October 2022 - Chimera-users - RBVI Mailing Lists

Question about save images
by Chang, Jufang 29 Apr '24

29 Apr '24

Hi, there, I used Chimera for a very short period of time. When I just started using Chimera I was able to save image by going to "file" and "save image" to save the image on the display window. For some reason, this stopped working. Now, after I did the same thing, the image I saved has complete blackness (attached). I wonder whether I might get be able to get help from you. I also tried using command line to save image. The result is the same. The exact procedure I used are: Go to "Presets", choose "publication 1" , then go to "File" and "save image" I used window system. Thank you J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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How to insert a nucleotide to a pdb
by Magdalena Riad 18 Nov '22

18 Nov '22

Hi, I have a pdb-file of the ribosome and would like to insert two nucleotides to one of the rRNA-chains. How do I do that? I’ve found the addaa command for amino acids, is there a similar one for nucleotides? Best regards, Magdalena När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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EULA modification request
by Smith, Lua J. 08 Nov '22

08 Nov '22

Hello UCSF Chimera creators, Our Chemistry department of Missouri University of Science and Technology would like to use your software. Our attorney reviewed the non-commercial software license agreement, and is requesting the legal jurisdiction be struck from the license agreement as well as other modifications. Due to the University being an instrumentality of the state of Missouri and having sovereign immunity under Missouri and federal law, we are not authorized to waive our legal jurisdiction (See Fowler v. Board of Regents, 637 S.W.2d 352 (Mo.App. 1982)). Would you please review the attached requested license agreement modifications, and initial if acceptable? Thank you! Lua Lua Smith Software Support, Information Technology 800 University Drive ljhqn8(a)mst.edu<mailto:ljhqn8@mst.edu> | 573-341-7990<tel:573-341-7990> | it.mst.edu<https://it.mst.edu> [Missouri S&T - 150 Years]<https://www.mst.edu/>

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xyz axis indicator
by Xiang Zhang 01 Nov '22

01 Nov '22

Hi all, I was wondering how I could hide the xyz indicator in the center of window when I was viewing the X-ray density from mtz file? It only appears in crystal unit view mode but disappears in EM projection side view. Best, Xiang

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AlphaFold Modeling
by S.M. RAIHAN RAHMAN 31 Oct '22

31 Oct '22

Hi! Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models? Please let me know. Thank you. Regards, Raihan

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How to invert a map values in UCSF Chimera
by Junha Song BA 31 Oct '22

31 Oct '22

Dear RBVI, I am currently looking into the ways to invert a map in UCSF Chimera so that I can flip the histogram of a map, but I cannot find a volume operation command that does the job. What command in UCSF Chimera allows creating a map with inverted map values? I thought it was vop but I cannot find a parameter that allows assigning negative value operation that would invert the map in UCSF Chimera command line documentation. Best, Junha Song.

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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. 21 Oct '22

21 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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Chimera-users October 2022