February 2024 - ChimeraX-users - RBVI Mailing Lists

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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Commands not working
by Heinen, Cobey J 28 Feb '24

28 Feb '24

Hello, I am new to this program and am learning the commands. However, when I type the commands from the tutorial, they don't work. For instance, when I do "start<https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/start.html> Side View" it registers it as an unknown command. Also, when I do the command "color hot pink :lys", it says it does not know what the residue is. Am I missing anything? Thank you for your time. Best, Cobey Heinen

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Fwd: protein-molecule contact log issue
by Eric Pettersen 27 Feb '24

27 Feb '24

> Begin forwarded message: > > From: Mario Rodriguez Monteverde <mrodriguez.81(a)alumni.unav.es> > Subject: protein-molecule contact log issue > Date: February 26, 2024 at 2:52:17 PM PST > To: "ChimeraX-bugs(a)cgl.ucsf.edu" <ChimeraX-bugs(a)cgl.ucsf.edu> > > Good afternoon. > > To whom it may concern. > > I am attempting to identify the residues with which a compound (A) is interacting with a target protein (B). I opened both pdb files in ChimeraX, I selected the compound and did as follows: Tools > Structure Analysis > Contacts (selected output info to log). > The results which I get are the contacts inside the same protein (prot(B) with prot(B)), instead of compound(A) with protein(B). > I have tried selecting only the target protein, selecting both, creating a new pdb file with the comp and the compound together, but nothing works, I still can not get to know which residues from the compound are contacting my target prot. > > How could I solve this? > > Thank you > > Best, > Mario

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Re: right-mouse clipping
by Daniel Larsson 27 Feb '24

27 Feb '24

Ok, by trial-and-error I figured out the answer to question 3. One right-clicks and hold while dragging the mouse up/down to change the radius. I would much prefer to be able to set the contour-level by right clicking-and-hold and drag, since that is something one needs to change much more frequenly than the Zone radius. Also, I realize that Zone does not hide atoms outside of the sphere, so one has to hide atoms first and then zone will show the atoms inside of the sphere. From: Daniel Larsson via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Reply to: Daniel Larsson <daniel.larsson(a)icm.uu.se> Date: Tuesday, 27 February 2024 at 09:42 To: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] right-mouse clipping 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 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ 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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Seeking help
by 林萌萌 27 Feb '24

27 Feb '24

What's the command for “colored by atoms by rmsd” ？

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Help saving a modified protein for 3d print
by Jana Villemain 23 Feb '24

23 Feb '24

Greetings, I have downloaded the attached .pdb. Also attached is a screenshot of same model, but sliced specifically at histidine 65. I need to export the edited file, sliced, as an .stl so that I can print it. However, try as I might, every time I save, or export the file, it is unedited - and includes the entire model. Any help you could provide would be great! [cid:image001.png@01DA667E.93B731E0] Thank you, Jana Jana Villemain, Ph.D. Associate Professor of Chemistry Dept. of Chemistry, Biochemistry, Physics and Engineering Indiana University of Pennsylvania Weyandt Hall 239D jvillema(a)iup.edu 724-357-2180

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ChimeraX Core module Issue
by Himal Godage 23 Feb '24

23 Feb '24

Dear ChimeraX Dev Team, I am currently in the process of developing a bundle for ChimeraX. I have clone the code from the git repository and made the necessary installations according to the documentation. But I have an issue with the location of the ChimeraX core module. I found that it's in the *ChimeraX > src > bundles > core > src* . But in most of the bundle codes it's located as a *chimerax.core * which gives me errors (screenshot is attached). Do I have to change the path to the above mentioned path or is there any other way I can locate the core module? Thank you Best regards Himal Godage

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Question regarding licensing
by Brandon Benson 22 Feb '24

22 Feb '24

Hello, I'm Brandon Benson and work in IT supporting the colleges of Engineering and Science. We would like to use your software on campus. To do so, we have to fill out some information and have the licensing agreement approved by our legal team and info sec teams. Who would be a point of contact that I can use for this? Thanks, Brandon B -- Brandon Benson Client Support Analyst Engineering and Science Computing University of Notre Dame

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