to the region of interest and resampling it onto the coordinate system of my protein of interest. Is there any possibility to transform the surface model into a (binarized) volume? Best, Lorenz

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Re: Advice on handling cofactor-protein electrostatic interactions
by Boaz Shaanan 08 Aug '23

08 Aug '23

Thanks Elaine, I'll do just that. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________ From: Elaine Meng <meng(a)cgl.ucsf.edu> Sent: Tuesday, August 8, 2023 11:57 AM To: �� <bshaanan(a)bgu.ac.il> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] Advice on handling cofactor-protein electrostatic interactions Hi Boaz, If you use Coulombic it will automatically calculate the charges, as in my example of 1qs0 with the TPP residue. I.e. you don't have to do it in a separate step first, and in fact it may be better if you do not: if you use Add Charge first, it will also add hydrogens and make the surface a lot bumpier. If you just use Coulombic the hydrogens are added only on a temporary copy that is in memory, not on your model, and the coloring will be applied to the smoother molecular surface without hydrogens. You just need to substitute the cofactor residue name for ":tpp" in my example, if it is not TPP. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 8, 2023, at 7:09 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > Thanks a lot for the detailed reply and (as always) very helpful suggestions. I'll experiment first with the Chimerax coulombic surfaces and trick to include the cofactor. This sounds attractive, certainly for the TDP case as a starting point. As for derivatives of TDP, which are already included in the pdb, I guess I should follow the 'Add Charges' guide, right? > > Thanks again. > > Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Monday, August 7, 2023 10:17 PM > To: �� <bshaanan(a)bgu.ac.il> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Advice on handling cofactor-protein electrostatic interactions > > Hi Boaz, > This answer addresses coloring by electrostatic potential (ESP). Calculating the electrostatic interaction per se (energy?) is somewhat different and not something that ChimeraX does. > > ChimeraX can color some surface, which could be a molecular surface, by the values in a 3D map, which could be electrostatic potential (ESP). See "color electrostatic" > <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%…> > > The ESP map can come from a Poisson-Boltzmann calculation (APBS, DelPhi, others) or from a more simplistic Coulombic calculation which can be done directly in ChimeraX. > > Poisson-Boltzmann calculations require atomic coordinates, partial charges, and radii, but the different programs differ in how you input these values. > > If I recall correctly, APBS takes as input a pqr file (q means charge, r means radii) which would usually be generated by PDB2PQR, but you said PDB2PQR throws out the nonstandard residues like cofactors, I guess because it doesn't have charges for them. ChimeraX assigns radii and can assign atomic partial charges (via lookup table for standard residues and Antechamber calculation for nonstandard residues like cofactors). However, ChimeraX does not write pqr format. Also in ChimeraX, these partial atomic charges are for all atoms (i.e. all hydrogens explicit) and not a united-atom model (in which hydrogens on carbons are merged with those carbons so that they become implicit) which is often used for Poisson-Boltzmann calculations. So if you wanted to go the APBS route, in ChimeraX you would add hydrogens and charges, then save the cofactor radii and atomic partial charges (atom attributes "radius" and "charge") in the attribute file format, and if you were using a united-atom charge model, manually generate united atoms from CH, CH2, and CH3 groups in the cofactor by adding the hydrogen charges to those of the carbons where they are attached and figuring out the appropriate united-atom radii, then reformat the cofactor atom coordinates, radii and charge values into pqr format and then add these lines to your protein pqr file from PDB2PQR, then use the resulting combined pqr file as input to APBS to get the ESP map that includes cofactor contributions. > > Actually I don't even know if APBS would accept that pqr file or not, but that is what I imagine you would try. So let's assume the APBS calculation will run using that pqr file. > > Then you would open the APBS ESP map that includes cofactor contributions in ChimeraX and color the molecular surface. If the cofactor is covalently attached to the protein then the protein molecular surface may already include it. However, if the cofactor is not covalently attached, you would need to tell ChimeraX specifically to lump it inside of the same surface as the protein with the "include" option of "surface" when you are calculating and displaying the molecular surface. > > The "coulombic" approach wil do more of these steps for you, given the "include" trick as well as the "surfaces" option of the "coulombic" command, but calculating ESP with the relatively simplistic Coulomb's law method. For example, 1qs0 chain A includes a noncovalently bound TPP residue and I could show the surface including the TPP and colored including its potential contribution: > > open 1qs0 > surf include :tpp > coulombic surfaces #1.2 > > <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%…> > <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%…> > > See first image attached with :tpp selected (green outline surface patch) > > If you don't use the "include" and "surfaces" options in these commands, the surface will be redrawn to include only the protein part with the TPP outside of it, like other ligands and the Coulombic ESP will not include the TPP contribution. See second image attached. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > <Screen Shot 2023-08-07 at 7.08.37 PM.png><Screen Shot 2023-08-07 at 7.12.43 PM.png> > > >> On Aug 7, 2023, at 4:10 PM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hi, >> >> I would like to present effects of mutations around cofactors (TDP derivatives) on the protein - cofactors electrostatic interactions. I use APBS and chimerax to display the electrostatic surface potential of the protein, but since PDB2PQR eliminates the cofactor from the pqr file I need a tool for the cofactor surface potential. I'm wondering what tool I should use for this. Is it Antechamber+chimerax or something else? >> Is there by chance a demo for such scenario? >> I'd appreciate your advice. >> Cheers, >> >> Boaz >> >> >> Boaz Shaanan, Ph.D. >> Dept. of Life Sciences >> Ben-Gurion University of the Negev >> Beer-Sheva 84105 >> Israel >> >> E-mail: bshaanan(a)bgu.ac.il >> Phone: 972-8-647-2220 >> Fax: 972-8-647-2992 or 972-8-646-1710 >> >> >> >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >> Archives: https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%… > > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%…

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Re: [Chimera-users] Saving phi psi values to a text file
by Elaine Meng 07 Aug '23

07 Aug '23

Hi Prathvi, In Chimera there is no command to save attributes. Instead you have to use the Render by Attribute dialog's File menu as described in the bottom section of this page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.ht…> In ChimeraX, as far as I know you can only save one attribute to a file at a time with the "save" command. However, it would probably work just to use the "save" command several times and then (outside of ChimeraX) concatenate the multiple files into one file afterward. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> Another idea is that in ChimeraX you can list attribute values in the Log with the "info" command, e.g. info residues protein attribute phi So an alternative approach if you don't need the file to be in the attribute-file format is to use "info" multiple times and then save the Log contents to an HTML file with "log save" -- see help pages for those commands: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 5, 2023, at 10:14 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > Is there a command to save the phi and psi angle values of each residue of a PDB file in a text file using UCSF chimera? > > I know we can do this in chimeraX using the command: save C:\myphi.defattr attrName phi format defattr model #1 > > Also, can we use chimeraX to save the phi and psi values in a single file? > > Thanks in advance >

2 1

Query regarding selection
by Prathvi Singh 04 Aug '23

04 Aug '23

Hi Elaine, I want to select all the atoms except the backbone oxygen and nitrogen atom of residues 100.A to 120.A . Is there a command to do this in either chimera or chimeraX? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 2

