August 2023 - ChimeraX-users - RBVI Mailing Lists

Saving the resolution of structure to a file
by Prathvi Singh 24 Aug '23

24 Aug '23

Hi Elaine, Is there a way to save the resolution of a protein structure to a file using command line, either in chimeraX or chimera? Thanks -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Equivalent to "ac ri" in ChimeraX?
by Oliver Clarke 24 Aug '23

24 Aug '23

Hi, In Chimera, the accelerator “ri” selects intervening residues. This is convenient because one can select two residues (let’s say at the start and end of a domain) and then select all the residues between them without having to explicitly specify a residue range (I have this bound to the alias “selbetween”) in Chimera. Is there any equivalent accelerator in ChimeraX? Cheers OIi

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Help with ChimeraX and dual extruder 3D printing
by Dye, Billy 24 Aug '23

24 Aug '23

I have been using ChimeraX to generate STL files for 3D printing models of a variety of protein structures that I use in my biology classes. I recently acquired a dual extrusion printer which should allow me to print models in two different colors. For example, I am currently trying to print a nucleosome from RCSB model 7PFX such that the DNA is printed blue from one extruder and the histones white from the second extruder. I am exporting two different STL files from ChimeraX, one with the DNA and one with the histones, and I am attempting to slice with FlashPrint 5 software for a FlashForge Creator Pro 2 printer. However, when I import the two STL files into the slicing software, they are not aligned. Even if I position both at 0,0,0 coordinates, it is obvious that the DNA and histones are not lining up properly. Is there a way to export the two STL files from ChimeraX such that they have a common reference point or origin and will thus align with one another when both are placed into the slicing software? Many thanks for your consideration and advice, Billy Dye [PastedGraphic-2.png]

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Trackpad modifier to translate in z?
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, In Chimera, I have shift-two-finger-drag set to translate the view in Z. This is very useful for precisely navigating around large structures without reorienting the camera, particularly when the cofr is bound to the center of view. Is there any way to replicate this behavior in ChimeraX? Cheers Oli

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Add shortcuts to Model panel, log and Volume viewer to toolbar?
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, I love the ability to customize the home tab of the toolbar, but there are some other things that I would like to add there and I don’t see how. Is there any way to add shortcuts/icons for the model panel, the log and the volume viewer? The use case is that I prefer to keep all panels undocked, in order to maximize screen real estate when working on a laptop - having shortcuts to bring these up would be convenient. It would also be great to have a shortcut for either a specific alias, or a dropdown menu of aliases, for custom lighting/visualization modes defined in the startup commands. Cheers Oli

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W-9 Request, Belharra Therapeutics | For Chimera
by Belharra Therapeutics Purchasing 23 Aug '23

23 Aug '23

Hello, I've recently tried to reach out regarding Chimera. All of my emails have been returned as undeliverable. Can I please get you assistance with the following information for Chimera? * A copy of your W-9 (or W-8, W-8BEN, W-8BENE for International) * Contact for your accounting department * Our account number for us to reference on our PO's, or if we are to refer to our company name. * Sales or email address to submit PO's Thank you, Heath Jarred Earle Belharra Therapeutics, Inc.. - Purchasing belharra(a)iabuyer.com<mailto:belharra@iabuyer.com> Innovative Advancement, LLC Brand & Vendor Specialist Ph: 425-686-9566 Ext. 703 www.innovativeadvancement.com<http://www.innovativeadvancement.com/> [cid:image001.gif@01D9D5BC.E5247540] <https://www.facebook.com/Innovativeadvancement/> [cid:image002.gif@01D9D5BC.E5247540] <http://twitter.com/innoadvance> [cid:image003.jpg@01D9D5BC.E5247540] CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential information and may be legally protected from disclosure. If you are not the intended recipient of this message, or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited

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Regarding use of attribute assignment files and difference between ChimeraX and ChimeraX daily build
by SUHANI BHATTACHARYYA 23 Aug '23

23 Aug '23

Dear Team Chimera, I am a second-year undergraduate student at IISER, Pune. I have been using ChimeraX for some time. Earlier I have also used some older Chimera versions. They had the kdHydrophobicity under Render by Attribute for residues. However, ChimeraX does not. On reporting a problem, I was told to use attribute assignment files for kdHydrophobicity. I downloaded the file as .txt file with .defattr suffix. Then, following the instructions in the user guide, I tried to use the open command to start using the attribute file. But I was shown an error that no such file existed. I even changed the file location and checked with multiple directories, including where ChimeraX files are stored on my PC to try to open the file, but nothing has worked. Kindly provide clearer instructions on where to save and open the attribute assignment files. Thank you. Regards, Suhani Bhattacharyya

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Fwd: Help with ChimeraX and 3D printing
by Elaine Meng 23 Aug '23

23 Aug '23

Dear Billy, Please use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list to ask ChimeraX questions (CC'd here so you don't need to re-send) -- I am not sure of the answer, and others on the list have more expertise in this area. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: "Dye, Billy" <Billy.Dye(a)volstate.edu> > Subject: Help with ChimeraX and 3D printing > Date: August 23, 2023 at 8:31:21 AM PDT > To: "meng(a)cgl.ucsf.edu" <meng(a)cgl.ucsf.edu> > > Hello > > I hope you might give some advice on using ChimeraX with dual extrusion 3D printing. > > I have been using ChimeraX to generate STL files for 3D printing models of a variety of protein structures that I use in my biology classes. I recently acquired a dual extrusion printer which should allow me to print models in two different colors. For example, I am currently trying to print a nucleosome from RCSB model 7PFX such that the DNA is printed blue from one extruder and the histones white from the second extruder. I am exporting two different STL files from ChimeraX, one with the DNA and one with the histones, and I am attempting to slice with FlashPrint 5 software for a FlashForge Creator Pro 2 printer. However, when I import the two STL files into the slicing software, they are not aligned. Even if I position both at 0,0,0 coordinates, it is obvious that the DNA and histones are not lining up properly. Is there a way to export the two STL files from ChimeraX such that they have a common reference point or origin and will thus align with one another when both are placed into the slicing software? > > Many thanks for your consideration and advice, > Billy Dye > > > >

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Regarding probeRadius
by Sakiat　Hossain 23 Aug '23

23 Aug '23

Dear Sir/Madam, Greetings. I am a nanomaterial chemist, and I would like to measure solvent accessible surface area (sasa) of my metal nanocluster using its single crystal x-ray diffraction structure. Specifically, I want to calculate H+ accessible surface area. I would appreciate it if you kindly let me know how to change probeRadius for calculating sasa in ChimeraX. I look forward to your kind help. Best, Sakia Hossain Tokyo University of Science, Japan Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Trackpad rotation
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, The trackpad zoom/rotation settings in ChimeraX seem very different from “old” Chimera. Is there any way to replicate the behavior from Chimera? Specifically, when I pinch to zoom in ChimeraX, I often find the view rotating a lot, unless I am very careful, which does not happen in Chimera. I have tried playing around with the trackpad twist sensitivity, but so far have been unable to find settings similar to the default in Chimera. Cheers Oli

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ChimeraX-users August 2023