- ChimeraX-users - RBVI Mailing Lists

How to gradually crop a volume with perframe command
by Edoardo D Imprima 24 Jun '22

24 Jun '22

Hi all, I would like to make a movie showing a volume gradually cropped along one axis .e.g. volume #1 region 0,0,0,410,375,336 (start) volume #3 region 0,0,0,410,375,31 (end). Could you please tell me how to provide the range in “perframe” command to perform this operation? Ie as trying something like this perframe "volume #1 region $1" 0,0,0,410,375,200 0,0,0,410,375,336 frames 10 without success though. Many thanks in advance, Edoardo ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

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user inputs for python scripts
by Pranav Shah 24 Jun '22

24 Jun '22

Hi Team, Is there a way to provide user input to python script files? I tried using sys.argv but I keep getting an out of list error message when I call the script from the ipython shell (accessed from within the chimeraX window) Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Version 1.4 for CentOS 7?
by Ricardo Righetto 24 Jun '22

24 Jun '22

Hi, First, apologies if this has already been announced elsewhere. I see on the download webpage that there is no production release for CentOS 7 and the latest daily release for this platform was built on 2022-05-06. Any chance we could get a production release of 1.4 and/or a newer daily build for CentOS 7? Thank you very much! Best wishes, -- Ricardo Diogo Righetto

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How to show fib-sem tomography data as solid volume
by Edoardo D Imprima 23 Jun '22

23 Jun '22

Hello, Could you please tell me how to display fib-sem tomography data as a compact volume that can be navigated by sliding planes? The data consists of a series of frames that I can convert as .mrc volume or .mrcs stack. I attach a snapshot taken from a review that illustrates (middle panel) the visualisation I would like to obtain. The medical-image panel in ChimeraX is very handy however, the “full” option shows the volume while I need to display the planes of each side to slice through them. Looking forward to your feedback, Best wishes, Edoardo ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

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where can I find the mesh option in chimeraX?
by 王超 23 Jun '22

23 Jun '22

Dear All,I want to setting the mesh option in ChimeraX like "Chimera way".Like "open Volume Viewer of a map, and click features-data display option".but I cannot find toolbar of Volume Viewer, I am puzzle where to find it?

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Chimera question
by Daniel VillanuevaAvalos 23 Jun '22

23 Jun '22

Hello, I am trying to create a spirosome, and I am entering *sym #1 h,56.5,164.4,12* but the radius of the helix is wrong. How can I change it? What I am trying to do is move my obj closer to origin but I cannot find a way to do that. I can only move the pivot to center with *cofr 0,0,0*. Thank you, Daniel.

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quality of life imporovement suggestion for view matrix output
by Pranav Shah 22 Jun '22

22 Jun '22

Hi Team, I use the view matrix command regularly to save orientation of the maps/models in a command file. As it currently stands, the output needs to be formatted appropriately so that the command can be run. As a one off, it is trivial to format the output from the log window into an appropriate format but, when it has to be done repeatedly as is my case it becomes quite annoying. Therefore, I was wondering if you would agree to format the output so that it can be directly copy pasted in a ready to use format? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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alphafold in Google colab
by Roberto Marabini 20 Jun '22

20 Jun '22

Hi, Starting today, when I try to execute AlphaFold calculations using Google Colab, I get the message: ====== ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. kapre 0.3.7 requires tensorflow>=2.0.0, which is not installed. xarray-einstats 0.2.2 requires numpy>=1.21, but you have numpy 1.19.5 which is incompatible. datascience 0.10.6 requires folium==0.2.1, but you have folium 0.8.3 which is incompatible. albumentations 0.1.12 requires imgaug<0.2.7,>=0.2.5, but you have imgaug 0.2.9 which is incompatible. Successfully installed absl-py-0.13.0 biopython-1.79 chex-0.0.7 dm-haiku-0.0.4 dm-tree-0.1.6 docker-5.0.0 flatbuffers-1.12 gast-0.4.0 grpcio-1.34.1 immutabledict-2.0.0 jax-0.2.14 keras-nightly-2.5.0.dev2021032900 ml-collections-0.1.0 numpy-1.19.5 pandas-1.3.4 scipy-1.7.0 tensorflow-cpu-2.5.0 tensorflow-estimator-2.5.0 typing-extensions-3.7.4.3 websocket-client-1.3.3 wrapt-1.12.1 + pip3 install --upgrade jaxlib==0.3.2+cuda11.cudnn82 -f https://storage.googleapis.com/jax-releases/jax_releases.html Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/ Looking in links: https://storage.googleapis.com/jax-releases/jax_releases.html ERROR: Could not find a version that satisfies the requirement jaxlib==0.3.2+cuda11.cudnn82 (from versions: 0.1.23, 0.1.29, 0.1.32, 0.1.40, 0.1.41, 0.1.42, 0.1.43, 0.1.44, 0.1.46, 0.1.50, 0.1.51, 0.1.52, 0.1.55, 0.1.56, 0.1.57, 0.1.58, 0.1.59, 0.1.60, 0.1.61, 0.1.62, 0.1.63, 0.1.64, 0.1.65, 0.1.66, 0.1.67, 0.1.68, 0.1.69, 0.1.70, 0.1.71, 0.1.72, 0.1.73, 0.1.74, 0.1.75, 0.1.76, 0.3.0, 0.3.2, 0.3.5, 0.3.7, 0.3.8, 0.3.10) ERROR: No matching distribution found for jaxlib==0.3.2+cuda11.cudnn82 ======= The error seems to be obvious but, can someone point me towards a solution? Thanks Roberto