Pseudobonds question
by Aleksei Solomonov 02 Aug '23

02 Aug '23

Dear ChimeraX Developers, I apologize for disturbing you, I have a question, how can I make pseudobonds in ChimeraX similar to Chimera? I mean when I try to create hydrogen bonds, by default, in Chimera (Tools->structure analysis->findHbonds) they appear as lines (or sticks), connected to the structure (left image). But if I export the model and import it in ChimeraX bonds become "disconnected". The same appeared if I place H-bonds directly in ChimeraX (right image). If I select pesudobond, an option of changing its length manually is unavailable. The structure is attached if needed. [cid:image002.png@01D9C590.A8D2F3A0] Thank you in advance! Best regards, Aleksei

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Missing functions for scripting
by Vincent Mallet 28 Jul '23

28 Jul '23

Hello, Thanks a lot for the awesome tool ! I have a question about how to use some commands that are not yet included in the python API : for instance "measure volume". I can run it using a cxc with : */usr/bin/chimerax --script measure.cxc --nogui --exit* Where *measure.cxc *contains looks like : *open test.mrc volume #1 level 0.42 measure volume #1* I don't understand how to do the same with a python script. Is there some way to use chimerax.tools(measure area/volume) to get this tool to work from within a python script ? My use case is that I am running this measurement for different thresholds, and I would like those thresholds to depend on the value of previous thresholds, hence I need looping. For now, I am calling subprocess on the .cxc command above from a python script, but this means that I need to load the mrc every time... Thanks in advance for your help ! Best, Vincent

3 3

Determining Chirality
by steffen＠sthomas.de 27 Jul '23

27 Jul '23

3 3

Download ChimeraX
by songlu 26 Jul '23

26 Jul '23

Dear ChimeraX developers, Thank you for taking the time to read my email. I have a question about downloading ChimeraX and I hope you can help me. When I downloaded the MacOS version of the ChimeraX1.6 on the official website, I found that the download always failed. After trying to switch the browser and the network, it still doesn't work. Perhaps you can help me solve the problem or send me the installation package for the MacOs version of the ChimeraX1.6. I would greatly appreciate it. Looking forward to your reply. Sorry again for the delay in your valuable time. Wishing you a pleasant day. Yours respectfully, Songlu

2 3

transparency for different selection
by Enrico Martinez 26 Jul '23

26 Jul '23

Dear ChimeraX users! I am dealing with the visualization of protein embedded into the plasmatic membrane (composed of water and lipids). Here is my script preset publication 1 rainbow protein palette $palette # for protein surface protein #color protein cornflower blue transparency 95 target s # for lipids surface :OL,PA,PE color :OL coral target s color :PA coral target s color :PE orangered target s hide bonds; hide atoms transparency 55 target s 1) I would like to set different values of the transparency for the surface of lipids and protein. For the moment I found only one possibility to set the transparency for the whole surface indicated above. Would it be possible to selectively apply a transparency command on the particular selection of the system ? 2) how would it be better to visualize the water in the same system in order to maintain the visibility of the protein ? Many thanks in advance Enrico

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How do you refine a structure with a new (or modified) amino acid residue in Isolde
by Trevor Sewell 25 Jul '23

25 Jul '23

Hi Everyone, I am adding residues (essentially modified cysteines ) to the polypeptide chain. e.g. HETATM 1 N2 PGR 0 1.743 -1.624 -0.731 1.00 0.00 N HETATM 2 C1 PGR 0 -0.077 -0.207 -0.018 1.00 0.00 C HETATM 3 C2 PGR 0 1.394 -0.544 0.203 1.00 0.00 C HETATM 4 C3 PGR 0 -0.485 0.927 -0.717 1.00 0.00 C HETATM 5 C4 PGR 0 -1.034 -1.073 0.503 1.00 0.00 C HETATM 6 C5 PGR 0 -1.840 1.189 -0.887 1.00 0.00 C HETATM 7 C6 PGR 0 -2.389 -0.810 0.331 1.00 0.00 C HETATM 8 C7 PGR 0 -2.794 0.323 -0.364 1.00 0.00 C HETATM 9 C8 PGR 0 2.379 0.585 -0.085 1.00 0.00 C HETATM 10 H1 PGR 0 1.529 -0.961 1.213 1.00 0.00 H HETATM 11 H2 PGR 0 0.232 1.599 -1.120 1.00 0.00 H HETATM 12 H3 PGR 0 -0.727 -1.940 1.035 1.00 0.00 H HETATM 13 H4 PGR 0 -2.145 2.053 -1.418 1.00 0.00 H HETATM 14 H5 PGR 0 -3.116 -1.477 0.733 1.00 0.00 H HETATM 15 H6 PGR 0 -3.837 0.527 -0.497 1.00 0.00 H HETATM 16 H7 PGR 0 1.655 -1.298 -1.705 1.00 0.00 H HETATM 17 H8 PGR 0 1.143 -2.449 -0.581 1.00 0.00 H HETATM 18 O18 PGR 0 3.393 0.026 -0.528 1.00 0.00 O HETATM 19 SG PGR 0 2.777 1.511 1.356 1.00 0.00 S HETATM 20 CB PGR 0 1.349 2.524 1.801 1.00 0.00 C HETATM 21 CA PGR 0 1.698 3.446 2.926 1.00 0.00 C HETATM 22 N PGR 0 0.565 4.254 3.182 1.00 0.00 N HETATM 23 C PGR 0 2.646 4.407 2.450 1.00 0.00 C HETATM 24 O24 PGR 0 2.145 5.309 1.717 1.00 0.00 O HETATM 25 O25 PGR 0 3.976 4.409 2.828 1.00 0.00 O HETATM 26 H9 PGR 0 1.980 1.252 -0.806 1.00 0.00 H HETATM 27 H11 PGR 0 1.044 3.140 0.942 1.00 0.00 H HETATM 28 H12 PGR 0 0.527 1.867 2.099 1.00 0.00 H HETATM 29 H13 PGR 0 2.043 2.881 3.803 1.00 0.00 H HETATM 30 H14 PGR 0 -0.245 3.721 3.480 1.00 0.00 H HETATM 31 H15 PGR 0 0.359 4.821 2.336 1.00 0.00 H TER My question is: How do I set up Isolde so that it can refine the structure? Many thanks, Trevor Sewell Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/report-incident

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Regarding replacing Aspartate with Isoaspartate
by Protya, Satirtha 24 Jul '23

24 Jul '23

Hi Everyone, Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. I am facing a new issue. In one of my peptide PDB file, I need to change the Aspartate Amino Acid with Iso Aspartate Amino Acid. I have been trying to do so, but not sure how to do that. Is there any way or package that can do that? Please let me know. Hope to hear from you soon. Have a great day. -- Yours sincerely Satirtha Saha He/Him/His Beloit College | Class of 2025 Triple Major | Biochemistry, Cognitive Science and Data Analytics Research Assistant | Sweedler Lab | UIUC Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_med…> sahass(a)beloit.edu<mailto:sahass@beloit.edu> [Image][Image]

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Questions on Visualizing Chromatin Structure and Gene Expression in ChimeraX
by 刘致远 24 Jul '23

