October 2020 - ChimeraX-users - RBVI Mailing Lists

Measure Motion / Blob Detection
by Scott, Brandon L. 09 Oct '20

09 Oct '20

Hello all, I had two questions: 1) I see there is now the option in measure area to ignore dusted objects, is it possible to have this feature in the measure motion as well? 2) For measure and mark blobs, Is there any way to use the output of the measure motion function to link the blobs since the triangle number changes in each frame, but following measure motion we know where it goes in the next frame. Thanks, Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor Nanoscience & Nanoengineering South Dakota Mines 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/> [South Dakota Mines on Facebook]<https://www.facebook.com/SouthDakotaMines/>[South Dakota Mines on Instagram]<https://www.instagram.com/southdakotamines/>[South Dakota Mines on Twitter]<https://twitter.com/sdsmt>[South Dakota Mines on Snapchat]<https://www.snapchat.com/add/sdsmt>

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Option Include non-water HETATM in Modeller Comparative
by Marta Martinez 09 Oct '20

09 Oct '20

Hi all, I am running a very simple example in Modeller Comparative (a small alignment including the template structure and the target sequence to model). Since the template harbors a HEME group, I decided to select the Advanced option "Include non-water molecules HETATM residues from template". However, no one of the retrieved models contains the HEME group. Does anyone know what could be happening? Thanks in advance: MARTA -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

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right mouse zone selection labels
by Sarah Piper 09 Oct '20

09 Oct '20

HI ChimeraX team, I really like the feature in ChimeraX that creates a map clipping zone in the right mouse tools - zone with automatic labelling. However, the default labels are black background and yellow text, and only the residue 3 letter code and number. Is it possible to change these labels to a white bg and customise the labels to include e.g. the one letter code and chain ID? I tried to do this with the selection - labels tool but it did not seem to change it for the zone labels. Many thanks and keep up the great work :) Sarah

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Error "Cannot determine format for"
by Karjalainen, Mikael 09 Oct '20

09 Oct '20

Hi! I am trying to get transparent background in png pictures, but it is not working and I get error "Cannot determine format for". Only way to get this is by using command line? I am writing something like: save C:\Users\a\Desktop\k [ format png ] [ supersample 4 ] [ transparentBackground true ] or save C:\Users\a\Desktop\k format png supersample 4 transparentBackground true Also, I have tried different variations. Regards, Mikael

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Exporting 3D models from ChimeraX?
by Karjalainen, Mikael 07 Oct '20

07 Oct '20

Hi! Is it possible to export 3D models from ChimeraX? Preferably in formats GLB (best for powerpoint), FBX, OBJ or 3MF? You can in old Chimera, but for powerpoint presentations it can only give STL files which do not have textures. Here are supported file formats for Office products: https://support.microsoft.com/en-us/office/3d-content-guidelines-for-micros… Regards, Mikael

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Request for access to ChimeraX GitHub repository
by Chen, Xiang 05 Oct '20

05 Oct '20

Dear Sir or Madam, I am a graduate student at the Memorial University of Newfoundland, and I am working on the development of virtual reality applications that can be used to visualize biological microscopic data. May I get access to the ChimeraX GitHub repository for further non-commercial research? Looking forward to your reply. Thank you very much! Best Regards, Xiang Chen --- Xiang Chen, Student # 201992538 Department of Computer Science Memorial University of Newfoundland St. John's, NL, Canada T (709) 219-2960 / E xiangc(a)mun.ca

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Access ChimeraX GitHub repository
by 唐翊国 05 Oct '20

05 Oct '20

Hi Dear, I'm learning Python 3 now, and I think one good way is to refer to a good application like ChimeraX, so please allow me to access ChimeraX repository, thanks a lot! BR, Eagle

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orientation
by Fabian Glaser 02 Oct '20

02 Oct '20

Dear chimerax experts, I have maybe a trivial question, I am willing to show a figure with several copies of the same protein, but when I move one copy of them using the "move x 10 model #1” etc command, they rotate upon probably the center of mass of all the models, such as when I separate all of them, they are rotated slightly different. I would like to show them in exactly the same orientation, is there a trick to move them in such a way that will be show in exactly the same orientation? Thanks a lot! Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701 Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ Tel +972 (0) 4 8293701

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Quest 2 Support?
by Blaine Hewitt 01 Oct '20

01 Oct '20

Hello, my name is Blaine Hewitt. Now I know that you have stated previously that you have no intention of bringing support to the Oculus Quest. Which is completely understandable since I know that not only would you have to develop around a completely new Operating System but another CPU architecture and much much more I assume. But with the soon release of the Oculus Quest 2 and it's new XR 2 chip-set makes a pretty good argument for it. As this would allow for much easier use in education (as is what I am attempting to do with it). I think it will be even easier now to push updates with SideQuest <https://sidequestvr.com/> being relatively simple to setup. I know that another (Naome <https://blog.matryx.ai/nanome-on-quest-public-beta-is-now-available-b546321…>) program is already available on the platform. But I do like your program a lot more since it is able to be used for free unlike Nanome Pricing <https://nanome.ai/pricing/> which is... as to say unappealing to public schools (such as mine). I was was also thinking (sorry if I am becoming annoying at this point) that if you do make a version of the Quest that you could make that GitHub branch available to the public. As for example while I may not be great at understanding complex protein structures I can help to make the whole experience more user friendly. Anyways if you read this far thank you for taking time from your day to read this. If you want to know who I am, my name is Blaine I am in my senior year of High School (Waynecsd <https://wh.waynecsd.org/>). I have to do a project by the end of the year where I have to present an area of study I want to pursue and I decided to research the effects of VR on the human's ability to learn and retain information. Budget..... None

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ChimeraX-users October 2020