May 2023 - ChimeraX-users - RBVI Mailing Lists

ChimeraX 1.5 Issue - Observations
by Ethan Crofut 22 May '23

22 May '23

Hello, I am Ethan Crofut, an undergraduate at UCLA and member of Professor Hong Zhou's lab. I wanted to comment on an issue brought up at the Stanford-SLAC Image Processing Workshop. I am using ChimeraX 1.5, but I have also experienced the issue where scrolling, panning, and zooming stop working in the middle of my session. In my experience, this issue is specific to Apple Macbook trackpads (as someone else commented, I haven't seen the same issue on Linux desktops). Here are my observations on the issue: - The problem can always be resolved by clicking on the ChimeraX window in which the 3D structures are being viewed. - A scroll, pan, and zoom functions are lost if I click on a separate ChimeraX window, such as the Log, an ISOLDE window, etc., but as stated above, I can rescue this by clicking on the main window again. This also occurs for windows that are embedded into the main window, as the Log usually is. - The scroll, pan, and zoom features are more likely to break right after I use a multi-fingered gesture on the trackpad, especially three fingered gestures. I think this may have to do with the Mac's three-fingered swipe shortcut. - Sometimes, some functions are lost but others are retained. I almost always retain the ability to rotate the model using the regular left click, but multi-fingered gestures, such as the zoom and panning options, break more frequently. I am not very technologically savvy, but my guess is that it is very easy for Macs to lose track of the main ChimeraX window being the currently active window, which causes the controls to stop working. For me, this is usually caused by using multi-fingered gestures or toggling between multiple different ChimeraX windows. Best, Ethan

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symmetry axis
by Tianyang Liu (Staff) 22 May '23

22 May '23

Dear ChimeraX team, I have attached my cryo-EM map with C2 symmetry. The symmetry axis is shown with a yellow rod, not along the z-axis. How can I save a new map in ChimeraX with the symmetry axis along z? Many thanks, T

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interfnal error toolshed
by steffen＠sthomas.de 19 May '23

19 May '23

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Support pages are not reachable
by Lars Hangartner 18 May '23

18 May '23

To whom it may concern: There seems to be issues with your web servers, as several pages cannot be reached, e.g. <https://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Sc…> cgl.ucsf.edu<https://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Sc…> [X]<https://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Sc…> Best, Lars –––––––––––––––––––––––––––––––––– Lars Hangartner, PhD Associate Professor The Scripps Research Institute Department of Immunology & Microbiology - IMM2 10550 North Torrey Pines Road La Jolla CA, 92037 U.S.A. Phone: +1 (858) 784 9876 Cell: +1 (858) 952 2282

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UCSF website
by Raneem Akel 18 May '23

18 May '23

Hello, I was trying to download ChimeraX but I’m getting an error saying that the website cannot be reached. Could you please advise. Thanks, Raneem

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Re: [chimerax-users] [Chimera-users] 3D_printing
by Elaine Meng 18 May '23

18 May '23

Dear François-Hugues Porée, In ChimeraX, there is no GUI tool but you can use the "cartoon style" command to increase ribbon (cartoon) width and thickness to specific angstrom values. For details see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> However, ChimeraX also has a "struts" command that will automatically increase ribbon thickness in addition to adding some stick pseudobonds specifically to make a 3D model stronger. So you may want to use "struts" instead : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/struts.html> Another thing to consider for 3D printing is the number of triangles of the object, which you can adjust with "graphics quality": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality> For ChimeraX questions in the future, you may want to use the other address chimerax-users(a)cgl.ucsf.edu (CC'd here) -- since the answers are different for the two programs, we try to not confuse people between them. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. you may also be interested in the NIH 3D website: <https://3d.nih.gov/> > On May 15, 2023, at 6:58 AM, Francois-Hugues Poree via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera Team, > first of all, I would like to thank you for providing a sotfware solution to molecular visualization and by the way 3D-printing. > > I send you this message concerning the UCSF Chimera X version. We usually are preparing our 3D-printing files from data collected from the pdb and to ensure the rigidity of the system, we thick the ribbon size and also add some H-bonds (mainly for helices). However, we are not able to find the way to do it in this version. > In the previous version (1.17), the command line was : Tools-depiction-ribbon style editor > > Could you explain us the new procedure to make this ? > > > We also noticed that the opportunity to save the file in a stl extension was not allowed in the 1.17 version. This option is running in the X version. > > Thank you very much for your reply > > Best regards. > > > fhporee > > François-Hugues Porée > Professeur de Chimie Thérapeutique > Institut des Sciences Chimiques de Rennes UMR CNRS 6226 > Faculté de Pharmacie - Université de Rennes > 2 Avenue du Pr Léon Bernard > F-35043 Rennes > France > Tel.02 23 23 41 87

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'Tunnel' hydrophobic colouring
by Kelly May Frain 16 May '23

16 May '23

Hello, Previously you were super quick and helping when answering my ‘tunnel’ question, so I thought I could try another question for chimeraX. I have a protein which via Caver I have found a tunnel which runs through. This tunnel has been exported as a pdb and using your help and python, the tunnel now changes diameter perfectly as it weaves through the structure. I had this idea to colour the tunnel according its surrounding residues and their hydrophobicity. So in chimeraX I can colour my model ‘hydrophobically’ from cyan to gold. Then I wanted to 'zone’ these colours into my tunnel pdb. But when I use color zone #2 near #1 distance 20 for example, the tunnel is coloured in red and blue patches? Even though the model is cyan and gold. Is there a way to achieve my goal please? Best wishes, Kelly

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Duplicate the model
by tim smith 15 May '23

15 May '23

Hello everybody, I would like to create copy of the model in the same session but with a different model number. Please, could you suggest how to do that. Thank you. Best Tim

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rendering of bond making/breaking along a trajectory
by Hassan, Sergio (NIH/NIAID) [E] 15 May '23

15 May '23

Hi, I am not sure whether this is a bug or something not yet implemented or else. I performed QM/MM simulations of a proton translocating along a water chain. This involves the breaking of a bond and the making of a new bond. The visualization of the trajectory does not show this process; instead, the original definition of bond is retained, without being updated at each timeframe. Is there a way to tell ChimeraX to automatically check covalent bonds at each snapshot and update the bond accordingly? A simple distance criterion will do. This is only for rendering purpose. In case further clarifications are needed: D—H.......A (with -- indicating the covalent bond between proton and domor and .... indicating the proximal acceptor) must be transformed to D.......H—A. Instead, it is rendered as D-------H..A (with an artificially elongated DH bond and no new HA bond) thanks s _____________________________________ Sergio A. Hassan https://bioinformatics.niaid.nih.gov/cmm/ BCBB/NIAID/NIH/DHHS 301 761 7221 (office) 301 741 5579 (mobile)

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Trajectory smoothing
by Shubham Devesh Ramgoolam 15 May '23

15 May '23

Hi all, Does chimeraX has a command for trajectory smoothing? Based on previous similar questions, I know a script was written for trajectory smoothing in chimera/chimeraX. However, I cannot not access this script because it is not found on the server anymore. Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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ChimeraX-users May 2023