24 Jul '23

Dear UCSF ChimeraX Team, I am a big fan of your program and I have been greatly impressed with its capabilities. I want to express my deep appreciation for the "soft" visualization option provided in ChimeraX - the aesthetics truly appeal to me. I've been utilizing ChimeraX to visualize my chromatin structure data. While I'm aware this might not be one of the intended uses, when I simulated the 3D structure of chromatin as a protein's cif file, the result looked fantastic. Now I've encountered a challenge and I am hopeful that you might be able to provide some guidance. I am looking to represent gene expression as the size of the spheres in my chromatin structure, all in one figure. I am aware that Chimera has a method using "vdwdefine", essentially using the size of the B-factor to represent the atomic radius. Could you guide me on how to achieve this in ChimeraX? Furthermore, if I want to include multiple columns similar to the B-factor, how can I add them to the cif? Using the "defattr" command feels a bit cumbersome. It would be very convenient if I could pack a lot of dimensional information (such as the gene density of this chromatin segment, CG content, chromatin opening degree, etc.) into a single cif file. Do you have any suggestions or strategies on how to achieve these somewhat unconventional functionalities? Your assistance would be greatly appreciated. Thank you for your attention and I look forward to hearing from you soon. Best Regards, Zhiyuan Liu

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Fwd: depicting contacts
by Eric Pettersen 24 Jul '23

24 Jul '23

> Begin forwarded message: > > From: Krishnan Raman <RKrishnan(a)BIOCRYST.com> > Subject: depicting contacts > Date: July 24, 2023 at 9:50:11 AM PDT > To: "chimerax-users-owner(a)cgl.ucsf.edu" <chimerax-users-owner(a)cgl.ucsf.edu> > > Hi all, > Any ideas to depict a dramatic improvement(200 nm to femtomolar) in binding affinities before and after mutations(about seven) in chimerax? > II have tried contacts , swapaa etc. nothing seems dramatic enough for visuals > Thanks > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows > > > > > 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. >

4 3

Fwd: RFdiffusion in ChimeraX?
by Tom Ferrin 24 Jul '23

24 Jul '23

2 1

Swapaa doubt
by Krishnan Raman 24 Jul '23

24 Jul '23

Hi, How do I use swapaa to do mutations on seven to ten residues in one 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 2

L-D isomers
by Íñigo Izal Azcárate 21 Jul '23

21 Jul '23

Hi everyone, Is there any way of changing the isomerism of protein residues from L to D? I use ChimeraX with students and it would be great to see what happens with some features of the structure like hydrophobicity after changing isomers. Thanks so much in advance Iñigo Izal Azcárate Personal de Apoyo a la Docencia, Coordinador del programa Science and Business Departamento de Bioquímica y Genética T: 948 425600, ext 6321 inizal(a)unav.es -- *Este mensaje puede contener información confidencial. Si usted no es el destinatario o lo ha recibido por error, por favor, bórrelo de sus sistemas y comuníquelo a la mayor brevedad al remitente. Los datos personales incluidos en los correos electrónicos que intercambie con el personal de la Universidad de Navarra podrán ser almacenados en la libreta de direcciones de su interlocutor y/o en los servidores de la Universidad durante el tiempo fijado en su política interna de conservación de información. La Universidad de Navarra gestiona dichos datos con fines meramente operativos, para permitir el contacto por email entre sus trabajadores/colaboradores y terceros. Puede consultar la Política de Privacidad de la Universidad de Navarra en la dirección: **https://www.unav.edu/aviso-legal* <https://www.unav.edu/aviso-legal>**** ** ** *This email message may contain confidential information. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. The personal information included in email messages exchanged with employees of the University of Navarra may be stored in the database of your interlocutor and/or the servers of the University for the time-period stipulated by its internal information storage policy. The University stores such data for purely administrative purposes, to facilitate e-mail contact between its employees and third parties. The University of Navarra Privacy Policy may be accessed at https://www.unav.edu/aviso-legal <https://www.unav.edu/aviso-legal> ***** ** ** _Antes de imprimir este mensaje o sus documentos anexos, asegúrese de que es necesario. Proteger el medio ambiente está en nuestras manos. Before printing this e-mail or attachments, be sure it is necessary. _It is in our hands to protect the environment.__

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Re: Chimera X: Protein-Ligand Docking
by khawar siddiqui 21 Jul '23

21 Jul '23

Hi Tom,We were wondering if it is possible to include Protein-ligand docking in the next ChimeraX version. That will benefit lots of researchers also by having it within the same package. Thanks and best wishes Dr K Sohail Siddiqui,School of Biotechnology and Biomolecular Sciences (BABS),Room 420, Building D26,The University of New South Wales (UNSW),Randwick, High Street, Sydney, Australia. NSW 2052Office: +61 2 938 55193email: z3030204(a)ad.unsw.edu.au; sohailsiddiqui1995(a)yahoo.com best wishes Dr Khawar Sohail Siddiqui On Friday, 7 July 2023 at 11:25:48 am AEST, khawar siddiqui <sohailsiddiqui1995(a)yahoo.com> wrote: Hi Tom,That will be really great if the next ChimeraX version has the Animation tool so less experienced researchers who find command line difficult can prepare protein structure movies using simple clicks. Thanks a lot for considering the suggestion. Waiting eagerly for the next version with animation tool.The ChimeraX is an amazing visualization tool. Best wishesSohail Sent from Yahoo Mail for iPhone On Friday, July 7, 2023, 5:15 am, Tom Goddard <goddard(a)sonic.net> wrote: Hi Sohail, We have funding to develop a ChimeraX animation tool like the one in Chimera but better. It is part of a 4 year NIH grant that started about 9 months ago that funds a lot of the ChimeraX development. We have not started on the animation tool and it will probably take about 6 months to develop once we start on it. Tom On Jul 4, 2023, at 11:46 PM, khawar siddiqui via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: Hi Developers,ChimeraX is a great tool for protein researchers and a vast improvement on the previous Chimera. However, ChimeraX has one limitation for users who dislike command lines. Kindly incorporate the Animation movie maker facility in a New Version under Tools/utilities as was in the previous version. It was so quick and simple by using GUI. Thanks a lot Dr K Sohail Siddiqui,School of Biotechnology and Biomolecular Sciences (BABS),Room 420, Building D26,The University of New South Wales (UNSW),Randwick, High Street, Sydney, Australia. NSW 2052Office: +61 2 938 55193email: z3030204(a)ad.unsw.edu.au; sohailsiddiqui1995(a)yahoo.com Sent from Mail for Windows _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu Manage subscription:

2 2

Regarding Usage of ChimeraX for PDB file creation
by Protya, Satirtha 21 Jul '23

21 Jul '23

Hello, Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. Currently, I am using ChimeraX for one of my research projects. I need to build structures and download the PDB files. I can do that for all L amino acid containing peptides, but I don’t know how to use ChimeraX for D amino acid containing peptides. For example, I have a sequence NWF. Now it is available in this standard L format and also in NdWF format. As ChimeraX is not case sensitive, I don’t know how I should give the command to build the structure with D amino acid containing peptide. Secondly, I have some peptides that have Amidation or NH2 at the C terminus. I don’t know how to add this to my structure. Please let me know how to solve this to issues. That will be really helpful for me. Have a great day. -- Yours sincerely Satirtha Saha He/Him/His Beloit College | Class of 2025 Triple Major | Biochemistry, Cognitive Science and Data Analytics Research Assistant | Sweedler Lab | UIUC Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_med…> sahass(a)beloit.edu<mailto:sahass@beloit.edu> [Image][cid:image002.png@01D9BB19.9CD8CA10]

