- Chimera-users - RBVI Mailing Lists

inquire about the capabilities of the UCSF Chimera software in visualizing bond atoms in a spring mode
by Wee Zhang 11 Sep '23

11 Sep '23

Dear RBVI Team, I hope you are doing well. I am writing to inquire about the capabilities of the UCSF Chimera software in visualizing bond atoms in a spring mode, similar to the exemplary images I have enclosed for reference. I have been using UCSF Chimera for various molecular visualization and analysis tasks, and I am particularly interested in exploring this feature for my research and projects. The visualizations I am referring to are those that effectively represent covalent bonds as springs connecting atoms in a molecular structure. These spring-like representations can provide valuable insights into the flexibility and dynamics of molecules, which are crucial aspects of my research in materials science. I have attached images that illustrate the visualizations I want to achieve with UCSF Chimera for your reference. These images serve as excellent examples of dynamic and informative representations that I believe could greatly enhance my research. I would appreciate it if you could provide information on whether UCSF Chimera can generate bond atom visualizations in a spring mode, and if so, any guidance on how to achieve this would be beneficial. Additionally, if any specific plugins or settings are required to create such visualizations, please let me know. Furthermore, if any workshops, tutorials, or resources can assist me in mastering this feature, I would be eager to participate in or access them. Thank you in advance for your time and assistance. I look forward to hearing from you regarding the feasibility of incorporating the spring mode bond atom visualization into UCSF Chimera and any guidance you can provide on achieving this. Please feel free to contact me via email at [your email address] or by phone at [your phone number] if you require additional information or clarification. Sincerely,

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Chimera will not start
by Secor, Maxim 06 Sep '23

06 Sep '23

Hello, I am a postdoc in the Lin lab at Tufts. We use Chimera for everything. Thank you for such wonderful software. Last week Chimera stopped working on my machine. I tried (1) restarting my machine (2) Updating my OS (3) reinstalling Chimera (4) Installing the daily release of Chimera. Nothing works… Thankfully ChimeraX is a good substitute. However, (A) I cannot seem to find all the features that I want in ChimeraX that I loved in Chimers, for example minimization tools, and (B) would really like the Chimera GUI to work. Any thoughts? Maybe there is a corrupted hidden cache file that I need to delete somewhere. Best Max

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Very big THANKS FOR SENT ME ACCESS to ;st version by CHIMERA X.IT IS FANTASTIC!!!Boris
by Boris Atanasov 02 Sep '23

02 Sep '23

-- Prof. BORIS ATANASOV <borisatanasov2(a)gmail.com> Institute of Organic Chemistry, Bulgarian Academy of Sciences, SOFIA 1113, Bulgaria

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Unable to run UCSF chimera using
by Prathvi Singh 30 Aug '23

30 Aug '23

Hi, Is it possible to use python to execute commands on the command line of UCSF chimera without actually opening its GUI on the Windows platform? If not, then how to use python to open its GUI and execute the commands? I tried the "subprocess.Popen()" and "os.system()" methods to run its GUI by passing the path of chimera executable (version 1.17.1) to them but chimera is displaying an error with exit code 1 (snapshot attached). However, I am able to launch chimeraX (version 1.6.1) via these methods. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Display of double/tripe bonds
by Ghislain Deslongchamps 29 Aug '23

29 Aug '23

Hi all, I wish to use Chimera for my students to view organic models that I created in MOE. How can Chimera display double/triple bonds? They appear as single bonds in .pdb, .mol, .mol2 formats. Thanks. Cheers, Ghislain GHISLAIN DESLONGCHAMPS Professor Department of Chemistry • Faculty of Science T 506 470-9976 F 506 453-3570 WWW https://www.deslongchamps<https://www.deslongchamps.ca/>.ca<https://www.deslongchamps.ca/> UNB campuses are open with strict adherence to New Brunswick Public Health requirements. Our priority continues to be providing high quality education while ensuring the health and safety of our community. [attachment.jpeg] [attachment.jpeg] /uofnb<https://www.facebook.com/uofnb> [attachment.jpeg] @unb<https://twitter.com/UNB> [attachment.jpeg] @discoverunb<https://instagram.com/discoverunb/> UNB.ca<http://www.unb.ca/> Confidentiality Note: This email and the information contained in it is confidential, may be privileged and is intended for the exclusive use of the addressee(s). Any other person is strictly prohibited from using, disclosing, distributing, or reproducing it. If you have received this communication in error, please reply by email to the sender and delete or destroy all copies of this message.

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How to show certain hydrogen bonds and hide others
by Karjalainen, Mikael 29 Aug '23

29 Aug '23

Hi! I am having problems to show certain hydrogen bonds and hide others. For example, I would like to hide some completely. Then others should be shown always. Even when atoms are not shown and only ribbon is. I couldn't find how to do this by googling or for example reading how to use hbonds command. I am using Chimera 1.16. I know that there is ChimeraX, but now I need to modify old project. Regards, Mikael

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Atlocs
by Hernando J Sosa 28 Aug '23

28 Aug '23

Dear ChimeraX, I have an atomic model with several chains that have residues with alternate locations A and B. I noticed that while Chimera by default displays alternate locations A. ChimeraX for some chains display alternate locations A and for other chains alternate locations B. Why is this behavior different in Chimera and ChimeraX? Is this a novel feature of ChimeraX? I this is the case how ChimeraX decides which of the two alternate locations A or B to display? Thanks Hernando ___________________________________ Hernando Sosa, PhD. Dept. of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 emai: hernando.sosa@einsteinmed.<mailto:hernando.sosa@einsteinmed.org>edu ___________________________________

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Saving the resolution of structure to a file
by Prathvi Singh 22 Aug '23

22 Aug '23

Hi Elaine, Is there a way to save the resolution of a protein structure to a file using command line, either in chimeraX or chimera? Thanks -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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dms from command line
by Guido Leoni 21 Aug '23

21 Aug '23

Dear list Is there an option to write dms from command line? I' m able to launch the command line interface with a pdb loaded within . Then I estimate the surface with this command surface #0 now I would write a dms ... Please do you have any tips that can help me? Thank you Guido

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non-integral charge warning
by Chris Ellis 21 Aug '23

21 Aug '23

Hi, After running the dock prep, I get the following warning in the reply log. Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log How can I fix this warning? Do I need to fix this? Thank you for any help you can provide. I truly appreciate it. Chris

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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 16 Aug '23

16 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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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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