October 2021 - ChimeraX-users - RBVI Mailing Lists

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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