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Matching ChimeraX color with the Adobe illustrator colors?
by Rayees Mattoo 20 Jul '23

20 Jul '23

Dear ChimeraX users, I am trying to match the colors of ChimeraX model to the Adobe illustrator drawing. I used Web safe colors to color my model in chimeraX and then used the same hex codes in the illustrator, but the colors did not match. Any thoughts or workarounds would be appreciated. Best Rayees

3 2

Re: Opening MTZ Files
by Elaine Meng 20 Jul '23

20 Jul '23

Hi Natalie, Everything I know on this topic is written in the documentation linked below, and yes, as it says therein, you do need to have Clipper installed. Then title of the section is "Open/Save Options from Clipper": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper> I can't think of anything else to say without getting more details from you. What is the problem? Which part are you confused about? What did you try? What happened? Did you follow the instructions in the link? Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 6, 2023, at 9:14 AM, Natalie Walsh <natalie.walsh(a)slu.edu> wrote: > > Hello, I previously asked a question (sent to the wrong email, oops!) about not being able to use MTZ maps in Chimera X (I was using 1.17.1, I just installed 1.17.2 today and still have the same issues). These were the instructions previously provided: > > "The instructions of how to open MTZ files with ChimeraX are here: > > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/comman… > > > "Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc." > > I read through the like and am still confused. I have also installed the Clipper Plugin (although I am unsure if it was installed correctly) since I saw somewhere that might be needed. > > Thanks, > Natalie Walsh

4 5

Running ChimeraX in batch mode on Mac OSX
by Enrico Martinez 20 Jul '23

20 Jul '23

Hello Greg, In addition to my previous message regarding running Chimera-X on Ubuntu, I have a similar question regarding MacOSX. In fact I have a macbook pro equipped with the Mojave (10,14.16) which I used with ChimeraX-1.3 that worked well in no-gui mode (without any additional flags like --offscreen). I've tried more recent releases of Chimera-X and found that it has not worked with Mojave. Anyway, if I do an update would it be possible to use the latest ChimeraX on Mac without gui ? Many thanks in advance Enrico

2 1

colour palette of multiple models
by Enrico Martinez 20 Jul '23

20 Jul '23

Dear Chimera-X users ! I am performing visualisation of multi domain protein loaded in the Chimera-X as different pdbs. In the model panel each pdb coloured differently according to the model ID and everythings is OK for the first 11 models, while starting from the 12th all of them are colored in green (please see the screen-shot). Would it be possible to quickly change the auto-colouring of the multiple pdbs when I load all of them directly using chimerax workdir/*.pdb ? Many thanks in advance Enrico

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Running ChimeraX in batch mode in the Ubuntu terminal
by Enrico Martinez 20 Jul '23

20 Jul '23

Dear ChimeraX users ! I have a quick technical question. Typically I run ChimeraX with a batch script in order to perform some manipulation with input pdb and print the output image / save chimera-X session. In my Ubuntu terminal I run it using: chimerax script.cxc where the script could be something like : ### open input.pdb # do some manipulation like view, orient etc save image.png exit ## It works OK but, while running from linux terminal I have a quickly open-closed Chimera-X window which is not very practical when I put this script in loop etc. Is there any possibility to fully suppress the Chimera-X gui when I run my script in batch mode from the terminal? Many thanks in advance Enrico

2 7

Feature request: support for MRC mode 12 (float16)
by Ricardo Righetto 20 Jul '23

20 Jul '23

Dear ChimeraX team, It seems that ChimeraX (tested version 1.6.1) does not yet support MRC data mode 12, corresponding to half-precision floating point (float16). This data mode is now supported in RELION-4 and IMOD, and is interesting to save storage in cryo-ET and subtomogram averaging workflows. Would it be possible to implement support for reading and writing this MRC data mode in ChimeraX? Thank you! Best wishes, -- Ricardo Diogo Righetto

2 3

Q3 Score Calculation Tool ChimeraX that is similar to MapQ Plugin in Chimera
by Thu Nguyen 19 Jul '23

19 Jul '23

Good afternoon, I am calculating the Q-Scores in cryo-EM density maps and found the MapQ Plugin <https://github.com/gregdp/mapq> in Chimera that does Q3-score calculation and visualization. I wonder if we have a similar plugin in ChimeraX that does Q-score calculation? Thank you very much. Best regards, Thu

2 5

Autodock Vina at ChimeraX
by ODA Natsuki 19 Jul '23

19 Jul '23

Dear all, Thank you for providing the license for ChimeraX. I have a question about ChimeraX for using Autodock Vina. Is it possible to use Autodock Vina at ChimeraX? I used to use Autodock Vina at Chimera before version of ChimeraX. I want to use Autodock Vina, so would you ask me the methods? Sincerely you. Natsuki ------------------------------------------------------------------ Name: Natsuki Oda Affiliation: Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University Student ID: number 1234521019 E-mail: oda.natsuki.i0(a)s.gifu-u.ac.jp ------------------------------------------------------------------

2 1

Question about energy minimization
by Luca Massaccesi 18 Jul '23

18 Jul '23

Dear Chimera team, Can you please tell me if it’s possible to do energy minimization with Chimera X as I used to in previous Chimera? I looked for it on the Chimera X page and in many tutorials but it looks like this tool was cut out of the software. Thank you very much for your help, Luca

2 2

view command to re-orient scene
by Enrico Martinez 17 Jul '23

17 Jul '23

Dear Chimera-X users! I would like to perform visualisation of the pre-oriented objects from a set of PDB filles. Briefly I load 20 pbs in chimera-x and the scene what I see, is depicted on the "initial.png" image attached to the mail. Then I need to orient it automatically in order that the scene would be perfectly parallel to the screen plane, as shown in the second enclosed image. What options for view command could be used to orient the object in the same way ? Many thanks in advance Enrico

2 1

mcopy command
by Matzov Donna 17 Jul '23

17 Jul '23

Hello, I'm trying to use the mcopy command (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mcopy.html) as such: mcopy #1 toAtoms #2 settings a However, I get the following error message: Unknown command: mcopy #1 #2 settings a Am I using the wrong syntax? I am using the latest chimerax release. Thanks, Donna Matzov, PhD Department of Structural Biology Weizmann Institute of Science The Shalev-Benami Lab<https://www.weizmann.ac.il/Structural_Biology/Shalev-Benami/home>

