- ChimeraX-users - RBVI Mailing Lists

Syncing up the movement of "plane" volumes.
by Mayer, Megan 30 Sep '21

30 Sep '21

Hi ChimeraX community. I have a reconstructed tomogram which has 92 ‘Z’ slices, and a segmentation volume that has ‘374’ slices. They are both displayed as “Plane” in the volume viewer (image attached). I would like to record a movie where they are showing the same features simultaneously. I have used the command: “volume #5 planes z,0,92; volume #2 planes z,0,374 ; wait 120 ; “ However, the volumes do not move at the same time: volume 5 completes before volume 2 begins. Is there a way around this, so that I can play both volumes at the same time? Thank you for any tips! Megan

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adding new trajectory format
by Radosław Giziński 30 Sep '21

30 Sep '21

Hi, Is there a way I can add custom, multi-frame trajectory format to ChimeraX so I can view multi frame trajectories? Is there some manual that could guide me through the process like this?: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html (scroll to the bottom) Best regards, Radosław Giziński

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movie encode bug on Rocky Linux 8.4
by Guillaume Gaullier 30 Sep '21

30 Sep '21

Hello, This time I am reporting what looks almost certainly like a bug. Using ChimeraX version 1.2.5 on Rocky Linux 8.4 (installed from the RHEL/CentOS 8 RPM package), I get the following error in the Log when trying to use the movie encode command (I attached a copy of the full error message in the Log): /usr/libexec/UCSF-ChimeraX/bin/ffmpeg: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory Turns out I definitely have libbz2 on my system, but not under the filename ChimeraX (or ffmpeg bundled with ChimeraX) is looking for: $ ls -l /usr/lib64/ | grep libbz2 lrwxrwxrwx. 1 root root 11 Apr 7 03:44 libbz2.so -> libbz2.so.1 lrwxrwxrwx. 1 root root 15 Apr 7 03:44 libbz2.so.1 -> libbz2.so.1.0.6 -rwxr-xr-x. 1 root root 73008 Apr 7 03:44 libbz2.so.1.0.6 If I create a symlink to libbz2.so.1.0.6 and name it libbz2.so.1.0, my movie encode command finishes fine and produces a movie file. So it was easy to work around this problem, but obviously it would be a lot better if it worked out of the box and the user did not have to mess with system files as root. Thank you in advance, Guillaume N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: 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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Trackpad scaling causes unintended rotation
by Oliver Clarke 29 Sep '21

29 Sep '21

Hi, In recent versions of ChimeraX (I don't think it always did this but can't be 100% sure), when one uses pinch-to-zoom on the trackpad to scale the view, this also changes orientation, causing quite a large and unintended rotation which can be a bit disconcerting. Comparing directly with Chimera using the same model, this does not happen in Chimera. Is there some difference in how the Chimera vs X are interpreting competing trackpad gestures, and could this be adjusted in ChimeraX? Because two fingers can be used both to scale and rotate... Chimera seems to be able to figure out which the user is intending, while ChimeraX presently applies both at the same time. Cheers Oli

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Possible to measure the shortest distance between two models?
by Vorländer,Matthias Kopano 28 Sep '21

28 Sep '21

Dear all, I am interested in measuring the shortest distance between two models (PDBs) without a priori knowledge of which atoms will be the closest ones. I am planning to do this for a large number of model pairs, therefore it would be great if this would be scriptable. Is this possible using ChimeraX? Thanks a lot in advance, Best, Matthias

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Have a map move with its model
by Bullitt, Esther 28 Sep '21

28 Sep '21

Hi, I renamed my map and model to be #9.1 and #9.2, thinking this would make them move together. However, when I used matchmaker to match the model to align it to another model, only the model moved and the map did not. To start with, I used fitmap #9.1 inMap #9.2, but now the model is elsewhere. If I go back and do fitmap again, it moves the wrong thing (I want to put the map where the model is now, not vice versa). Is there something I am missing, or is there a different way to do this? Thanks very much. Sincerely, Esther

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Flat transparency setting absent
by David William Kastner 27 Sep '21

27 Sep '21

ChimeraX community, I noticed that in ChimeraX, the “flat” transparency option that was present in Chimera has been either moved or renamed in ChimeraX. This setting made it so the transparency setting wasn’t overwhelming/distracting when focusing on details. In Chimera, it is accessed with Tools > Viewing controls > Effects > transparency > flat. Does anyone know how to achieve this effect in ChimeraX? I find the default ChimeraX transparency option to be disorienting when visualizing details. Here is a rendering comparing the two rendering styles with and without “flat” option. I look forward to your thoughts! https://www.dropbox.com/s/xrjyjnzegeeltap/transparency_comparison.png?dl=0 David --- David Kastner Ph.D. student | Bioengineering MIT | Kulik Lab kastner.io

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Error on installing isolde
by benhaijing＠sina.com 27 Sep '21

27 Sep '21

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

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Compound Docking in UCSF Chimera
by Ayush Patel 25 Sep '21

25 Sep '21

Sir or Madam; Recently, I was having issues with docking a ligand into a receptor due to surface calculation failures. A quick search told me to use ChimeraX. However, I am not sure how to carry out docking in ChimeraX. Could you please explain how to do this? As a side note, I do currently have AutoDock Vina. Thank you so much, Ayush Patel

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Hi. I have a question about Chimera X program
by dongyoung kim 24 Sep '21

24 Sep '21

Hi. I'm researching protein 3D structure to develop the new drug. In recent, I'm using the Alphafold function in Chimera X daily version. I have 4 questions. First, if I use Alphafold to predict my important project data, is it keep secure privately? I want to keep my data secret. It shouldn't be open to anybody without me. Second, when I using Alphafold in ChimeraX, I faced some error messages that mean 'Not enough disk volume. please remove past data.'. I'm not familiar with google colab...how can I manage the disk to remove past data or expand disk volume? Third, how can I improve the speed of alphafold prediction? ChimeraX shows some resources like ram, disk. fourth, I want to operate simultaneously Alphafold prediction to predict 2 or more structures. Is it possible? If there need some pay to improve the second, third, fourth question, please let me know methods. Many thanks. -from KDY

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