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Research associate / Group leader position at the University of Luebeck (Northern Germany)
by Guido Hansen 20 Jun '22

20 Jun '22

The Institute of Biochemistry (Director: Univ.-Prof. Dr. Thomas Krey) at the University of Luebeck has an opening for a position as a *Research associate / Group leader (m/w/d)* in full-time (currently 38.7 hours per week) for an initial period of 4 years. Within the position, the opportunity for further qualification (habilitation) is given. *Main areas of activity:* * Own research (incl. acquisition of third-party funding) on topics in structural infectiology * Supervision of technical assistants, bachelor, master and doctoral theses * Co-responsibility for the cryo-electron microscope planned at the site * Organisation and implementation of teaching (in English) in biochemistry for the Molecular Life Sciences programme (lectures, practicals, seminars, performance review and booking, preparation of certificates) * Participation in teaching (in German) in biochemistry for medical students (lectures, practicals, seminars and their performance review and booking) *Requirements:* * Completed university degree in a natural science or medical programme, e.g. biochemistry, molecular life sciences, chemistry or biology. * Completed or nearly completed PhD thesis in natural sciences (defense in 2022), preferably in the field of structural infectiology * Proven research focus in the field of structural infectiology * Experience in the field of cryo-electron microscopy * Experience in teaching natural sciences and/or human medicine (in German and English) More information can be found here https://www.biochem.uni-luebeck.de/fileadmin/files/pdf/Ausschreibung1043-22… Please contact Prof. Dr. Thomas Krey (krey(a)biochemie.uni-luebeck.de) for any further questions, and send your written application with the usual documents (cover letter with research interests, curriculum vitae, references) summarised in a single PDF document by July 4^th , 2022 (*date of receipt*) at the latest to*bewerbung(a)uni-luebeck.de*, quoting the reference number*1043/22*. Best wishes Thomas *Prof. Dr. Thomas Krey* University of Luebeck *University of Lübeck Institute of Biochemistry* phone: +49-451-3101-3100 fax: +49-451-3101-3104 e-mail: krey(a)biochem.uni-luebeck.de <mailto:krey@biochem.uni-luebeck.de> www.biochem.uni-luebeck.de <http://www.biochem.uni-luebeck.de> Ratzeburger Allee 160 23562 Lübeck Germany -- Re: email signature

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The ChimeraX Toolshed is temporarily down
by Greg Couch 17 Jun '22

17 Jun '22

Due to database corruption. Hope to have it back up soon. -- Greg

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ChimeraX: chashes in no-gui execution
by Enrico Martinez 17 Jun '22

17 Jun '22

Dear ChimeraX users! I noticed that sometimes ChimeraX crashes while being executed in batch mode using bash script. Here is an example of my script that calculates hbonds and contacts between protein and ligand open mypdb.pdb #calculate h-bonds and contacts in each frame hbonds #1.1-24&protein restrict #1.1-24&ligand coordsets false interModel false makePseudobonds false log true distSlop 0.5 angleSlop 20 intraRes false saveFile hbondsALL_rep1.log clashes #1.1-24&protein& :41,49 restrict #1.1-24&ligand overlapCutoff 0.3 interModel false makePseudobonds false log true intraRes false saveFile contactsALL_rep1.log wait wait exit as you may see I added two times wait in the end of the script that could reduce the frequency of crashes. May you specify what is the default value for each wait (in seconds??) and how I could use just one wait command to set up the pause in the proper way? Many thanks in advance! Cheers Enrico

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Centos7 version of ChimeraX version 1.4 possible?
by Martin Moche 16 Jun '22

16 Jun '22

Dear ChimeraX developers, Thanks for an outstanding piece of software! Is it possible to have a CentOS7 variant of version 1.4 of ChimeraX? Best regards, Martin Head of Macromolecular X-ray Crystallography<https://ki.se/en/mbb/psf-mx> | Protein Science Facility<https://ki.se/en/mbb/protein-science-facility> Medical Biochemistry and Biophysics<https://ki.se/en/mbb/department-of-medical-biochemistry-and-biophysics> 171 65 Solna | Solnavägen 9 +46 8 524 868 43 | +46 73 322 93 27 martin.moche(a)ki.se<mailto:martin.moche@ki.se> | ki.se<https://ki.se/> ______________________________________ Karolinska Institutet - a medical university När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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ChimeraX 1.4
by Eric Pettersen 11 Jun '22

