August 2023 - Chimera-users - RBVI Mailing Lists

San Jacinto College Software Intake Form Chimera
by Yates, Michael 18 Aug '23

18 Aug '23

Greetings. I am the Supervisor of Desktop Support Services for San Jacinto College. Information Technology Services (ITS) has been asked to evaluate Chimera to ensure that the San Jacinto College computing environment meets the requirements for the service as well as to ensure that the service offering complies with our requirements. As part of our standard process we reach out to software vendors to request the completion of the attached form after the requestor has completed section 1. At this time we request that you complete section 2 or 3 of the attached form and return it to us by August 21st so that we may complete our evaluations and grant purchase eligibility if the service qualifies. Additional questions may follow. In addition to what is in the form, please include (if applicable) any information / documentation that you have available regarding the options below and please indicate if there are any additional charges for the implementation of such: * Azure AD Single Sign On capability * Office 365 Integration features * Ellucian Banner Integration features [Description: Description: cid:image001.png@01CEC8EF.F2E97C50] Michael Yates San Jacinto College Supervisor of Desktop Support Services 4624 Fairmont Pkwy, Pasadena, TX 77504 Direct: (281) 998-6150 X7325 | Technical Support: (281) 998-6137 Web<http://blogs.sanjac.edu/its> | Facebook<http://www.facebook.com/sanjacits> | ITS Twitter<http://www.twitter.com/sanjacits>

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Moving atoms of a protein
by Abril Gijsbers 18 Aug '23

18 Aug '23

Hi Elaine, I have this alphafold structure (see picture) that is basically a huge string/thread and then a folded domain. I wanted to stretch the string to make its length more obvious. Is it possible to pull the residues without messing with the connections (peptide bond)? I am using chimeraX and I saw that you can "move atoms" but when you pull one you don't pull the others. If chimera cannot do this, do you know if another program will allow me to do it? Thank you in advance for your help, Best regards, Abril Gijsbers [image: image.png]

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Re: ChimeraX license and download
by Elaine Meng 17 Aug '23

17 Aug '23

Please disregard and delete the previous message. I messed up and accidentally CC'd the chimera users list instead of the licensing address. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2023, at 12:56 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > [...] > Thank you for licensing the commercial version of ChimeraX, the next-generation molecular visualization and analysis program from our research lab. ChimeraX is under active development, with version 1.6.1 released in May 2023. As new features are added, daily development builds are also available for download. Daily builds are not tested as thoroughly as production releases, but in practice are highly usable. > [...]

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Requesting protocol to find protein configuration units
by Panapakam, Jyotheeswaran 17 Aug '23

17 Aug '23

Dear Officail, This is Jyo writing from UNT biological sciences at Denton, TX, USA. I have been using your software for my research project for about an year. I was looking for a help/instructions about how to find out the configuration change in the protein after docking with a ligand. I have heard about RMSD docking value, that will be given in Amstrong units, could you kindly instruct me the process to perform it. It would be more glad if you are able to answer me withing a week from now : ) Sincerely, Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas. Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas.

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Re: [chimerax-users] re error with Movie recorder utility
by Elaine Meng 17 Aug '23

17 Aug '23

Hi Anna, This chimerax-users email address is for questions about ChimeraX, but it sounds like you are using the Chimera program instead, since only Chimera has a Movie Recorder tool. So I am CC-ing the chimera-users email address on this reply, and you do not need to re-send your question. There is no separate "freeware version" -- Chimera is free for academic use and the download is the same for academically or commercially licensed users. (This is also the case for ChimeraX). The Command Line is always for entering one command at a time, i.e. that is the normal situation, not a problem or bug. If you have just a few commands you can enter them as one line with semicolons between them. However, if you mean that you have a script that contains many Chimera commands, you do not enter them one at a time into the command line. Instead you use some text-editing program (outside of Chimera) to create a plain text command file containing those commands, then you open that file using either the Chimera menu File... Open, or the Chimera "open" command. Normally command files are named with the filename extension ".com" or ".cmd" so that Chimera knows what kind of file you are trying to open. See Chimera help pages and tutorials on making movies, namely: Making movies: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html> Movie Recorder help page (you can just click the Help button on the tool, or see the copy of the same thing at our website here): <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorde…> Chimera movie-making tutorials: <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies09/moviemaking.html> <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 16, 2023, at 6:31 PM, Anna Lohning via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi > I have the freeware version installed and trying to make a movie using the Tools/Utilities/Movie recorder window. > At this stage, I seem to only have the command line available for commands one at a time. > Anyway, under the Tools/Utilities, the only options there currently are > Register > Updates > > Be grateful for some clarification as I cant seem to find anyone having this issue. > Many thanks > Kind regards > > Anna > Dr Anna Elizabeth Lohning > Associate Professor - Biochemistry > Faculty of Health Science & Medicine > Bond University > ROBINA 4229 > (07) 5595 4779 > alohning(a)bond.edu.au >

