October 2021 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Error on installing isolde
by benhaijing＠sina.com 08 Oct '21

08 Oct '21

Hi Greg!Thanks very much! After I deleted the two directories: (1) site-packages\ChimeraX_UI-1.2.1.dist-info and (2) site-packages\chimerax\ui in my computer, I have successfully reinstalled chimerax and isolde! It works now!Best regards, Haijing Ben ----- 原始邮件 ----- 发件人：Greg Couch <gregc(a)cgl.ucsf.edu> 收件人：benhaijing(a)sina.com, chimerax-users <chimerax-users(a)cgl.ucsf.edu> 主题：Re: [chimerax-users] Error on installing isolde 日期：2021年09月28日 06点24分 Actually, it worse than I thought. Uninstalling the user-installed version of the UI bundle is not doable from within ChimeraX. And uninstalling ChimeraX and reinstalling it doesn't help, because that only takes care of system files, not any of the user's customization. To get rid of the user installed bundle, the first step is to find where on the filesystem the files are. So start the Shell tool from the Tools / General menu. And then type in it: import chimerax chimerax.app_dirs.user_data_dir That will show where to go. For example, for me on Windows, it prints: 'C:\\Users\\gregc\\AppData\\Local\\UCSF\\ChimeraX\\1.2' So using the Windows file brower, I would navigate to C:\Users\gregc\AppData\Local\UCSF\ChimeraX\1.2. You may need to check "Hidden Items" in the View menu to navigate into AppData directory. macOS and Linux users should have an easier time going to the correct directory. And they would use forward slash, /, instead of backslash, \. The next step is to remove two directories: (1) site-packages\ChimeraX_UI-1.2.1.dist-info, and (2) site-packages\chimerax\ui. And then, when you restart ChimeraX, you'll be back to the version that came with ChimeraX. HTH, Greg On 9/27/2021 2:22 PM, Greg Couch via ChimeraX-users wrote: Hi Haijing, The output you pasted says that ISOLDE is already installed, so you don't need to install it again. It should be reinstallable, so that is a bug. If you use the graphical toolshed interface (click on More Tools... in the Tools menu), you would have seen that the install button for ISOLDE said Installed, meaning it is already installed. In this particular case, it looks you made things worse by deliberately installing an older version of the UI bundle from the toolshed than the version that came with ChimeraX. Using the graphical toolshed interface, you would have seen that it was a downgrade, which means do not install it unless necessary. Or maybe you used the Updates tool to do that? If so, you should have seen that installed version was 1.7.6 and the version on the toolshed is 1.2.1, so much older. Regardless of how you did it, to fix it, give the command: toolshed uninstall ui And that should revert back to version of the UI bundle that came with ChimeraX. The fact that you could install an older, incompatible, version of the UI bundle is a bug that is difficult to fix in the general case. Best regards, Greg On 9/26/2021 5:55 PM, benhaijing--- via ChimeraX-users wrote: Hi all！ I can’t install the plugin isolde using command 'toolshed install isolde'. Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Requirement already satisfied: ChimeraX-ISOLDE==1.2.2 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (1.2.2) Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3) Requirement already satisfied: ChimeraX-Core~=1.2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5) Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-Clipper~=0.16.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-ISOLDE==1.2.2) (0.16.0) Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1) Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.5) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.4) Requirement already satisfied: ChimeraX-IO~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.2.1) INFO: pip is looking at multiple versions of chimerax-pdblibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-pdb to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-opencommand to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-nucleotides to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-io to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-dataformats to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-mmcif to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-graphics to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-geometry to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-core to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomsearchlibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-connectstructure to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-clipper to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomiclibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomic to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-arrays to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-isolde to determine which version is compatible with other requirements. This could take a while. The conflict is caused by: chimerax-nucleotides 2.0.1 depends on ChimeraX-UI~=1.0 chimerax-opencommand 1.5 depends on ChimeraX-UI~=1.0 chimerax-savecommand 1.4 depends on ChimeraX-UI~=1.4 To fix this you could try to: 1. loosen the range of package versions you've specified 2. remove package versions to allow pip attempt to solve the dependency conflict ERROR: Cannot install chimerax-nucleotides==2.0.1, chimerax-opencommand==1.5 and chimerax-savecommand==1.4 because these package versions have conflicting dependencies. ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies WARNING: You are using pip version 21.0.1; however, version 21.2.4 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command. Thanks, Haijing Ben _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

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Mol2 file conversion
by Marcus Agyin 06 Oct '21

06 Oct '21

Hello, I am emailing to get clarification on how I would convert a chimera file into a Mol2 file. If I’m understanding correctly, I would need to click on “File” and in the pop-up menu there would be a “save as Mol2” option, however, all that it is showing the generic “Save” option. Thanks in advance, Marcus Agyin

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Measuring Colocalisation using ChimeraX
by BINGHAM Dominic 06 Oct '21

