October 2020 - ChimeraX-users - RBVI Mailing Lists

Set transparency on DNA stubs
by Siyu Chen 16 Oct '20

16 Oct '20

Dear chimerax developers, I am writing to ask about an issue regarding to the transparency of DNA bases. I set the double strand DNA as stubs and colored cyan, and I wanted to set it as transparent (trans 70 tar c). However, it looks like only the DNA backbones become transparent, and the bases are still bright and solid. I even tried to throw in all possible targets into the 'trans' command (acrsbpfl) and got the same looking images. I am just wondering if this is because of the style or color that makes the bases look solid? Also, do you have other suggestions to get around this issue? Thanks in advance for your time and help! Best, Siyu Chen

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Chnage Chain IDs
by Kazan Ramy (M.) 13 Oct '20

13 Oct '20

Greetings to all, In UCSF Chimera tools, there's an option to change chains ID/names. Unfortunately, I can't save my model under a cif format. While in Chimera X , I can save a model under a cif format but can't change the name of my chains, or at least I'm not able to find the command for that. My main goal is to have my model under a cif format with my new naming system, any idea on how I can solve this problem? Ramy Kazan PhD Student

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Assistance: ChimeraX save scene
by Priyanka Abeyrathne 12 Oct '20

12 Oct '20

Hi All, Is there a save scene command in ChimeraX? Thanks, Priyanka

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Resources to get started with toolshed development
by Florian Wernert 12 Oct '20

12 Oct '20

Hi there, I'm looking forward to integrate a processing algorithm I coded into a toolshed for ChimeraX. Are there any available resources in order to get started with plugin/toolshed development for ChimeraX ? Thanks, Florian Wernert

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Measure Motion / Blob Detection
by Scott, Brandon L. 10 Oct '20

10 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 06 Oct '20

06 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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