- ChimeraX-users - RBVI Mailing Lists

need Section 508 compliance statement
by Weiss, Carol 06 Mar '24

06 Mar '24

Hello, I would like to use ChimeraX, but the FDA IT administrators will not download the Chimera X software without a statement about its Section 508 compliance for users. Would you please send me available Section 508 compliance information for this software? Thank you, Carol Weiss

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Improvement suggestion: single letter code for swap
by Vorländer,Matthias Kopano 05 Mar '24

05 Mar '24

Dear ChimeraX team, A small feature request: It would be helpful if the swapaa command could accept the single letter code for amino acids as well as the three letter code. This makes it easy to quickly fix a sequence, i.e based on a sequence that is open in the sequence viewer. Many thanks, Matthias

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Mainchain and sideonly atom names
by Sabrina Moffit 05 Mar '24

05 Mar '24

Dear ChimeraX team, So far I've found that these are the atom names classified as mainchain atoms by ChimeraX: ['H3', 'HA2', 'H2', 'CA', 'H', 'H1', 'HA', 'C', 'O', 'HA3', 'OXT', 'N'], by using such command: sel #1 & mainchain; info atoms sel. I'm not sure if there are more atom names classified as mainchain atoms by ChimeraX. Could you please provide me with a comprehensive list of all the atom names of the mainchain atoms (and sideonly atoms as well, if possible) of all types of amino acids? Thank you.

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Conctac map in ChimeraX?
by PABLO HERRERA NIETO 05 Mar '24

05 Mar '24

Hi everyone, I started using chimera after some years. In the new ChimeraX I could not find an option to calculate contact/distances heatmaps for proteins or protein complexes. Is that old funcionality gone for good? However, to check AlphaFold's pLLDT there is a really nice intereactive chart. Is there any option/hack to use that to visualize contacts/distances for any structure? Thanks Pablo -- Pablo Herrera Nieto Dpto. de Estructura de Macromoléculas, lab 15 Centro Nacional de Biotecnología - CSIC

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movie record / encode
by Enrico Martinez 05 Mar '24

05 Mar '24

Dear ChimeraX users! I noticed that there is some difference in the quality of the molecular movies produced in Ubuntu or MacOSX environments. Are there some tricks to improve the quality of the animation produced on ubuntu ? Here are the commands which produced the best results: movie record size 1920,1080 supersample 4 movie encode format h264 quality higher bitrate 25000 how could I modify / add something more with the aim to obtain the best molecular animations ?? Yours sincerely Enrico

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Question
by 张楠 04 Mar '24

04 Mar '24

Dear developers, I have a question I'd like to ask. The structure after refinement appears as helices when opened in PyMOL, but in ChimeraX, it doesn't display as helices, as shown in the figures. What could be the reason for this? Is there a way to make it display as helices in ChimeraX? Looking forward to your answer, thank you！ Best regards, Nan 张楠 zhangnan(a)nankai.edu.cn

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Inquiry - UCSF ChimeraX
by Fumi JINUSHI 04 Mar '24

04 Mar '24

Dear Sirs, We are a sales agent and a custom made computer manufacture in Japan. We focus on R&D sector as a key business area and help researchers and engineers in universities, research institutes and large companies, and provide them with a good selection of industrial products. I wonder if we can sell UCSF ChimeraX and provide our customers with the software installed on our custom made computers. We look forward to your reply. Thank you ! Kind regards, Fumi +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Fumi JINUSHI web_delivery(a)tegara.com Tegara Corporation 211-17, Higashimikata-cho, Chuo-ku Hamamatsu-shi, Shizuoka, 433-8104 Japan T +81-53-543-6691 F +81-53-543-6689 UNIPOS https://en.tegara.com/service/unipos/ TEGSYS https://en.tegara.com/service/tegsys/ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

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right-mouse clipping
by Daniel Larsson 01 Mar '24

01 Mar '24

Hi all, I have some question and comments regarding the very useful right-mouse Clipping tools. I feel they are poorly documented (or documentation is very difficult to find by Google searching). For the Clip tool, it took me forever to realize how to “undo” the clipping (click again). The Zone clipping is a very nice feature, which shows atoms, residue labels and volume inside of an approximately 10 Å sphere and hides the volume and only show cartoon outside of the sphere. Right-clicking on the background hides the labels. Some questions 1. How do I change the back/far clipping plane using the Clip tool (the icon suggests that you can clip into a slab)? 2. If so, is it possible to set a default thickness of that slab? 3. Is it possible to change the radius of the Zone clipping tool? 4. Is it possible to disable the cartoon outside of the sphere of the Zone clipping tool? 5. Alternatively have the ability to have an extra front clipping plane, which “intelligently” follows the camera when zooming in (hiding things closer to the centered region when zoomed in more)? 6. I use the mouse mode to center the view and camera pivot point (mousemode middleMode "center or translate"). It is possible to make the Zone clipping tool also center the view + pivot point so that I don’t have to also middle-click every time? Regards, Daniel 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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Isolde add nucleotide?
by Vorländer,Matthias Kopano 01 Mar '24