2 1

Slowing down a movie
by Leyre Marin Arraiza 17 Jul '23

17 Jul '23

Dear ChimeraX, I want to make a movie using ChimeraX, in which I can see the map of my protein complex rotating 360 degrees, plus a full rotation of the same map after zooming in. I managed to do so with the following command: movie record ; turn y 2 180 ; wait 180 ; zoom 1.5 ; turn y 2 180 ; wait 180 ; movie encode However, in the final .mp4 file I get, the rotation is quite fast. I would like to create the same movie, but with slower rotation. I have tried figuring it out reading through the guide and trying different commands, but I am not successful. Could you help me with this issue? Thanks in advance 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 2

bond: merging two models within new model
by Enrico Martinez 17 Jul '23

17 Jul '23

Dear Chimera-X users ! I need to fuse two models in the entire construction. Precisely having a water soluble domain with a linker in the first model #1 as well as transmembrane alpha helix segment in the #2 I load the both in chimera-x and then use the bond command with the aim to create a peptide bond between the last residue of the #1 and the first residue of the #2. Here is my command: # select the last residue from the core and the first residue from the TM helix; build join peptide #1:182@C #2:1@N move large The problem is that on the text step I will need to add the membrane in the TM part, but the orientation of the created construction is not optimal. How could I easily modify the mutual orientation between #1 and #2 ? I join the both initial pdbs to this message, in order that my model could be checked :-) Many thanks in advance Enrico

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Re: [Chimera-users] Chimera-X inteprhase of the AlphaFold
by Tom Goddard 17 Jul '23

17 Jul '23

Hi Enrico, The ChimeraX AlphaFold interface does not allow specifying your own structure template. But the ColabFold web server does allow this https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/Alph… using "template mode: custom" on that web page and follow instructions they list on that page for using custom templates https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/Alph… I have tried custom templates with AlphaFold in the past and it has never changed the predicted structure. AlphaFold only uses the template as a first guess at the structure then it does multiple rounds (by default 3 recycles) of creating new models. If AlphaFold is pretty confident about a different conformation than the template it simply replaces the starting structure with the conformation it prefers. Possibly if AlphaFold has low confidence in a prediction a template could bias it to get a different conformation but I've never seen that happen. This is a basic limitation of AlphaFold that it is not designed to optimize an existing structure. The input that dominates the calculation is the sequence and the deep sequence alignment that it computes, not template structures. Possibly AlphaFold could be prodded to predict different conformations by changing the deep sequence alignment to include just the sequences known to fold in the desired conformation and excluding sequences known to fold in a different conformation. Tom > On Jul 13, 2023, at 3:43 AM, Enrico Martinez via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera-X users! > > In parallel to the modeller, I am trying to use the Alpha fold > interface with the aim to full model starting from the sequence using > template. > > The problem is that I can not define manually which template I would > like to use for each prediction so the interphase takes its > automatically based on the input sequence and the final prediction is > not very precise. Would it be possible rather to specify a specific > pdb ID additionally to a given sequence ? > > Many thanks in advance > > Enrico > _______________________________________________ > 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/ >

3 2

ChimeraX in Debian v-12
by Stephen P. Molnar 15 Jul '23

15 Jul '23

I would lie to install ChimaeraX on my Debian v-12 desktop. However, he installer requires libffl7 which is not available. Please advise. Thais in advance -- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

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Re: [Chimera-users] hiding a model slowly in ChimeraX
by Elaine Meng 14 Jul '23

14 Jul '23

Hi Andy! I added "in ChimeraX" to the subject line to make it more obvious to the Chimera users. We recommend sending ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here so you don't need to re-send) instead of chimera-users so that people don't get confused between the two programs - thanks! Here are some thoughts on how to do it in ChimeraX: (1) is anything in the view moving (rotation, translation, conformational change) while this model fades? If not, you can simply use "crossfade" or if you are recording a movie anyway, better to use "movie crossfade", in the script between where the model is shown and where it is hidden. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#crossfade> (2) if you want motions of the view or of individual models at the same time as the fading, then crossfade won't work. Instead you have to do something fancier. Instead of hiding the model you could try gradually changing its transparency from 0% to 100% over some number of frames. This requires combining the "transparency" command with a "perframe" command to iterate over different transparency levels, since you don't want to have to put in 100 (or more) transparency commands. For example, if the model is currently completely opaque (0% transparent) then you can make it completely transparent (100% transparent) over 240 image frames with something like roll y 0.1 perframe 'transparency #7 $1 target abcsp' range 0,100 frames 240; wait 240; ~perframe The "roll" command is only included above as an example so you can see how this fading works during motions. See the help pages for "transparency" and "perframe": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html> However, it will require experimentation with how you specify the other commands for the motion (view, turn, roll, zoom, coordset, etc.) in your command script to make this fading happen at the same time as those motions. Even experts don't get their movie scripts right on the first try; I usually have to change and re-run my script several times. I don't even add the movie-recording commands until after I get all the motions and display changes right. Carrying on from the example above, you can stop the roll and make the model opaque again with something like stop transparency #7 0 target abcsp You stay safe too! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 14, 2023, at 3:09 PM, Sen, Anindito via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera X team, > > Is there a way I can hide one of the models in a ChimeraX session slowly (like fading it off) while making a movie. > > typically I use > > hide #7 model > > Stay safe & Regards > > Anindito Sen. Ph.D > > Microscopy and Imaging Center > Texas A&M University > 301 Old Main Dr > College Station, TX 77843-2257 > > Office: ILSB Room 1133 > Tel. 979-458-9881 > fax: 979-847-8933 > http://microscopy.tamu.edu

1 0

getting RSCC validation scores
by Das, Abhinaba 14 Jul '23

14 Jul '23

Hi ChimeraX community: I’m trying to get real space correlation coefficient value of map-model fit as done in this paper from DiMaio’s group https://elifesciences.org/articles/17219 (Table 2, RSCC validation map column). It is possible to do so in Chimera but I’m not sure how. Although the alternative might be the Map-Q & Q-score plugin in chimera (or Model-Map Q score in ChimeraX) from Greg Pintilie which “uses a real-space correlation approach to assess the resolvability of each model atom in the map” (-http://doi.org/10.1038/s41592-020-01051-w), I would like to get the RSCC values. Is it possible to obtain those values? Thanks in advance for any advice. -abhi

2 1

installation problem with MacOS
by Fabienne Charbit-Henrion 13 Jul '23

13 Jul '23

Hello! I tried to install Chimera X on my Macbook (2016), with MacOS Sierra, but i have this message: [image: image.png][image: image.jpeg] "Image damaged" is there an older release I should install? I tried 1.6 and 1.5 i SO hope it will work!! thanks a lot for your help Fabienne CHARBIT-HENRION

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Re: [Chimera-users] Chimera-X inteprhase of the AlphaFold
by Elaine Meng 13 Jul '23

13 Jul '23

Hello, Since this is a ChimeraX question it should go to chimerax-users(a)cgl.ucsf.edu instead of chimera-users(a)cgl.ucsf.edu (we don't want to confuse the Chimera users). But since the answer is short I will try to give it now: sorry, there is no ChimeraX option to control which template(s) the alphafold calculation uses. There is an option "Use PDB templates when predicting structures" but that is only to control whether it uses any templates or not. Default is off, do not use any templates. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#options> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 13, 2023, at 3:43 AM, Enrico Martinez via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera-X users! > > In parallel to the modeller, I am trying to use the Alpha fold > interface with the aim to full model starting from the sequence using > template. > > The problem is that I can not define manually which template I would > like to use for each prediction so the interphase takes its > automatically based on the input sequence and the final prediction is > not very precise. Would it be possible rather to specify a specific > pdb ID additionally to a given sequence ? > > Many thanks in advance >

