- Chimera-users - RBVI Mailing Lists

Inquiry regarding file opening issue
by LEE JIA QI . 26 Jan '24

26 Jan '24

Dear Ms/Mr, I hope this email finds you well. I am writing to bring to your attention an issue I am experiencing with your software. I have been attempting to open my protein file using Chimera, but unfortunately I have encountered difficulties. The file opened with nothing, but I can open it last time I will send my file here, and I would appreciate it if you could provide guidance for me as soon as possible. I look forward to your assistance in resolving this issue. Best regards Jia Qi -- *PENAFIAN*: E-mel ini dan apa-apa fail yang dikepilkan bersamanya ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat, rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Kebangsaan Malaysia (UKM) adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut. _*DISCLAIMER *: This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of The National University of Malaysia (UKM) shall be understood as neither given nor endorsed by any of the aforementioned._

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RMSD related query
by Dhindwal, Poonam 16 Jan '24

16 Jan '24

Hello, I was wondering if there is a way in Chimera to generate RMSD values for individual C alpha after structure alignment. I want to plot a graph of RMSD vs individual Amino acids. I performed 'Matchmaker' to generate the structure alignment and in the output tab, I can see rmsd bars on top of aligned sequences but I am unable to get the exact values of RMSD. Any help would be greatly appreciated. Thank you, Poonam Dhindwal, Ph.D. Post-doctoral fellow Department of Veterinary Microbiology Western College of Veterinary Medicine University of Saskatchewan 52 Campus drive Saskatoon SK S7N5B4 Phone: 639-317-4702 Email: pod898(a)usask.ca

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CAN NOT RECORD VIDEO
by akmalyati sulong 16 Jan '24

16 Jan '24

Dear Sir or Madam, I am trying to record a movie in Chimera 1.17.2, but I consistently get the following error without a proper error message: "An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: ". Please help me to solve the problem Regards, Akmalyati email : nays5098(a)gmail.com

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Query on the force field for energy minimization
by Prabuddha Bhattacharya 15 Jan '24

15 Jan '24

Dear Sir I would be grateful if you kindly let me know what force field is used by Chimera to optimize the geometry of a small organic molecule (not peptide) if I minimize the structure using the parameters as shared in the attached file. Thank you Kind regards *Prabuddha Bhattacharya * [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 13/01/24, 15:02:51

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LIGAND ENERGY MINIMIZATION
by DR. SHAZIA DAWOOD 12 Jan '24

12 Jan '24

Dear Sir , I want to minimize ligand and protein energy (pre docking step) . which chimera should be downloaded. I have an ucsf chimera for windows but currently it is not working. mention me chimera for my laptop windows 10. Thanking You -- *Dr. Shazia Dawood* Assistant Professor Pharmacy And Allied Health Sciences M.Phil. PhD. Biochemistry (UOK) North Karachi Campus, Plot No. 204-205 Sector 7B/1, North Karachi, Karachi, Pakistan. 7580 03319764733 +9221-36723221-6/111-11-IQRA shazia.dawood(a)iqra.edu.pk <saad.saleem(a)iqra.edu.pk> --

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how to play trajectory frames ?
by Mitch Murphy 11 Jan '24

11 Jan '24

i tried "open 3ft6.psf coordsets true coords 3ft6.xtc" but i get "*'coordsets' has no suffix*" error message. and with "open 3ft6.psf coords 3ft6.xtc coordsets true" i get "*Expected a keyword*". how do i play frames of a trajectory. i have the psf and xtc or dcd trajectory files available.

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Chimera export morph animation to 3D software
by Rebekah Moore 09 Jan '24

09 Jan '24

Hi, I was wondering if it's possible to export a morph animation to a 3D software like C4D, Maya, or Blender? I don't wish to render a "movie" in Chimera, as I would like to add the protein morph to a 3D scene in C4D with other animated objects and render it using Redshift. Is this possible? I've tried exporting in vrml xmd and glb formats, which in theory can have animation data, but when I import the files into C4D or Blender the protein has no keyframes and is static. Thanks for your help! Best, Rebekah

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Finding interacting residues between receptor and ligand
by Prathvi Singh 04 Jan '24

04 Jan '24

Hi Elaine, I used the HPEPDOCK server (http:// huanglab.phys.hust.edu.cn/hpepdock /) to dock a ligand onto a receptor and downloaded the conformation (pose) of the ligand with lowest energy. Next I opened the receptor and ligand structure in UCSF chimera. The ligand fitted perfectly in the binding site. Now is it possible to know which residues of the ligand are interacting with the receptor and what is the type of non-covalent interaction between them? Thanks in advance, Prathvi

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Need help using AutoDock Vina with Chimera on Mac
by Kush Unadkat 04 Jan '24

04 Jan '24

Greetings I am a student and I just got a new Mac and I am having a difficult time using AutoDock Vina in Chimera on my Mac. When working with two proteins (.mol2) format, I use AutoDock Vina in tools, input the required values and describe the path to “vina” using the browse button but instead of getting a pop up with the docking possibilities, I get an error like this: [Errno 30] Read-only file system: ‘docking.receptor.pdb’ I tried to look into the problem and if I can understand this correctly, I has something to do with Mac not allowing users to Write on the disk but I’m not sure. Can you please tell me what I’m doing wrong or how I can solve this issue? I am currently working on a project and I have a deadline so it is really important that I find a solution soon. Thank you. Your assistance is really valuable to me.

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Unrecognized command: "hide"
by Gourav Das 03 Jan '24

03 Jan '24

Greetings everyone! I am trying to hide the hydrogen atoms of a molecule using the command line in Chimera. But the software does not recognize the "hide" command. In addition, it could not recognize the "undo" command. Please help me regarding this issue. With regards, Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

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