11 Jun '22

UCSF ChimeraX version 1.4 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/ This will be the last release to support macOS 10.14 (Mojave). Also, ChimeraX 1.4 is not available for CentOS 7, Ubuntu 16.04 and 18.04 because the Qt 6 window toolkit does not support those older Linux distributions. Updates since version 1.3 (Dec 2021) include: - search/retrieve from EBI AlphaFold DB 3rd release, ~1 million structures - display AlphaFold predicted aligned error (PAE) plots - can BLAST UniRef100,90,50 (+ previous choices AlphaFold, PDB, NR) - AlphaFold prediction of multimers (of limited size) on Google Colab - independent centers of rotation available as mouse mode - join models with Build Structure tool or command - define axes for display and/or use in measurements - increase/decrease VDW radii relative to their current values - switch PDB residue numbering scheme (author/canonical/uniprot) - align sequences with Clustal Omega or MUSCLE - calculate % identity in sequence alignments - window toolkit updated to Qt 6.2.3 from 5.15.2 For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

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Saving PDB file as a string
by Sophie Liu 08 Jun '22

08 Jun '22

Hi, My organization has some extra information at the end of a PDB file that I would like to be printed onto the Log Console of ChimeraX. I am currently writing a bundle to do so by adding a command (however if this is best implemented by overriding the open command for PDB files then I would switch to that). I am wondering how I can have the bundle work like so: 1. the user types a command call it, "showdata" 2. the bundle would read all Models (that are pdb files) that are being displayed 3. for each model it would read the PDB text file, and say go to indices 200-251 of the string and display that in the Log console I hope this makes sense. I am mainly struggling on how to access the original PDB text of the model. Best, Sophie

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Licensed software source
by Jeya Priya Senthilkumaran 07 Jun '22

07 Jun '22

Hi Community, To use ChimeraX licensed software. I have few queries Do we have a separate source {tar file} to be downloaded or the same source from https://www.cgl.ucsf.edu/chimerax/download.html should be used? While purchasing the license, will we be provided with separate source to download the software? We have bought license, now we need to upgrade to newer version of ChimeraX ,do we have instructions to upgrade to the newer version? In case, we have installed open source of the software, how should we upload the license to the ChimeraX? Kind Regards, Jeya Priya Scientific Cloud Computing [cid:image001.png@01D874F0.89D1F100]<https://www.zifornd.com/> [cid:image002.png@01D874F0.89D1F100] M +91 8098223555 [cid:image003.png@01D874F0.89D1F100] www.zifornd.com<http://www.zifornd.com/> [cid:image004.png@01D874F0.89D1F100] IST (Time Zone) [cid:image005.png@01D874F0.89D1F100] Follow us on [cid:image006.png@01D874F0.89D1F100]<https://www.linkedin.com/company/zifo-technologies/> ******************* CAUTION ******************* This e-mail is intended exclusively for the individual(s) to whom it is addressed and may contain information that is PRIVILEGED and CONFIDENTIAL. If you are not the intended recipient, please notify the sender and delete the original message. Further, you are not to copy, disclose or disseminate this e-mail or the information contained to any other person and any such actions are unlawful. Zifo Technologies has taken every reasonable precaution to ensure that this e-mail and attachment(s) has been swept for viruses, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment(s). Zifo Technologies is neither liable for the proper and complete transmission of the information contained in this e-mail nor for any delay in its receipt. *************************************************

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Save the map after surface dust
by Dai, Xin 07 Jun '22

07 Jun '22

Dear ChimeraX developers, I'm trying to save a density map following the command "surface dust". However, the map saved remains to be the original one. Is there any command to save the cleaned map? I found this old post http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html asking the same question using Chimera. But unfortunately, it's not working for me. Thank you, Xin

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Analog of Chimera "addcharges" command in ChimeraX
by Rafi Brent 07 Jun '22

07 Jun '22

To whom it may concern, I have about 20,000 pdb files to which I'd like to add Hydrogens, add partial charges, and convert to the mol2 format using either Chimera or ChimeraX. I have not had much success with Chimera, as the process slows down quite drastically over time when run through the GUI, and when I run Chimera from the terminal (using chimera --nogui python_script.py), I run into errors with ANTECHAMBER that do not occur when my script is run through the GUI. I'll write to the Chimera support email with more details, and I'd appreciate any advice if you have any, but based on these errors I'm thinking that there is likely a better way to perform this task using ChimeraX. I noticed that the "addcharges" command no longer exists in ChimeraX, and the "write" command which I was using to convert to mol2 files in Chimera appears to have been replaced as well. Because of this, any recommendations about how to run my operation using the closest analogs to the original Chimera methods would be greatly appreciated. Thanks so much for any advice you may have. Sincerely, Rafi Brent

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Docking window for html viewer automacially
by Shubham Devesh Ramgoolam 04 Jun '22

04 Jun '22

Hi all, I hope you are doing well. I am using the following code to open chimeraX along with an HTML file when a condition is met: subprocess.call([path_chimeraX, path_html]) Now, in this scenario, is it possible include some codes(perhaps as arguments for subprocess?) that will dock the window for the HTML viewer automatically while also hiding the log and command line interface upon startup of chimeraX? Or should I use a different approach? Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Rescaling IMOD segmentation models in ChimeraX
by Martinez, Matthew 03 Jun '22

