- Chimera-users - RBVI Mailing Lists

EULA modification request
by Smith, Lua J. 08 Nov '22

08 Nov '22

Hello UCSF Chimera creators, Our Chemistry department of Missouri University of Science and Technology would like to use your software. Our attorney reviewed the non-commercial software license agreement, and is requesting the legal jurisdiction be struck from the license agreement as well as other modifications. Due to the University being an instrumentality of the state of Missouri and having sovereign immunity under Missouri and federal law, we are not authorized to waive our legal jurisdiction (See Fowler v. Board of Regents, 637 S.W.2d 352 (Mo.App. 1982)). Would you please review the attached requested license agreement modifications, and initial if acceptable? Thank you! Lua Lua Smith Software Support, Information Technology 800 University Drive ljhqn8(a)mst.edu<mailto:ljhqn8@mst.edu> | 573-341-7990<tel:573-341-7990> | it.mst.edu<https://it.mst.edu> [Missouri S&T - 150 Years]<https://www.mst.edu/>

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Finding disulphide bonds
by Prathvi Singh 08 Nov '22

08 Nov '22

Hi Elaine, I have found out a way to select the disulphide bonded CYS residues in UCSF chimera using the command: *select disulphide*. However, is there a way to count the number of disulphide bridges in a protein and save in a variable? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Question regarding 2dlabels in Chimera
by leonard.maurer＠uni-bonn.de 07 Nov '22

07 Nov '22

Hi, I am using Chimera for several years now and I really enjoy it, but there is one issue I could not solve until now: Is it possible to have subscript/superscript for the 2D labels? For example something like "subunit A\_{1}" and "subunit A\^{1}" that I can type either in the 2d labels GUI text part or with the 2dlabels command, which gives me the raised and lowered versions of the "1"? I am confident that this feature might be already implemented given Chimera's impressive amount of tools, but I was not able to find it in the documentation so far. Thanks in advance! Best regards, Leonard

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Running the Modify Structure tool using command line in UCSF Chimera
by Prathvi Singh 03 Nov '22

03 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 03 Nov '22

03 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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AlphaFold Modeling
by S.M. RAIHAN RAHMAN 31 Oct '22

31 Oct '22

Hi! Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models? Please let me know. Thank you. Regards, Raihan

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How to invert a map values in UCSF Chimera
by Junha Song BA 31 Oct '22

31 Oct '22

Dear RBVI, I am currently looking into the ways to invert a map in UCSF Chimera so that I can flip the histogram of a map, but I cannot find a volume operation command that does the job. What command in UCSF Chimera allows creating a map with inverted map values? I thought it was vop but I cannot find a parameter that allows assigning negative value operation that would invert the map in UCSF Chimera command line documentation. Best, Junha Song.

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Question regarding protein-protein interactions in ChimeraX
by Lake, Camille (NIH/NIAID) [C] 31 Oct '22

31 Oct '22

Hello, My name is Camille Lake and I have used ChimeraX to model proteins. I was wondering - if I load two completely separate proteins from PDB, what is the nature of their interaction as shown by ChimeraX? The two proteins I'm interested in, TIM-3 (5f71) and CEACAM1 (5dzl), are predicted to interact in the literature, but if I load them separately into ChimeraX, is this predicted interaction what displays automatically? It seems that they are, but I can't find anywhere on the web whether this is automatically done in ChimeraX. Other proteins I randomly add in generally keep far away from each other in space. Thank you, Camille Camille Lake, PhD Emerging Leaders in Data Science (ORISE) Fellow National Institute of Allergy and Infectious Diseases (NIAID) - Office of Data Science and Emerging Technologies (ODSET) National Institutes of Health (NIH) 5601 Fishers Lane, 6C5 Rockville, MD 20871 camille.lake(a)nih.gov 301-761-7976 ---------------------------------------------- The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender’s own and not expressly made on behalf of the NIAID by one of its representatives.

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