- Chimera-dev - RBVI Mailing Lists

Python interpreter for Chimera X
by Shivam Gupta 27 Jun '22

27 Jun '22

Hello Development Team, Greetings of the day! I am a commercial license holder of ChimeraX and want to explore its application for high throughput analysis by writing python script. I searched a lot but I couldn't find a way to write a script for chimeraX in python3.8. Could you please help me out by guiding me over the python script for chimera X. Thanks -- 株式会社ファーマフーズ Biomedical Department グプタシヴァム Gupta Shivam 〒615-8245 京都市西京区御陵大原1-49 TEL:075-748-9811 FAX:075-948-9818 E-mail: *shivam-gupta(a)pharmafoods.co.jp <a-higashiyama(a)pharmafoods.co.jp>* URL: http://www.pharmafoods.co.jp/

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Chimera source code
by Haleh Shahbazi 14 Jun '22

14 Jun '22

Hello Chimera Developer Team, I am Haleh, a PhD student at University of Toronto. For my research, I downloaded Chimera and tried to install and execute its bin file using my SSH terminal on the server (Compute Canada, Mist) which didn’t work due to differences in processing architecture. Chimera was built for Intel x86_64 CPUs, but I’ve been trying to run it on Mist which is a different architecture (IBM Power9). Now, I wonder if it requires recompilation of the source code or any recommendation to fix it. Thanks in advance for your support! Haleh HALEH SHAHBAZI PHD STUDENT @GARTON LAB • she/her • [Personal/Lab LinkedIn] <https://www.linkedin.com/in/haleh-shahbazi> IBME, University of Toronto haleh.shahbazi(a)mail.utoronto.ca<mailto:haleh.shahbazi@mail.utoronto.ca> www.gartonlab.org<http://www.gartonlab.org/> • bme.utoronto.ca<https://bme.utoronto.ca> • [LinkedIn] <https://www.linkedin.com/school/bme-uoft> [Twitter] <https://twitter.com/bme_uoft> [Instagram] <https://www.instagram.com/bme_uoft/> [signature_3600261848]<https://bme.utoronto.ca/>

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Chimera assistance
by Elliott, Luc 17 Nov '21

17 Nov '21

Hello, I'm a first year PhD student with the University of Liverpool and I have a query regarding chimera. I'm trying to write some code which selects all the regions of a segmented map (.seg) and saves each region to its own .mrc file, similarly to how it works in the program but without needing to interact with the GUI. Would there be a way to make this happen? Thank you for your time. Kind regards, Luc Elliott

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Is it possible to use Chimera on linux_arm64?
by Chen Zhiqiang 15 Nov '21

15 Nov '21

Dear chimera-dev Thank you for making Chimera open source and free to noncommercial use ! It is a great software ! The official website cannot download the binary executable programs for Linux_arm64. I tried to compile from source, but it failed. Is there any good way to use Chimera on the Linux_arm64, please? Regards, Chen Zhiqiang

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Chimera extensions request
by Jacopo Carbone - jacopo.carbone2＠studio.unibo.it 09 Nov '21

09 Nov '21

Hello, We are two post-graduate students of the University of Bologna in the department of chemistry. We are working in CADD field and we have written some tools which help the user before and after the molecular docking. We would like to know if it is possible to collaborate with you on this project. Thanks in advance for your time, J.C.

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Unable to open the software
by Lakshmi G Rao 06 Sep '21

06 Sep '21

Hi I have downloaded chimera-1.15-win64.exe in my windows 10, I could install the software but After installing I am not able to open the application, I get a error message as below , pfa Regards Vijayalakshmi Research Scholar St Aloysius College Mangalore India

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Hardware Requirements
by John Joshua Gutierrez 06 May '21

06 May '21

Dear Chimera Developers, Just a quick question regarding the hardware that Chimera/ChimeraX needs. Are these programs CPU and/or GPU heavy? How much memory is recommended? Is the program storage heavy? Essentially, what are the specs needed to run Chimera/ChimeraX comfortably? Thank you for your time, John

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job opening for ChimeraX developer
by Elaine Meng 06 May '21

06 May '21

Hello everybody, We're looking for somebody to join the ChimeraX development team! Please see this posting for details: <https://sjobs.brassring.com/TGnewUI/Search/Home/Home?partnerid=6495&siteid=…> On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Chimera Error
by Vishakha Kamble 02 May '21

02 May '21

Dear Sir/Madam, I am facing this error while doing Minimization step on my protein.(5ULP) "Correct charges are unknown for 1 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms Details in reply log No MMTK name for atom "HXT" in standard residue "VAL" " Please could you help me solve this issue Thanks & Regards Vishakha Kamble

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Building custom nucleotides
by Divita Mathur 09 Jan '21

09 Jan '21

Hello! I am using the Build structure to create DNA duplexes with ATGC bases. However, I want to insert Ts that are slightly modified. I can go in and modify each T but I was wondering if I can make a modified-T “template” , assign it a new letter (say X) and then use it in the Build structure function. The backbone and base pairing rules of the new T would be the same. For example, I want to create a T that has an amino linker… Regards, Divita

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