03 Jun '22

Hi everyone, I have a question regarding the rescaling of data in ChimeraX. I'm depicting a subtomogram average at their aligned positions in a tomogram, which doesn't contain scaled pixel information, and I want to also load in IMOD segmentation data to depict with the subtomogram average. I'm able to readjust the pixel size of the tomogram easily with the Map Coordinates dialog box, but is there a way to rescale IMOD segmentation models once in ChimeraX? I can do this within IMOD, but it would be more convenient to do it in ChimeraX with the volume. Thanks in advance for any help! Best regards, Matt

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Isolde | ARG Sidechain Bond Angle Outliers
by Anderson, Jacob 31 May '22

31 May '22

I have been using Isolde inside Chimerax 1.3 - it works fantastic! However, when I go to validate on OneDep, invariably all the ARG have outliers, specifically the NE-CZ-NH1 bond angle. Has anyone else observed this and overcome it? Perhaps something wrong with my build?

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ChimeraX - XMAS pluggin modification questions
by Moya Clark, I.O. de (Isabel) 31 May '22

31 May '22

Good morning, I am a student intern at the Richard Scheltema Laboratory, and I am going to be continuing with the modification of the XMAS bundle submitted to ChimeraX recently. Right now, we are trying to extend the bundle to be able to extract specific distances between specific amino acids for two different proteins but for a molecular dynamics simulation. Either by loading a trajectory coordinates + topology files or by using the “morph” command and then “coordset slider”. So, the idea would be to extract the distances between the alpha carbons, of a set of pre-selected amino acids, in each frame of the simulation. Do you have any suggestions about any modules or methods that I should look into to extract this information in each frame? I saw there is a CooordSets class but I do not know if this would be the right way to go about it. Kind regards, Isabel de Moya Clark

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no text in log gui after ubuntu 22.04 upgrade
by Sean Connell 30 May '22

30 May '22

Hi, I was wondering if you have some suggestions for me to solve a problem I have after upgrading to ubuntu 22.04. I am running UCSF ChimeraX version: 1.3 (2021-12-08) and after upgrading ubuntu the log window in the GUI has no text. If I use the command "log save chimerx.html" and open chimerax.html in a browser I can see everything I expect in the log. It is just not being displayed. I installed using the Ubuntu 20.04 (Linux) 64-bit deb on the download page. many thanks for your help in advance sean -- --------------------------------- Sean Connell, PhD Ikerbasque Associate Structural Biology Unit, BioCruces Bizkaia Health Research Institute, Plaza Cruces s/n, 48903, Barakaldo, Spain Phone: +34 634 623 493 sean.connell(a)gmail.com https://www.biocrucesbizkaia.org <https://www.biocrucesbizkaia.org/areas-investigacion/bc3.19> frozenribosomes.com ---------------------------------

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Filled helix tube when clipped
by Zheng Ruan 27 May '22

27 May '22

Dear ChimeraX users, I'm curious to know if there is a way to have the helix tube filled when after using the clip command? I know that the clip plane of surface representation can achieve this as found in this example (https://www.rbvi.ucsf.edu/chimerax/feature_highlights/pmc.png) However, I'm not able to make it when I display my structure in cartoon cylinder representation. I attached an example image that I made. Thank you for your input. Best, Zheng

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Nonstandard residues
by Abhilash Padvannil 27 May '22

27 May '22

Hi, I am trying to open PDB (multi subunit complex) from phenix refinement in ChimeraX. One of the chains is A7. While the PDB’s open normally in coot, ChimeraX recognizes a couple of chains as nonstandard residues and is showing XXXX for the entire length of the amino acid sequence (ALA as ALAA 7 , MET as META 7) and so on. The residues correspond to subunit with chain ID A4. Attached is the sequence view Please suggest how to fix this. Thanks Abhilash. [cid:10AB2EAB-7B93-4DBA-8BFF-7329E82724B0@mcb.ucdavis.edu]

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lighting Flat + ambiant Occlusion ?
by Thibault TUBIANA 27 May '22

27 May '22

Dear Chimera X community and developpers :) I would like to create a flat representation for a protein but with ambiant occlusion, a little bit like on the example joined (made with [ https://3dproteinimaging.com/ | https://3dproteinimaging.com ] ). Is it something that it is possible with ChimeraX ? I've been playing with the shaddows but the "flat effect" is disappearing then :/ Thank you :) Thibault. -- Thibault Tubiana, PhD Postdoctoral Fellow @ [ https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism… | IMAPP ] Institute for integrative biology of the cell ( [ https://www.i2bc.paris-saclay.fr/ | I2BC ] ) - CNRS UMR 9198

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chimerax-1.4-rc2022.05.25 generic Linux 64-bit doesn't work
by Xiaoguang Xue 27 May '22