1 0

Modeler interphase of the Chimera-x
by Enrico Martinez 13 Jul '23

13 Jul '23

Dear Chimera-X users ! I am trying to use the Modeller interphase of the Chimera-X, with the aim to model missed segments from the input PDB structure. I have very basic questions: 1) In the top, there is a Sequence Alignment dialog box but I don't understand how to provide the alignment there. Should it be the alignment of the sequence of the target pdb (template) ? If so, how could it be obtained supposing that I have i) a pdb with missing fragments as well as ii) the full sequence. Many thanks in advance Enrico

2 1

PDB coordinates missing--how to add residues to N-terminus
by stevensb＠ufl.edu 12 Jul '23

12 Jul '23

The first few N-terminus residues of a seq are grayed out in the PDB sequence viewer and are missing in the PDB chain. It is even possible for ChimeraX to make the peptide bonds to glue on the missing residues in the helix in accurate XYZ positions tacked on at N-terminus without resorting to generating an Alphafold model? I am also thinking ISOLDE won't work.

3 2

Problem using a python script to run chimeraX (installation?)
by Collignon, Bar /FR 12 Jul '23

12 Jul '23

Hello, I am picking up an old code that used chimera and updating it to use ChimeraX. Our code writes a python script file that looks like : import chimera from chimera import runCommand runCommand("open ../4ZKC_H_reduce.pdb") runCommand("swapaa LYS #0:11.B&:LYS lib dynameomics") runCommand("swapaa TRP #0:51.B&:TRP lib dynameomics") runCommand("write #0 ../4ZKC_H_reduce.pdb") and executes chimera --nogui --nostatus --script python_script.py I installed ChimeraX on Ubuntu 22.01 with the .deb from your website and "sudo apt install chimerax.deb" When i execute ChimeraX with my script, i get : available bundle cache has not been initialized yet Executing: runscript chim_4ZKC_H_reduce.py Traceback (most recent call last): File "chim_4ZKC_H_reduce.py", line 2, in <module> from chimera import runCommand ModuleNotFoundError: No module named 'chimera' Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/scripting.py", line 84, in open_python_script _exec_python(session, code, argv) File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/scripting.py", line 61, in _exec_python exec(code, sandbox.__dict__) File "chim_4ZKC_H_reduce.py", line 2, in <module> from chimera import runCommand ModuleNotFoundError: No module named 'chimera' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 747, in init run(sess, 'runscript %s' % script) File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/runscript.py", line 38, in runscript open_python_script(session, open(script_file, 'rb'), script_file, argv=argv) File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/scripting.py", line 90, in open_python_script raise UserError('Error opening python file %s' % stream.name) chimerax.core.errors.UserError: Error opening python file chim_4ZKC_H_reduce.py I tried installing chimera using pip but it installs Chimera (the one in python 2.7) and crashes during the installation. Any ideas on how to fix this? Did i do something wrong somewhere? Thanks you very much for your help, Bar Collignon

2 3

Chimera X: Gui based Movie making Function
by khawar siddiqui 06 Jul '23

06 Jul '23

2 2

color interior of helix on cartoons?
by Barrett, Susanna Elizabeth 06 Jul '23

06 Jul '23

Hello, On the old chimera, it was very simple to color the interior of cartoon helices, but I cannot seem to find the documentation for this on chimeraX. Could you please tell me how to do this? Thank you! Best, Susanna Barrett (she/her/hers) PhD candidate in chemistry at UIUC - Mitchell lab NSF Graduate Research Fellow Chemical-Biology Interface Training Program Fellow

3 3

Graphical Window
by Shubham Devesh Ramgoolam 06 Jul '23

06 Jul '23

Hi all, I hope you are doing well. If I hover my mouse over a structure in the graphical window of chimeraX, a short text is loaded revealing information about the residue/atom/bond my mouse is hovering on. I want to take advantage of this feature, but I want to perform a task different from the default one but still specific to the part of the structure my mouse is hovering on. As of now, I don't really know how to go about this and I am trying to locate the scripts that encode the original feature just so I can get an idea of how to go about this. Could you please help locate those scripts (if possible)? Regards, Shubham

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help
by Walton, Travis Steven 06 Jul '23

06 Jul '23

Dear ChimeraX, Please unsubscribe me from the mail list. Thanks. Travis ________________________________ From: chimerax-users-request(a)cgl.ucsf.edu <chimerax-users-request(a)cgl.ucsf.edu> Sent: Tuesday, July 4, 2023 3:00 PM To: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Subject: ChimeraX-users Digest, Vol 79, Issue 2 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. Re: [Chimera-users] Opening MTZ files on Mac OS (Elaine Meng) 2. Coloring proteins by Ca rmsd when they have different sequences (Vorländer) 3. Re: Coloring proteins by Ca rmsd when they have different sequences (Elaine Meng) 4. Re: Coloring proteins by Ca rmsd when they have different sequences (Elaine Meng) 5. Extract settings/parameters from a chimerax cxs session file (alan.cheung(a)bristol.ac.uk) ---------------------------------------------------------------------- Message: 1 Date: Mon, 3 Jul 2023 19:24:07 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: [chimerax-users] Re: [Chimera-users] Opening MTZ files on Mac OS To: Natalie Walsh <natalie.walsh(a)slu.edu> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu>, ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Message-ID: <56AC7019-083A-43B6-97DE-B674733A0561(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Natalie, This is a ChimeraX question, although sent to the chimera-users list -- although unnecessary this time, for future reference please send chimeraX questions to the chimerax-users(a)cgl.ucsf.edu list CC'd here (we try not to confuse Chimera users with ChimeraX answers and vice versa). The instructions of how to open MTZ files with ChimeraX are here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper> "Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 3, 2023, at 8:52 AM, Natalie Walsh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > > I am having troubles opening MTZ maps from PDB on ChimeraX 17.1. on Mac OS. I read somewhere that you need to download the Clipper plug-in. I went ahead and installed that (although I am not sure that I was successful) and am still struggling to open these files. > > Thank you, > Natalie Walsh ------------------------------ Message: 2 Date: Tue, 4 Jul 2023 14:02:10 +0000 From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at> Subject: [chimerax-users] Coloring proteins by Ca rmsd when they have different sequences To: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> Message-ID: <3944043A-628C-43CD-8A65-67B361695EDB(a)imp.ac.at> Content-Type: multipart/alternative; boundary="_000_3944043A628C43CD8A6567B361695EDBimpacat_" Hi all, I would like to color proteins by the Ca-RMSD after aligning them, and found the Youtube tutorial on how to do this for proteins with identical sequence. However, I would like to compare structures from different species, as for example done in Figure 2 in this paper https://www.sciencedirect.com/science/article/pii/S0959440X16302408?via%3Di… . Is this possible in ChimeraX? Many thanks, Matthias

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Fourier transform tool in chimeraX?
by Das, Abhinaba 06 Jul '23