06 Oct '21

Hello, I have a problem with which I’m trying to use chimeraX to solve. I have some images of synapses with which I have super-resolved two proteins in 3D (so two images/channels). I want to quantify the colocalisation of a structure of one protein to the blobs of the other protein within a certain distance. Shown below is the non-segmented map of the 2 images of proteins. So for example I would want to quantify the colocalisation of the red blobs within a certain distance of specific larger green blobs. I want to then compare these between different conditions. [cid:5E6B5354-093F-44B8-BCD8-9C01AFDEAF72] I have segmented the images already using "segmentat map ». I have been trying to start with the « distance » tool to measure how far one blob of protein is from the structure (Image shown below of two selected structures in just the map of one protein to practice). [cid:ED6171EE-E03F-47C8-A3AE-81A7E5FC9177] However, this doesn’t seem to work functionally as no distance is shown when I try to perform the function. Also, this function may possibly be too basic for what Im trying to do. That said, any help on how to use this function would still be greatly appreciated. Ultimately, I think the best thing for what I would like is to be able to select a specific structure and have a measurement of all the blobs of the other protein within a defined 3D radius of this structure, and then compare this value between different conditions. I have been looking through the user manual and I can’t seem to find anything that will do something like this… I (and my PhD) would be monumentally grateful if you could possibly help me with this problem? Either by pointing me to the correct function, or even a thread that has discussed a similar problem that I may have missed? Thanks and have a wonderful day, Dominic Bingham PhD student at Aix-Marseille University

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Hidden points present in gltf file
by Scott, Brandon L. 06 Oct '21

06 Oct '21

I'm having an issue with gltf exporting with hidden objects. The surface that is exported looks correct; however, when querying the points in the exported file all the hidden ones are there as well which is hindering a downstream analysis. Exported gltf: [cid:18a58daf-6676-4fe8-ab6c-935e631e379d] Rendered points from gltf: [cid:3bd25148-70ad-4079-885b-368e0d2c57af] Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor Nanoscience & Nanoengineering South Dakota Mines 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/> [South Dakota Mines on Facebook]<https://www.facebook.com/SouthDakotaMines/>[South Dakota Mines on Instagram]<https://www.instagram.com/southdakotamines/>[South Dakota Mines on Twitter]<https://twitter.com/sdsmt>[South Dakota Mines on Snapchat]<https://www.snapchat.com/add/sdsmt>

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Error messages when executing command file with chimerax --exit
by Guillaume Gaullier 05 Oct '21

05 Oct '21

Hello, When I run the attached command file from within ChimeraX 1.2.5 on macOS 10.15.7 (open 7otq_figure-2-supplement-2.cxc), it completes without any error. However, when I run it from the shell with 'chimerax --exit 7otq_figure-2-supplement-2.cxc', I get the attached errors in the terminal. In both cases, the figures are generated correctly, so as far as I am concerned it seems I can simply ignore these errors. But I thought you (ChimeraX developers) might need to know that this happens. This does not happen with other command files (I have been happily making movies without ever seeing these error messages), which makes me think maybe the problem is specific to this particular one? Cheers, 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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Structure Prediction on ChimeraX
by Chang Jang 05 Oct '21

05 Oct '21

Hi ChimeraX users, I am trying to find Structure Prediction -> AlphaFold but there seems no such tool. Would you please guide me on how to add the "Structure Prediction" tool on ChimeraX? Thank you. Best regards, Chang Woon Jang

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can isolde work with ChimeraX 1.3 developer versions?
by Sindelar, Charles 04 Oct '21

04 Oct '21

Hi all, any chance I can persuade ChimeraX v1.3 (i.e. nightly downloads) to use the current version of Isolde? I would love to use some of the newest features of ChimX together with Isolde, but the toolshed does not allow this (says only ChimX 1.2 is allowed). Are they really incompatible? Can I perhaps "trick" the toolshed somehow? Thanks for all your work to make these fabulous tools. By the way, Tom, Eric, Elaine and team, I *love* the new tool-switching shortcuts, i.e. shift-esc and control-tab. They make my life so much easier and this is a primary motivation for my request (but other new features in 1.3 also). Cheers! Chuck --------------------- Charles V. Sindelar, Ph.D. Dept. of Molecular Biophysics and Biochemistry Yale University Bass 335 New Haven, CT 06520-8114 Lab (203) 432-3095 Fax (203) 432-5175 http://medicine.yale.edu/mbb/faculty/charles_sindelar.profile

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crossfade command not working from a command file
by Guillaume Gaullier 01 Oct '21

01 Oct '21

Hello, I am using ChimeraX version 1.2.5 (2021-05-24) on macOS 10.15.7. When trying to generate a simple movie with the attached command file, I get the attached wrong result in which the crossfade command seems to fail (instead of a smooth transition, I only get a flashing black screen for a few frames). A similar problem happens with the same version of ChimeraX on Rocky Linux 8.4. Instead of loading the command file from a fresh session (with 'open command-file.cxc'), I tried to prepare my models first, and then sent the commands generating the movie all at once (separated by semi-colons). When I did it this way, I got the correct result (also attached). Is there anything I am doing wrong, or is this a bug? I am pretty sure the command file version worked correctly in a previous version of ChimeraX, because I have done this before. Unfortunately, I don’t remember which version it was (but probably 1.1, since it was just last year). I would appreciate any help with this. 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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Tiling images are stepped
by Pranav Shah 01 Oct '21

01 Oct '21

Hi, I want to create an image of multiple volumes that are tiled horizontally. However, when I run the command "tile columns 6" the volumes get arranged in a step-like manner (attached image). I do not see this happen in chimera so I am wondering if this expected behaviour in ChimeraX? I am on UCSF ChimeraX version: 1.2.5 (2021-05-24) on the M1 MacBookPro, MacOS 11.6. 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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ChimeraX-users October 2021