27 May '22

Dear developers, It seems the most recent chimerax-1.4-rc2022.05.25 generic Linux 64-bit doesn't work correctly for me. I got the following errors: NOTE: Traceback (most recent call last): File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/ChimeraX_main.py", line 1021, in <module> exit_code = init(sys.argv) File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/ChimeraX_main.py", line 573, in init from chimerax.ui import initialize_qt File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/chimerax/ui/__init__.py", line 21, in <module> from .gui import MainToolWindow, initialize_qt, menu_capitalize File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/chimerax/ui/gui.py", line 130, in <module> from Qt.QtWidgets import QApplication ModuleNotFoundError: No module named 'Qt' BUG: ModuleNotFoundError: No module named 'Qt' File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/chimerax/ui/gui.py", line 130, in from Qt.QtWidgets import QApplication _See log for complete Python traceback._ Best, XG

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Coordset command not working in nogui mode
by Shubham Devesh Ramgoolam 26 May '22

26 May '22

Hi all, I hope you are doing well. I have a python script for measuring the distance between aromatic rings of specific residues for different frames of a trajectory. To measure the distance, I am first defining centroids at the center of aromatic rings and then use the command distance. This process is repeated for each frame to be analyzed. To navigate between frames, I am using the command ‘coordset #1 {desired frame}’. When executing the script in no gui mode, the centroids are always defined with respect to the residue’s location in frame 1 even though the command coordset has changed the frame. In gui mode, the script only works if a delay is created between changing the frame and defining the new centroids. I introduced that delay by asking for a dummy user input (I ran the script from python Shell): run(session, 'coordset #1 ' + {new_frame}) y = input('dummy') run (session, 'define centroid /A:8 & aromatic-ring radius 0.3 color yellow mass false name d1’) My chimeraX version: 1.4rc202205060510 (2022-05-06) Should I be using a different command for changing frames of trajectories when in nogui mode? Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Display the boundary of a density map
by C.J. 25 May '22

25 May '22

Hi, If a similar function to chimera to show the boundary of a density map in ChimeraX? In Chimera, it is in "Volume viewer" > "Features" > "Data display options" > "Show outline box using color" option. Thanks! Jianhao

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relative position of a marker
by C.J. 25 May '22

25 May '22

Hi, I place a marker in a cryoEM map with "Volume Tracer" tool. How can I know the relative position of the marker to the origin or center of the map? Thank you! Best, Jianhao

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Surface Coloring of EM density maps by radius
by Das, Sayan 25 May '22

25 May '22

Hi, I'm trying to figure out if there is any way to color the electron density map by radius(something similar to the surface color feature on Chimera) in ChimeraX. I'm trying to color the map of a virus from the center to the outside of the capsid proteins using a series of color range based on its radius from the center. Is this feature available in ChimeraX? Any leads will be helpful. Thanks, Sayan.

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Executing a script in chimerax python shell for an interactive session
by Shubham Devesh Ramgoolam 25 May '22

25 May '22

Hi all, I hope you are doing well. I have a python script that allows the user to visualize specific residue pairs. Here is an overview of how the script functions: * Ask the user to input the path of a .cxs file (created previously) and a text file containing the pairs to be visualized * Print the names of the pairs along a uniquely assigned number * Ask the user to input a number in order to visualize the pair assigned to it To run the script currently, I have to do the following: i)Open chimerax ii)Show the shell iii) Call the script from the shell Now, is it possible to include some codes in the script that would allow me to just open chimerax, click on File -> Open -> this script, and then the shell would show up and the execution would continue there? Right now, if I ran the script using File -> Open -> this script, I would get this error: Traceback (most recent call last): File "C:/Users/Shubham/Desktop/this_script.py", line 8, in session_path = input('Enter file (.cxs) to be visualized with path: \n') RuntimeError: input(): lost sys.stdin Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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How to get all values from Fit List table
by Ioannis Skalidis 25 May '22

25 May '22

Hello all, I am doing some fit searches in Chimera X and I would like to use the values reported not only for "Correlations and times found" (which is reported in the log and can be copied) but also the "Ave" and "Inside" values reported for each fit in the Fit list. But unfortunately, I cannot copy any of the values in the Fit List. Is there any workaround available so I can get all these values? Thanks a lot, Yiannis. -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

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Multi color information export for 3D printing in ChimeraX
by M. Elizabeth Stroupe 24 May '22

24 May '22

Hi- Is there a way to export the multi-color information in ChimeraX for 3D printing? I have figured out how to combine the .mtl and .x3d information in Chimera, but would like to use rendering in ChimeraX that is not available in Chimera. Thank you (and sorry if you have answered this a million times - I couldn't find it in the archive despite my best efforts!). Beth --- Dr. M. Elizabeth (Beth) Stroupe Professor, Department of Biological Science Director, Graduate Program in Molecular Biophysics Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306

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Assembling 2 proteins
by SANTOSH RAMA BHADRA RAO TATA 24 May '22

24 May '22

Hi, I would like to create a pentamer, how can I assemble 5 different proteins subunits into a pentamer. I was trying to use matchmaker but I couldn't. can you please help me with some video how to get in use it or if there is any other way to use the software and create pentamer please let me know. Thanking you, With best wishes, Tata Santosh Rama Bhadra Rao, PhD Scholar, C/O Prof Helen Irving, La Trobe university, Bendigo, Vic-3550, Australia. Email: 19807877(a)students.latrobe.edu.au; S.Tata(a)latrobe.edu.au Phone: 0499263974