06 Jul '23

Dear ChimeraX community, I stumbled upon a link<https://www.cgl.ucsf.edu/chimera/data/downloads/1.2470/docs/ContributedSoft…> discussing a Fourier Transform tool in Chimera. However, I encountered an issue while trying to locate it in my Chimera version (running the command "start Fourier Transform" resulted in an error). My objective is to generate a Fourier space diffraction pattern of a helical reconstructed volume by performing its Fourier transform. I am curious to know if this functionality is available in either Chimera or ChimeraX. Could you kindly provide some guidance on this matter? Thank you in advance for any advice. Abhi

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Coloring proteins by Ca rmsd when they have different sequences
by Vorländer,Matthias Kopano 05 Jul '23

05 Jul '23

Hi all, I would like to color proteins by the Ca-RMSD after aligning them, and found the Youtube tutorial on how to do this for proteins with identical sequence. However, I would like to compare structures from different species, as for example done in Figure 2 in this paper https://www.sciencedirect.com/science/article/pii/S0959440X16302408?via%3Di… . Is this possible in ChimeraX? Many thanks, Matthias

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Extract settings/parameters from a chimerax cxs session file
by alan.cheung＠bristol.ac.uk 04 Jul '23

04 Jul '23

Hi All - apologies if this has been answered before, couldn't find it with search. I have a session file with very nicely formatted views/lighting/graphics settings, but i'd like to duplicate them for another (new) session. I can't remember what i set! And it's not in the log. Is there a way to get ChimeraX to return these values (or indeed, all parameters) for the current session? I imagine this might be useful generally too. Alan

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Re: [Chimera-users] Opening MTZ files on Mac OS
by Elaine Meng 03 Jul '23

03 Jul '23

Hi Natalie, This is a ChimeraX question, although sent to the chimera-users list -- although unnecessary this time, for future reference please send chimeraX questions to the chimerax-users(a)cgl.ucsf.edu list CC'd here (we try not to confuse Chimera users with ChimeraX answers and vice versa). The instructions of how to open MTZ files with ChimeraX are here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper> "Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 3, 2023, at 8:52 AM, Natalie Walsh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > > I am having troubles opening MTZ maps from PDB on ChimeraX 17.1. on Mac OS. I read somewhere that you need to download the Clipper plug-in. I went ahead and installed that (although I am not sure that I was successful) and am still struggling to open these files. > > Thank you, > Natalie Walsh

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Re: ChimeraX-users Digest, Vol 78, Issue 54
by Fabian Bumbak 30 Jun '23

30 Jun '23

leave On Sat, 1 Jul 2023 at 10:45, <chimerax-users-request(a)cgl.ucsf.edu> wrote: > Send ChimeraX-users mailing list submissions to > chimerax-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via email, send a message with subject or > body 'help' to > chimerax-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimerax-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of ChimeraX-users digest..." > > Today's Topics: > > 1. Re: Volume Series tool missing (Elaine Meng) > 2. Re: Volume Series tool missing (Jarrett Bowman) > 3. ChimeraX Questions (Bani Kaur) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 Jun 2023 13:14:56 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: [chimerax-users] Re: Volume Series tool missing > To: Jarrett Bowman <jarrettbow(a)gmail.com> > Cc: chimerax-users(a)cgl.ucsf.edu > Message-ID: <D9C12F1F-8A96-428D-B572-4D0E83ACD5EA(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Jerry, > The picture shows that the video tutorial you are viewing is for Chimera, > not ChimeraX. Chimera and ChimeraX are two different programs. > > ChimeraX does not have a GUI tool, as you said, but it does have volume > series capabilities via the "vseries" command, see both of the following > and links therein: > > <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html> > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jun 30, 2023, at 12:46 PM, Jarrett Bowman via ChimeraX-users < > chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hello, > > I am trying to use the volume series tool on ChimeraX version 1.6.1 for > Windows. It doesn't appear to be in my download of ChimeraX possibly along > with other tools. A tutorial I am following shows this picture: > > > > <image.png> > > > > While this is what I have: > > > > <image.png> > > > > Any help would be greatly appreciated! > > > > Jerry Bowman > > > > ------------------------------ > > Message: 2 > Date: Fri, 30 Jun 2023 14:49:14 -0600 > From: Jarrett Bowman <jarrettbow(a)gmail.com> > Subject: [chimerax-users] Re: Volume Series tool missing > To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Message-ID: > <CAFN=EO2pGxSNMRJ=ChH+QTG+WSH-G8oshP41fJtKbTBD= > DF_aw(a)mail.gmail.com> > Content-Type: multipart/alternative; > boundary="000000000000d3119b05ff5ef3b8" > > Elaine, > > Thanks! The links helped a bunch > > On Fri, Jun 30, 2023 at 2:15 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > Hi Jerry, > > The picture shows that the video tutorial you are viewing is for Chimera, > > not ChimeraX. Chimera and ChimeraX are two different programs. > > > > ChimeraX does not have a GUI tool, as you said, but it does have volume > > series capabilities via the "vseries" command, see both of the following > > and links therein: > > > > <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html> > > > > Best, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Jun 30, 2023, at 12:46 PM, Jarrett Bowman via ChimeraX-users < > > chimerax-users(a)cgl.ucsf.edu> wrote: > > > > > > Hello, > > > I am trying to use the volume series tool on ChimeraX version 1.6.1 for > > Windows. It doesn't appear to be in my download of ChimeraX possibly > along > > with other tools. A tutorial I am following shows this picture: > > > > > > <image.png> > > > > > > While this is what I have: > > > > > > <image.png> > > > > > > Any help would be greatly appreciated! > > > > > > Jerry Bowman > > > > >

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ChimeraX Questions
by Bani Kaur 30 Jun '23

30 Jun '23

Hi, I hope you are doing well! My name is Bani Kaur and I am an active user of ChimeraX for a research project concerning protein modeling, specifically with the CFTR protein. I have been running into issues with showing atoms on my residue, specifically after I change the romater. I am not sure what to do about this as I have downloaded the latest version of ChimeraX. I have attached a photo where the left one is the selected residue (Thr) and the right photo is the residue when it is changed to Ile. [image: Screen Shot 2023-06-30 at 5.38.22 PM.png] Additionally, I am not able to see clashes for some very reason and am only able to see it when limit by selection is unchecked, but for my research project, we require that it is checked in the clashes settings. I have attached a photo of the settings. [image: Screen Shot 2023-06-30 at 5.39.01 PM.png] Thank you so much for your help! Best, Bani Kaur

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Volume Series tool missing
by Jarrett Bowman 30 Jun '23

30 Jun '23

Hello, I am trying to use the volume series tool on ChimeraX version 1.6.1 for Windows. It doesn't appear to be in my download of ChimeraX possibly along with other tools. A tutorial I am following shows this picture: [image: image.png] While this is what I have: [image: image.png] Any help would be greatly appreciated! Jerry Bowman

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toolshed plugin upload - disk quota exeeded
by Lugmayr, Wolfgang 30 Jun '23