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.msi chimera
by Yanni Goudetsidis (Staff) 11 Aug '23

11 Aug '23

Good morning Is there a .msi installer for chimera I could download, please? Thank you

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making composite map using vop maximum command
by ytakagi＠iu.edu 10 Aug '23

10 Aug '23

Hi I want to make a composite map using two locally refined maps. I tried Phenix but did not work well. So, I like to do it by Chimera. Apparently, a composite map can be made using Chimera's vop maximum command. But I could not find the instruction of how to do it. Can you tell me how to do it? Thanks

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San Jacinto College Security Evaluation
by Melendez, Aaron 09 Aug '23

09 Aug '23

Good afternoon, San Jacinto College, as part of its new application/vendor procurement process, is evaluating the security posture of Chimera and would like to ask for your help in procuring documentation that proves the security controls in place for the company. If you have any Information Security documentation you can share with us, it would be greatly appreciated. If an NDA needs to be signed, we would be happy to provide that to you. Documents that help: * HECVAT (one will be attached that can be filled out) * SJC Vendor Questionnaire (one will be attached that can be filled out) * Information security policies and procedures * Datacenters or Hosting Providers used. * Incident response plan * Disaster recovery plan * Business continuity plan * System and network architecture diagrams * Penetration testing reports * Vulnerability scan reports If you can provide the Data Centers that are used and the Hosting Providers, it will also help our evaluation process. Thank you in advance for your help. Please reach out if you have any questions. Regards, e Aaron C. Melendez Third-Party Risk Analyst The Office of Cybersecurity Cell: (281) 635-2940 (Please call x 2 or Text) San Jacinto Community College 4624 Fairmont Pkwy, Pasadena, TX 77504 Technical Support: Get help at SanJac ITS<https://www.sanjacits.org/> | call (281) 998-6137 www.sanjac.edu<https://www.sanjac.edu/> | www.facebook.com/sanjacintocollege<http://www.facebook.com/sanjacintocollege> | @SanJacCollege [2z5cr1lnO9iMtMLfMHSAYwzcMySsBwfq8SYpRxc6xBeRPF2c+m+YTgIc8IdrhL4f1IjMkJpGrM5AAAAAElFTkSuQmCC] “Under pressure, you don’t rise to the occasion, you sink to the level of your training.”

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Secondary structure editing of molecules
by GABRIELLE LUPETI DE CENA 08 Aug '23

08 Aug '23

Good morning! I have doubts about how to turn the peptide structures of the four images below (A), (B), (C), and (D) into a cartoon model like figure (E). I've tried, but I'm not succeeding. Thank you very much. -- ---- É obrigatória a utilização do e-mail @unifesp em todas as correspondências oficiais, institucionais e no acesso aos equipamentos e sistemas da Universidade Federal de São Paulo, conforme a portaria Reitoria n. 1182/2022 <https://sti.unifesp.br/documentos/termos-de-uso-do-email> que define a Política de e-mail institucional da Unifesp. <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=pub…>

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Saving phi psi values to a text file
by Prathvi Singh 06 Aug '23

06 Aug '23

Hi Elaine, Is there a command to save the phi and psi angle values of each residue of a PDB file in a text file using UCSF chimera? I know we can do this in chimeraX using the command: save C:\myphi.defattr attrName phi format defattr model #1 Also, can we use chimeraX to save the phi and psi values in a single file? Thanks in advance -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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