- Chimera-users - RBVI Mailing Lists

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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Need guidance
by Naima syed 30 Oct '22

30 Oct '22

Hello I am trying to find the RMSD between docked ligand and original ligand but I am not able to do it. When i tried the command "match" it showed the error atom spec missing. Can you please tell me how to fix this problem? Thank you

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Question about use of Chimera to view data from SALIGN program
by Edmund Marinelli 26 Oct '22

26 Oct '22

Helllo: I used SALIGN to obtain alignment / superposition of peptides. On the SALIGN webpage there is a link for Launch Chimera. When I click this I get a download of a file named "show.chimerax". Then nothing happens. The file contents appear to be directing ChimeraX to the data on the web and are as follows: <?xml version="1.0"?> <ChimeraPuppet type="std_webdata"> <web_files> <file name="alignment.pir" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/str-str_out.…" /> <file name="model1_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model1_fit.p…" /> <file name="model2_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model2_fit.p…" /> <file name="model3_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model3_fit.p…" /> <file name="model4_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model4_fit.p…" /> </web_files> <commands> <py_cmd>chimera.processNewMolecules(chimera.openModels.list(modelTypes=[chimera.Molecule]))</py_cmd> <py_cmd>import MultAlignViewer</py_cmd> <py_cmd>mols = chimera.openModels.list()</py_cmd> <py_cmd> m=chimera.extension.manager for i in m.instances: if isinstance(i, MultAlignViewer.MAViewer.MAViewer): mav = i </py_cmd> <py_cmd> for m in mols: if not m in mav.associations.keys(): mav.associate([m]) mav.match(mols[0], mols[1:], iterate=True)</py_cmd> </commands> </ChimeraPuppet> What am I supposed to do with this file. ChimeraX does not have a file extension .ChimeraX hence I do not know how to proceed next. Can anyone help? Thanks in advance.

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Set a reference coordinate for a viral structure?
by Feng, Y. 20 Oct '22

20 Oct '22

Hi there, I am a fresh new user of Chimera and have literally no experience in it. So I was wondering how to perform the process as mentioned in the Figure S4 of the following article: DOI: 10.1021/acs.jpcb.6b10131. My questions would be: In Chimera, 1. How to make an appointed atom in a viral structure with coordinates of (0,0,1)? 2. How to rotate the target point to the coordinates (0,0,1) and read out the original coordinates of the target point? What I want to do in Chimera is exactly the same as mentioned in the above article. But I don't have much experience with Chimera. So if you could explain how to do that step by step, that would be very much helpful. Sincerely appreciate! With best regards, Yuzhen Feng

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Set a reference coordinate and rotate target point to the reference coordinate?
by Feng, Y. 18 Oct '22

18 Oct '22

Hi there, I am a fresh new user of Chimera and have literally no experience in it. So I was wondering how to perform the process as mentioned in the *Figure S4* of the following article: DOI: 10.1021/acs.jpcb.6b10131. My questions would be: In Chimera, 1. How to make an appointed atom in a viral structure with coordinates of (0,0,1)? 2. How to rotate the target point to the coordinates (0,0,1) and read out the original coordinates of the target point? What I want to do in Chimera is exactly the same as mentioned in the above article. But I don't have much experience with Chimera. So if you could explain how to do that step by step, that would be very much helpful. Sincerely appreciate! With best regards, Yuzhen Feng

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Question: Why hydrogen bonds are not displayed?
by Kenji MATSUI 16 Oct '22

16 Oct '22

Dear Chimera I am sorry to interrupt your busy schedule. My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day. I am now looking at protein-ligand interactions. We found in the paper that His 421 interacted with another ligand. Therefore, the interaction between His-421 and the ligand. Problem :However, no hydrogen bonds were displayed.(first figure) I would like you to ask why this is caused. ---------------------------------------------------------- <detail> This is because the distance between the His-421 and OH oxygen atoms was 3.7 Å. A ligand with a structure similar to this one in the paper formed a hydrogen bond with His-421 at 3.8 Å. The thing I tried The Relax H-bond constraints section was adjusted from 3.0 to 5.0. [image: image.png] you can show this figure when you open the attached file Wheat: Ligand the other color:protein [image: image.png] H-bond parameter [image: image.png] --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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UCSF Chimera Non-Commercial License Agreement
by Sarah Haar 14 Oct '22

14 Oct '22

Hi, Bowling Green State University would like to use UCSF Chimera Non-Commercial License Agreement. As part of our University review process, all legal Terms need to be examined to assure that we stay in compliance with Ohio law. Please provide all Terms (i.e. Terms and Conditions, Master Service Agreement, EULA, SAAS, etc.) that we need to accept in order to use your product. Because we are a State-owned University there are some Terms that we cannot accept. For example, we cannot indemnify or agree to arbitration. Would you consider Amendment to your Terms if needed? Best regards, Sarah Haar Procurement Specialist Bowling Green State University 1851 N. Research Dr. Bowling Green, OH 43403 Office: 419-372-7926 [cid:image001.jpg@01D8DFDF.BAD37170]

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fit into map global
by Dieter Blaas 12 Oct '22

12 Oct '22

Hi, I am struggling to fit a model of a single protomer into a viral cryo-EM map. I usually succeed after a very long process of manually positioning the model approximately and then running 'fit into map' that arranges it in the best way. I filtered the map to low resolution and used the option to generate a density map of the pdb file which makes it easier but it is still complicated. However, I believe that there is a routine to globally fit that does not require the very cumbersome first manual fitting. Can anybody please give me a hint? Thanks a lot, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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how to find size of a molecule using Chimera
by Aditi Laddha 10 Oct '22

10 Oct '22

Hi Elaine, I wanted to find the size of a molecule which acts as a substrate (consisting of multiple elements) for my protein, I want to know the diameter of the molecule. But I am unable to find a way to do it. Can you please guide me through the process of determining the size of a molecule? -- Regards, Aditi Laddha PhD Scholar Indian Institute of Technology, Kanpur, Uttar Pradesh 208016

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Enquiry about the ligand library generation by scripts in Chimera
by Zhenjiao Du 07 Oct '22

07 Oct '22

Good morning, Dear Professor, My name is Zhenjiao Du, from Kansas State University. I am employing molecular docking for peptide screening and need to build peptide ligands for docking screening. I used to generate ligand by VMD and then energy minimized by molecular dynamics simulation, but the final conformation is not that matchable to the crystallography results. Chimera generated ligands perform a better job. I find Chimera provides amazing ligand energy minimization protocols, but there is no any resource for the scripts based ligand generation and minimization since I might need to generate thousands of peptide ligands for virtual screening. I find Chimera also supports python programming. Could you please provide me some information for the ligand generation by Chimera based on python scripts? I really appreciate it. I am looking forward to your reply. Sincerely, Zhenjiao Du Vice president of CAFS Student Committee Ph.D. student, Cereal Chemistry Grain Science & Industry, Kansas State University 150A Waters Hall, Manhattan, KS 66502 Pronouns: He/His

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