- Chimera-users - RBVI Mailing Lists

.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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Query regarding selection
by Prathvi Singh 04 Aug '23

04 Aug '23

Hi Elaine, I want to select all the atoms except the backbone oxygen and nitrogen atom of residues 100.A to 120.A . Is there a command to do this in either chimera or chimeraX? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Re: [EXTERNAL] Chimera-users Digest, Vol 243, Issue 22
by Reza Khayat 01 Aug '23

01 Aug '23

Hi Elaine, Thanks for the help. This will speed things up quite a bit. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________________ From: chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Tuesday, August 1, 2023 3:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: [EXTERNAL] Chimera-users Digest, Vol 243, Issue 22 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Measure rotation without writing PDB (Reza Khayat) 2. Re: Measure rotation without writing PDB (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 1 Aug 2023 18:23:19 +0000 From: Reza Khayat <rkhayat(a)ccny.cuny.edu> Subject: [Chimera-users] Measure rotation without writing PDB To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Message-ID: <1690914198332.72284(a)ccny.cuny.edu> Content-Type: multipart/alternative; boundary="_000_169091419833272284ccnycunyedu_" Hi, I'm trying to measure the movement of a domain between two structures of the same protein. Here are the conditions: 1. There are two domains in each structure 2. I want to overlay the first domain and measure the rotation of the second domain 3. There are lots of structures, so I want to minimise the number of steps 4. I'd like to do this with a script and the --no_gui option on headless Chimera Here is my current script for the routine: open pdb1 open pdb2 match #1:1-50 #0:1-50 write format pdb relative #1 #0 t.pdb delete #1 open t.pdb match #1:55-80 #0:55-80 measure rotation #1 #0 delete #1 open pdb3 ... Is it possible to not have to write, delete, and open #1 after the first match step? If I don't do this, then the measure rotation #1 #0 will measure rotation of the initial match rather than the second match. Thanks for the help. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Measure rotation without writing PDB
by Reza Khayat 01 Aug '23

01 Aug '23

Hi, I'm trying to measure the movement of a domain between two structures of the same protein. Here are the conditions: 1. There are two domains in each structure 2. I want to overlay the first domain and measure the rotation of the second domain 3. There are lots of structures, so I want to minimise the number of steps 4. I'd like to do this with a script and the --no_gui option on headless Chimera Here is my current script for the routine: open pdb1 open pdb2 match #1:1-50 #0:1-50 write format pdb relative #1 #0 t.pdb delete #1 open t.pdb match #1:55-80 #0:55-80 measure rotation #1 #0 delete #1 open pdb3 ... Is it possible to not have to write, delete, and open #1 after the first match step? If I don't do this, then the measure rotation #1 #0 will measure rotation of the initial match rather than the second match. Thanks for the help. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Silent install?
by Jim Richard 27 Jul '23

27 Jul '23

Hello, We are using MECM (SCCM) to install Chimera and need to suppress ALL windows. I have tried the /verysilent flag but a command prompt still pops up with what looks to be the compiling portion. Is there a way to have ALL windows silent? -- *Jim Richard* Pronouns: he/him/his Client Systems Administrator

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Saving Animations on Mac OS
by Natalie Walsh 25 Jul '23

25 Jul '23

Hello, I am having troubles saving my animations on my Mac OS. I get this error when I record and save my animation: An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: -1 Error message: Could not find ffmpeg executable —————————————— I googled some solutions regarding “ffmpeg” and I believe I successfully installed it to my terminal, but I am still receiving the same error. Thank you, Natalie Walsh

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