November 2022 - Chimera-users - RBVI Mailing Lists

Running the Modify Structure tool using command line in UCSF Chimera
by Prathvi Singh 04 Nov '22

04 Nov '22

Hi Elaine, Is there a way to run the *Modify Structure *tool in UCSF Chimera using command line? I want to substitute a S-atom with O-atom in more than 100 structures and doing it for each structure using the GUI looks very time consuming. Please help. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Jagged edges in chimera X
by Prathvi Singh 04 Nov '22

04 Nov '22

Hello Elaine, Is there a way to smoothen the jagged edges seen around ribbons and sheets in ChimeraX? The jagged edges can be removed in UCSF chimera by setting the *subdivision *value to 20 and enabling multisampling but I do not see these features in chimeraX. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Doubt regarding Copyright for the use of UCSF Chimera free software in research paper
by aiswarya tressa chacko 03 Nov '22

03 Nov '22

Sir/Madam, I am a post graduate student who is working on a research article which involves molecular docking and analysis. I am using the free software of UCSF Chimera (version 1.16) for obtaining results and analysing them. I am wondering whether using these results and images that I acquired from Chimera in my research study, will subject me to Copyright Issues. Kindly address my doubt as soon as possible.

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xyz axis indicator
by Xiang Zhang 01 Nov '22

01 Nov '22

Hi all, I was wondering how I could hide the xyz indicator in the center of window when I was viewing the X-ray density from mtz file? It only appears in crystal unit view mode but disappears in EM projection side view. Best, Xiang

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