30 Jun '23

hi, i tried to upload a new starmap release and run into the following error: OSError at /submit_app/ [Errno 122] Disk quota exceeded: '/usr/local/projects/chimerax/www/production/cxtoolshed3/media/pending_releases/ChimeraX_StarMap-1.2.15-py3-none-any.whl' Request Method: POST Request URL: https://cxtoolshed.rbvi.ucsf.edu/submit_app/?expect_app_name=ChimeraX_StarM… Django Version: 4.2.1 Exception Type: OSError Exception Value: [Errno 122] Disk quota exceeded: '/usr/local/projects/chimerax/www/production/cxtoolshed3/media/pending_releases/ChimeraX_StarMap-1.2.15-py3-none-any.whl' Exception Location: /wynton/home/ferrin/cxtoolshed/production-site/lib/python3.8/site-packages/django/core/files/move.py, line 63, in file_move_safe Raised during: cxtoolshed3.submit_app.views.submit_app Python Executable: /usr/bin/python3 Python Version: 3.8.16 Python Path: ['/usr/lib64/python38.zip', '/usr/lib64/python3.8', '/usr/lib64/python3.8/lib-dynload', '/wynton/home/ferrin/cxtoolshed/production-site/lib64/python3.8/site-packages', '/wynton/home/ferrin/cxtoolshed/production-site/lib/python3.8/site-packages', '/usr/lib64/python3.8/site-packages', '/usr/lib/python3.8/site-packages', '/usr/local/projects/chimerax/www/production'] Server time: Fri, 30 Jun 2023 04:53:50 -0700 can you please have a look at the problem? cheers, wolfgang -- Multi-User Cryo-EM Facility @ Centre for Structral Systems Biology (CSSB) @ Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 Gebäude 15 (E.247) 22607 Hamburg, Germany Tel.: +49 40 8998-87706 Email: wolfgang.lugmayr(a)cssb-hamburg.de http://www.cssb-hamburg.de/

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Constrained Movement
by Derek Ng 29 Jun '23

29 Jun '23

Hi, Thanks so much for ChimeraX! The tool is amazing so far. Is it possible to do the Constrained Movement GUI feature from the old Chimera in ChimeraX? I couldn’t find it in the GUI nor documentation. Thanks in advanced! Derek

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alphafold PAE map color (bluered), alphafold contacts palette option and selecting interacting residues under certain PAE values
by ahramkim1128＠gmail.com 29 Jun '23

29 Jun '23

Dear ChimeraX team, I have been working with analyzing AlphaFold-predicted structures in ChimeraX and have a few queries/suggestions. 1. Color palette for PAE Maps: One of the outputs from ColabFold is a PAE map rendered in a blue-white-red color palette. I find this color scheme very useful, and the command "alphafold pae #1 palette bluered" is working well for changing the color gradient into blue-white-red in PAE map. I was wondering if it could be integrated as a clickable option in the PAE map settings in ChimeraX, similar to the existing "Color plot rainbow" or "Color plot from structure" options. 2. Alphafold contacts color palette: I'm also interested in changing the color palette for alphafold contacts to match the bluered color scheme. While I attempted to change the color palette using the command "alphafold contact #1 /A to /B distance 5 palette bluered", it resulted in all contacts being colored red, without the expected color gradient. I'm curious if there's an alternative approach or if this could be an added feature in future updates. 3. Residue selection and visualization based on PAE cut-off: Lastly, I'm looking for a method to selectively visualize the connections between certain residues based on a PAE cut-off. For example, using the command "alphafold contacts /A to /B distance 5", I can visualize all the residue connections between A and B under a distance of 5. However, this also displays connections that are poorly predicted (i.e., yellow or red lines corresponding to PAE >15). I'd appreciate if you could suggest a way to filter these poorly predicted connections or provide an option for this in the software. Thank you in advance! Best regards, Ah-Ram

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Measuring Tilt of Helices
by Das, Abhinaba 29 Jun '23

29 Jun '23

Dear ChimeraX users, I’m trying to measure the tilt of the helices with respect to the helical axis (i.e. the z-axis). As depicted in the image below, I was wondering if it would be possible to draw a line parallel to the z-axis, traversing through the stack of helices, and another perpendicular to the z-axis and finally measure the angle between the axis passing through the helix (generated by define axis command) and the perpendicular drawn to the z-axis. [cid:image001.png@01D9A9E2.A0B8D0F0] Thanks in advance Abhi

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Daily build issues
by BARRY E DEZONIA 29 Jun '23

29 Jun '23

Hello, My colleague and I are trying to install daily build(s) of chimerax. A few weeks ago, on Ubuntu 20.04, I installed the daily build for that OS just fine. Now I am trying to show my work to a colleague. We need a daily build because our work relies on a bug fix that was recently made. Anyhow he is on ubuntu 22.04 and needs to install the version appropriate for his OS. When we do so it complains that "libssl3" is missing. And when we find instructions on how to install it apt says the dependency for "glibc" can't be satisified because the version required is newer than the one installed. Now rather than messing with my colleague's system too much I'd like to know your recommendations for getting the daily build installed. Thanks.

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IMOD Generated Model and Tomogram are Offset
by Guilliams,Bradley 29 Jun '23

29 Jun '23

Hi All, I have been working with a tomogram and corresponding model in IMOD and when I load these files into ChimeraX the model and tomogram are offset (see included image). At the highest plane of the tomogram, it intersects roughly halfway up the model. Any advice on how to fix this would be much appreciated! Cheers, Bradley Bradley Guilliams (he/him/his) PhD Candidate Ackerson Research Group Analytical Resources Core - Imaging & Surface Science (ARC-ISS) Department of Chemistry Colorado State University

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Save only the sequence that is present in the model
by Eric Pettersen 28 Jun '23

28 Jun '23

> Begin forwarded message: > > From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> > Subject: Save only the sequence that is present in the model > Date: June 28, 2023 at 6:53:11 AM PDT > To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> > > > Dear ChimeraX team, > > I would like to save only the sequence of a chain that is actually modelled. As I would like to do this for many files it would be great if this would work via scripting. Is this possible? > > Many thanks, > Matthias

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Docking scores only as integers??
by thomas.wein＠lmu.de 28 Jun '23

28 Jun '23

Dear all, I'm reading glide Docking results into ChimeraX. In the ViewDockX table or charts the docking score is displayed only as integers. However, typical score valus are "-4.1234" or "-8.9876", I only see the "-4.000" etc. For the correct numbers I have to go into the original files which is somehow time consuming. Is there any possibility to get a "real" score value displayed? Thanks Thomas

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Combining two volumes
by Tom Goddard 28 Jun '23

28 Jun '23

Tatiana writes: Dear ChimeraX developers, I would like your help to combine two volumes in ChimeraX while keeping the properties of each volume (colour, threshold...). I know it's borderline in ChimeraX, but it seems feasible. I have been playing with morph, vop commands and a lot of information found on the web for several days, but I fail. I'm also asking chapGPT... but I can't manage to combine my two volumes. Could you please help me to combine these two attached volumes. If yes, could you please send me the procedure And one more questions related to this question, How to know the name of the slider after vop morph command to synchronise 2 morph and record a movie. I found a way to do it on the web (via the Tools menu and selecting General Controls to open the General Controls panel. In the General Controls panel you will find various sliders) but I don't have this General Controls menu in ChimeraX. Thank you very much if you have time to help me. Tatiana

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