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(no subject)
by Andrea Dallapè 24 May '22

24 May '22

Dear ChimeraX Team, I would like to ask you if there's a simple and easy method (without using external software) to label the steric clashes, as in the attached image (the red line between the ball densities). Thank you for your help and attention! Andrea

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Colouring submodels using a palette
by Lorena Zuzic 24 May '22

24 May '22

Hi all, I have a model that contains 256 submodels of a ligand across trajectory frames. I would like to colour the individual models using a palette (e.g., blue:orange) so that the time progression across frames is depicted in colour. Is there a way to assign palette range to submodels? Best wishes, Lorena

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Asking copyright for one of your picture
by Catherine Duverger 23 May '22

23 May '22

Hello, I'm a French artist and I want to ask you for using one of your picture in a project. How it's possible to use it for a double exposure photography in order to prepare an exhibition in Rennes France. I probably made a book in 200 ex. Thanks a lot to answer if it's possible. Catherine

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Selecting atoms outside (or inside) a density map's contour
by Mateusz Dobrychłop 23 May '22

23 May '22

Dear ChimeraX Team, I'm a structural bioinformatician working on my PhD thesis. I've been a long time user of Chimera, and I'm now using ChimeraX to create figures for my dissertation. I genuinely love both programs. Thank you for creating them. I found myself stuck trying to perform one operation in ChimeraX that is very easy to perform in Chimera. What I'm trying to do is select (and color) all atoms of an atomic model, that are located outside of a density map's contour. In Chimera, I was able to just select the model and use the shortcut "ac oa" and that was it. Unfortunately I am not able to find a way to do that in ChimeraX. I even tried to select the atoms in Chimera, then save the selected atoms as a PDB file, and then the inverted selection as a separate PDB file, and then open the two files in ChimeraX and color them separately. This could even work for a full atom representation, but does not work well for ribbon representation. That said, if the solution to my problem could be to somehow transfer the list of atoms that are outside the map from Chimera to ChimeraX, that would work for me as well. I will appreciate any tips and suggestions! Kind regards, Mateusz

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OpenGL woes on Windows
by Pranav Shah 21 May '22

21 May '22

Hi Team, I have installed the latest RC of chimerax on a windows box running v10 Pro. The box has an Nvidia RTX6000 GPU card as well. I have updated the Nvidia drivers to the latest version yet when I start ChimeraX, i see the following error message - ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 3.0 Try updating your graphics driver. Nvidia driver version - Version: R510 U6 (512.78) WHQL; Release Date: 2022.5.16; Operating System: Windows 10 64-bit, Windows 11 Do you guys have any suggestions for trouble shooting? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Problems with the first installation
by mykalxxxxx 20 May '22

20 May '22

Deer developer, This is my first time install ChimeraX. What should I do if I get this prompt after installation .Thanks. (QT 5.12.12 was already installed,windows 11,ChimeraX 1.4rc202205060510). | | mykalxxxxx | | 邮箱：mykalxxxxx(a)163.com |

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Map "Blobs" tool - Generate objects?
by Ricardo Righetto 20 May '22

20 May '22

Hi again, Pardon for resurrecting another old thread: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001139.html I have needed to extract selected blobs as separate surfaces (and also separate volumes) recently and found a way to do it within ChimeraX version 1.3 (2021-12-08), here's how: 1. Right mouse → Blob → right click desired blob to color it (any color different from the rest of the volume) 2. Split the surface based on colors: sop splitbycolor #1.2 3. Use the desired split surface to mask the original volume data: vol mask #1 surf #2.2 fullMap true 4. Save as a new volume: save my_segmented_piece.mrc #3 Hope this helps :-) Best wishes, -- Ricardo Diogo Righetto

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feature request : yellow/ochre clipping planes
by Pranav Shah 18 May '22

18 May '22

Hi Guys, Would it be possible to reinstate the same color scheme used to delineate the clipping planes in Chimera into ChimeraX. The current lines are too thin and have the same color as the default map color value. This makes the manipulation of the planes harder especially when working on a smaller screen. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Re: [chimerax-users] [Chimera-users] interface plot
by Elaine Meng 18 May '22