01 Mar '24

Dear all, Is it possible to add nucleotides to existing chains, similar to Isolde add aa? Many thanks, Matthias

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Re: Seeking Assistance with PyCharm Debugging Configuration
by Zachary Pearson 28 Feb '24

28 Feb '24

Hi Himal, I'm confused by a couple of things. First, your system packages should list all of ChimeraX's packages, like the screenshot attached to this email. Did you build ChimeraX (make build-from-scratch) and subsequently use ChimeraX's internal Python, not your system Python, to make your virtual environment? Second, the path to your interpreter looks like it's a path to a virtual environment inside ChimeraX itself. In /the base directory of the git repository:/ ./ChimeraX.app/bin/python.exe -m venv .venv --system-site-packages Then in PyCharm -> Settings -> Project: ChimeraX -> Python Interpreter Add a new interpreter path/to/ChimeraX/.venv/Scripts/python.exe Use that as the interpreter for your run or debug configuration. -- Zach On 2/27/2024 1:36 PM, Eric Pettersen wrote: > Nudge, nudge... :-) > >> Begin forwarded message: >> >> *From: *Himal Godage <himalgodage2759(a)gmail.com> >> *Subject: **Re: [chimerax-users] Seeking Assistance with PyCharm >> Debugging Configuration* >> *Date: *February 20, 2024 at 11:34:54 PM PST >> *To: *pett(a)cgl.ucsf.edu >> *Cc: *chimerax-users(a)cgl.ucsf.edu >> >> Hi Eric, >> Thank you for the reply and I appreciate your assistance. >> >> I've been using the internal Python to create a virtual environment >> in my project’s folder, and I've set the Python interpreter path as >> outlined in the documentation. The first attached screenshot is my >> interpreter configuration. >> >> However, my current challenge lies in the debugging section. I've >> created a new Run/Debug Configuration(third attachment) following the >> instructions , as shown in the second attached screenshot. >> Regrettably, when attempting to run the configuration, I encountered >> an error in the console: "No module named chimerax.core" (refer to >> the fourth attached screenshot). >> >> I believe that the issue is regarding a module named chimerax.core >> which I couldn’t find on the project. >> Thank you in advance for your help. >> >> Himal >> >> On Wed, Feb 21, 2024 at 12:39 AM Eric Pettersen <pett(a)cgl.ucsf.edu> >> wrote: >> >> Hi Himal, >> The person on our team that uses PyCharm and that wrote >> that documentation is on a trip to NIH this week and may not be >> able to respond promptly. Reading that page myself, it seems >> that the Debugging section assumes that you set up a virtual >> environment as outlined in the preceding "IDEs" section. Did you >> do that? >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> > On Feb 19, 2024, at 9:40 PM, himalgodage2759--- via >> ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> > >> > Dear ChimeraX Dev Team, >> > >> > I'm Himal Godage, and I am currently in the process of >> developing a bundle for ChimeraX software. I have been thoroughly >> following the provided documentation, successfully completing the >> steps related to setting up a ChimeraX development environment, >> obtaining the code, and compiling ChimeraX. However, I have >> encountered a challenge in the IDEs, Debugging, and Profiling >> section, specifically within PyCharm. Following the provided >> steps, I am instructed to: >> > 1. Create a new Run/Debug Configuration. >> > 2. Set the script path field to point at a module. >> > 3. Set the module to “chimerax.core”. >> > 4. Set the Python interpreter to ChimeraX’s internal Python. >> > 5. Uncheck “Add content roots to PYTHONPATH”. >> > 6. Uncheck “Add source roots to PYTHONPATH”. >> > While attempting to follow these instructions, I encountered >> difficulty in locating the "chimerax.core" module. Unfortunately, >> the provided directory structure or module seems to be difficult >> to find in my current project. However there is a module named >> core in the following path. ChimeraX > src > bundles > core >> > >> > I am reaching out to seek your guidance on resolving this >> issue. Could you please provide insights on how I can locate or >> create the necessary "chimerax.core" module or suggest an >> alternative approach to address this problem? >> > >> > Thank you in advance for your time and support. >> > Best regards, >> > >> > Himal Godage >> > himalgodage2759(a)gmail.com >> > _______________________________________________ >> > 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/ >> > >> >

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