18 May '22

Oops, I meant to send this to chimerax-users(a)cgl.ucsf.edu , not chimera-users(a)cgl.ucsf.edu (apologies to the latter folks)! Elaine > On May 12, 2022, at 12:27 PM, Elaine Meng via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Pranav, > If you mean that you wanted a list of the interface residues, you can use the "interfaces" network diagram edge context menu to select the residues, then list them in the Log with "info residues sel" ... and either cut-n-paste from the Log to text file or use "log save" to save it as an HTML file. The "info" command should really allow saving a text file directly, but it doesn't do that yet. I believe we have an open ticket to fix that omission. > > In the chain-chain network diagram, e.g. when the mouse cursor is over the edge representing the chain B-C interface, context-menu choices include > > Select Contact Residues of B and C > Select Contact Residues of B with C > Select Contact Residues of C with B > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#diagram> > > Or if you get a new daily build, another way to select the residues is to use menu: Select... Contacts, the Chains section of the resulting dialog: > <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> > > Then use "info residues sel" and possibly "log save" as mentioned above. > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save> > > Alternatively, you could use "measure buriedarea" specifying the two chains and "list true", which also reports each residue's buried area. (thus avoiding having to select and use "info") > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> > > Example: > measure buriedarea (/A&protein) with (/B&protein) list true > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On May 12, 2022, at 9:06 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: >> >> Indeed! Although, as a suggestion, would it be possible to highlight >> in the description that in order for the plot to inherit residue >> colors, one needs to invoke the plot _after_ the residues have been >> identified and colored? Also, could I save the output of the analysis >> to a text file? >> Best, >> Pranav >> -- >> Pranav Shah >> Postdoctoral Research Fellow. >> >> Division of Structural Biology, >> Wellcome Trust Centre for Human Genetics, >> University of Oxford, >> Roosevelt Drive, Oxford OX3 7BN, >> UK >> >> On Thu, May 12, 2022 at 4:53 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>> haha, glad you like it!! >>> >>> Best, >>> Elaine >>> >>>> On May 12, 2022, at 8:27 AM, Pranav Shah via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>> >>>> <3 >>>> <3 >>>> <3 >>>> <3 >>>> <3 >>>> >>>> Best, >>>> Pranav >>>> -- >>>> Pranav Shah >>>> Postdoctoral Research Fellow. >>>> >>>> Division of Structural Biology, >>>> Wellcome Trust Centre for Human Genetics, >>>> University of Oxford, >>>> Roosevelt Drive, Oxford OX3 7BN, >>>> UK >>>> <image.png>_______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users(a)cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimerax-users] exporting crosslinks histogram
by Tom Goddard 18 May '22

18 May '22

Hi Pim, I added a Save Plot As... menu entry to the crosslinks histogram, can save as svg or pdf or png. I also added bins, maxLength, minLength and height options to the command to control how many bins, the x scale and height of y scale (in counts per bin). These changes will be in tomorrow's ChimeraX daily build which will become ChimeraX 1.5 eventually. Too late to make it into ChimeraX 1.4. Tom > Dear ChimeraX team, > > I am analysing multiple datasets generated using crosslinking-ms, loaded as separate pseudobond files on my model. The crosslinks histogram plots works just fine and I’d now like to put some plots neatly side-by-side. My questions: > > - can the histogram be saved or exported? Ideally as an svg or pdf file. But png or jpg would also already be useful. > I could export the .pb files and plot them elsewhere, but that seems like a workaround. > > - is it possible to specify the x and the y axis of the generated histograms, as well as the bin size? This would be helpful to show them side-by-side. > > Many thanks in advance, > > Pim > -running v1.2.5 on mac os catalina 10.15-

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Re: [chimerax-users] [Chimera-users] Set scale factors from displayed contours?
by Tom Goddard 17 May '22

17 May '22

Hi Oliver, In tomorrow's daily ChimeraX builds you can use volume maximum #1,2 scale fromlevels and it will scale each map by 1/level where level is the displayed surface level before taking the maximum. This allows merging maps that have different intensity levels. Thanks for the suggestion. This will be in ChimeraX 1.5 but not in 1.4 and is not in Chimera. Tom > On May 6, 2022, at 2:38 PM, Elaine Meng via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Oli, > Oh, I see, you already figured out the scale factors (essentially) by adjusting thresholds interactively. So the automation would simply be doing the math of taking the ratio of the thresholds and scaling the map(s) according to that, which sounds more feasible. > > I can make a feature request ticket (probably ChimeraX), but can't make promises as I would not be the one to triage it. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On May 6, 2022, at 1:42 PM, Oliver Clarke via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >> >> Hi Elaine, >> >> I don't think I explained very well - I mean to say, calculate the scale factors from the displayed thresholds. >> >> E.g. if the user has set map1 to a threshold of 1.0, and map2 to a threshold of 2.0, in order to make them visually equivalent in a combined map, map1 needs to be scaled by a factor of 2. >> >> It would be great if this could be done automatically as a flag for the volume or vop command (as there is already a flag to provide per map scale factors). >> >> Cheers >> Oli >> >>> On May 6, 2022, at 4:39 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>> Hi Oli, >>> Our volume expert Tom is on vacation until mid-month and might not be reviewing questions for a while... so I will give my not-so-expert thoughts: >>> >>> To me, the initial identification of "overlapping bits" sounds quite subjective and thus difficult to encode. If the user could designate the boundaries of this area (by drawing a box?), perhaps automatic scaling of one map to make its values as similar as possible to the values of another map inside that box could be done. However, drawing the box would probably be just as time-consuming as the process that you are already using. >>> >>> Also, new developments/agorithms would be going only into ChimeraX, not Chimera. ChimeraX has mostly the same "vop" options as Chimera, except included in the "volume" command instead of "vop": >>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#vop> >>> >>> Best, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>>> On May 6, 2022, at 1:23 PM, Oliver Clarke via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>>> >>>> Hi, >>>> >>>> When combining maps using vop maximum (or volume maximum in chimerax), we often want to adjust the scale factors of the maps such that the overlapping bits of two aligned maps are visually on the same scale. It is possible to calculate the appropriate scale factors from the displayed thresholds, but this becomes a little time consuming when combining many maps. >>>> >>>> Would it be possible to add a flag, something like "get scalefactor from display thresholds" that would take care of this automatically? >>>> >>>> Cheers >>>> Oli >>> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

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Removing text labels generated with command distance
by Shubham Devesh Ramgoolam 17 May '22

17 May '22

Hi, I hope you are doing well. I have a python script, to be executed in nogui mode, which does the following: -open a pdb file -define centroids for specific residues -draw pseudobonds between specific residues -> I am using the command distance for this purpose The issue arises when I have to save the session (.cxs) when in nogui mode, I am getting this error: QGuiApplication::font(): no QGuiApplication instance and no application font set. I believe it is because of the text labels created by the command distance. So, I included the following in my code: run(session, ‘hide #2.*’) and I can now save the session. I noticed in the model panel that the pdb file is assigned to #1 and the pseudobond to #2. The text labels are created as a submodel of the pseudobond (so #2.1, 2.2,..), hence why the ‘hide #2.*’ Will this fix always work? Is the model assignment also dependent on the pdb file being opened? Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Where is the renumber sequence tool in ChimeraX?
by Phan, Isabelle 17 May '22

17 May '22

The sequence of my structure includes a tag and I want to renumber from -7 so that the first residue is the start Met. I tried the old chimera command resrenumber = FAIL. I googled and searched the docs, read the list of commands one by one, and still could not figure it out. The API has a renumber_sequence() function but I don't understand the description (what’s "the given residues”? The chain?) and was unable to find an example on how to call this from the interface. I opened the python shell and typed: from chimerax.core.commands import run run(renumber_residues('#1/A:*', -7)) # FAIL Sorry if this is trivial, I am still completely baffled by ChimeraX despite using it for years. Thanks, Isabelle CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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align 400 copies of the same density map into a circle
by SHIQING LIAO 16 May '22

16 May '22

Hi there, I am a new user and would really appreciate any input on the task I want to do using Chimerax. Currently I have a mrc map, and it is a part of a cylindrical tube-shaped structure (like the area I drew in the picture). The map looks like a curved plane from the side of the cylinder, if it helps. If I piece 400 identical copies of map with some rotation and transition, I would ideally get a cynlider shaped strutcure, without top and bottom (like the picture below). The reason why I want to piece the mrc together is that I don't have the full look of the tube, but I know the rough radius (that's how 400 was derived), and I want to make a model for the full tube, using the model of the composing protein. I managed to manually fit the models of individual protein into one map. For the other mrc copies, I tried to do the same again but it took a lot of time and not very accurate, so I'm looking for any coding solutions that might help. I'm currently thinking if it is possible for me to place a marker at the center of one mrc map. Then make 400 copies of the map with the marker. Then write a code to tell each 1/400 mrc map to rotate 0.9 degrees around the marked center and move to a coordinate. Then I can repeat the same for the protein models I mapped to one mrc map. But I have no idea how to achieve it, and any suggestions would be greatly appreciated! Thank you so much for helping me!!! Best, Shiqing [image: cf23fde5-632f-4568-9700-9307f24e0f6c.png]

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crossfade issue
by Omid Haji-Ghassemi 16 May '22

16 May '22

Dear ChimeraX community, I am having some issues with the crossfade command while making a movie. For some reason the command stretches out the image while running the transition. I am just doing a simple transition for a movie as part of a more complicated movie. To illustrate the problem I made a simple script that reproduces the issue. movie record supersample 3 size 640,480 wait 60 crossfade; cartoon hide #1/D-F; wait 60 movie encode framerate 60 output test.mov Be great if someone can let me know what I am doing wrong. Best, Omid --------------------------------------------------- --------------------------------------------------- Dr. Omid Haji-Ghassemi Assistant Professor, Biological Sciences Department University of Calgary https://hajighassemilab.org

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Re: [chimerax-users] [Chimera-users] Making a movie from map series while keeping map's colors
by Elaine Meng 16 May '22

16 May '22

Hi Michal, Since this is a ChimeraX question I'm putting it on chimerax-users(a)cgl.ucsf.edu -- otherwise the Chimera users will be confused! In the future you may want to use that address for ChimeraX questions. If I remember correctly, "vseries" re-renders the surfaces at the time of playback, unless you specify storing more of them with the "cacheFrames" option -- so try using "vseries" with "cacheFrames 20": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html> See previous answer to a similar question: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003271.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 16, 2022, at 12:45 AM, Michal Arie Shmuelov via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi everyone, > I have 20 maps (from 3D variability analysis) that I open as series in chimeraX. > I’m coloring the map series using the command “color zone #X near #X distance X” (coloring the map according to pdb model). > Next I’m trying to make a movie of this map series while retaining the map colors. > For some reason when the morph/ vseries starts to run the colors disappear. > Can someone help me to solve this problem? > What are the commands that I should write? > Thanks, > Michal >

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