- ChimeraX-users - RBVI Mailing Lists

Guidance on aligning models with overlapping aa subsequences
by Martin Gordon 07 May '24

07 May '24

Hi everyone, I'm hoping to get some assistance from the community for visualizing structures from multiple AF runs with overlapping subsequences. We have been using AlphaFold monomer to try to identify structure and domains of a large (+3000aa) human protein. Our AF runs fail to model the full structure (possibly insufficient resources), so we have tried 'breaking' up the protein into overlapping subsequences. I was wondering if there is a sensible way to combine these substructures based on their overlapping regions? I have tried matchmaker, which I believe constructs a MSA and attempts to align the structures, but it seems a significant region of the overlap is not aligning correctly (img below with the overlapping subsequences highlighted). Any guidance is greatly appreciated. Thank you, Martin [image: image.png] Thank you, Martin

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Inquiry on the vertex_convexity function
by Yoseph Loyd 07 May '24

07 May '24

Hi ChimeraX Team, My name is Yoseph, I'm a student. I saw that your measure convexity function 'vertex_convexity' is documented to report the vertex convexity from ' 2pi - half cone angle of the incident vertex and all triangles the incident vertex is a part of'. Is the half cone angle generated by averaging all half cone angles? Thank you for taking the time to read this and I hope your day goes well. Best regards, Yoseph Loyd

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Making movie of whole cell model with EM images
by George Schaible 07 May '24

07 May '24

Hello, My name is George Schaible and I am a post doc at Montana State University. I would like to use ChimeraX to make my movies of whole cell serial block face EM data I have modeled in IMOD/3dmod and I was wondering if someone could point me towards a tutorial or some way that I can make the movie using both the model and the original EM data. Any information is helpful and thank you! -- George A. Schaible, Ph.D Dept. of Chemistry & Biochemistry Montana State University Google Scholar profile <https://scholar.google.com/citations?user=_M2xvYIAAAAJ&hl=en>

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No version number in Add- Remove Program (Windows)
by Gruhm, Sebastian 07 May '24

07 May '24

Hello, I manage the software distribution at the Frei Universität Berlin, and I noticed that after installing ChimeraX 1.7.1, the entry in "Add-Remove Programs" (ARP) does not include a version number (see attached Screenshot). This is problematic because I cannot create a query for the version number in the software distribution (SCCM). All that would need to be done to display the version number under ARP is to create the RegKey "DisplayVersion" under "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\UCSF ChimeraX_is1". Would be great to see this implemented in the next version of ChimeraX. Mit freundlichem Gruß Sebastian Gruhm [cid:image001.jpg@01DAA061.0DA8A940] Zentraleinrichtung für Datenverarbeitung Server Infrastructure (SI) Fabeckstraße 32, 14195 Berlin Raum: 110 Phone: +49 30 838 58668 sebastian.gruhm(a)fu-berlin.de

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Adjust the Rotation Axis Size in ChimeraX
by AARON FERRELL 07 May '24

07 May '24

Hello, Is there a way to adjust the size of the rotation axis generated by the command line "measure rotation #2 toModel #1, in ChimeraX? I am looking to adjust both the length and diameter of the axis display. Please let me know! Best, Aaron

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Issue with Recurring Update Notifications in ChimeraX
by ahmed morsy 07 May '24

07 May '24

Dear ChimeraX Support Team, I hope this message finds you well. I am writing to ask for help with an ongoing issue I've been having with ChimeraX. Despite having downloaded and installed the most recent version of ChimeraX, I continually receive prompts to update the software each time I launch it. This occurs even though I am certain I am running the latest version. Could you please help me understand why this might be happening, and advise on how to resolve this issue? It would be helpful if you could provide steps or recommendations to ensure that the software recognizes the current version installed on my system. Thank you for your time and assistance. I look forward to your prompt response. Best regards,Ahmed Morsy=========================Ahmed Morsy, Ph.D. Assistant Professor, Department of Stem Cell & Regenerative Biotechnology,Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, KoreaTel.: 02-450-0498C.P.: +82/10-5299-5844E-mail: ahmed_morsy86(a)yahoo.com; ahmed(a)konkuk.ac.kr Orcid id: https://orcid.org/0000-0003-3873-9903 Scopus id: 55258308400 (https://www.scopus.com/authid/detail.uri?authorId=55258308400) Researchgate: https://www.researchgate.net/profile/Ahmed-Abdal-Dayem GoogleScholar: https://scholar.google.co.kr/citations?user=NevFBgMAAAAJ&hl=en

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Alphafold
by Chang, Jufang 06 May '24

06 May '24

Dear Sir Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back? Thank you Ju-Fang ________________________________ 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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Amber output pdb file - can't open... bad PDB record
by Alexander Hung Lee 06 May '24

06 May '24

Hi! I have a large system containing >100k atoms w/o water. Amber produced a pdb file, and I have a trajectory file for it. When I try to open the pdb in chimeraX, most of it loads but with warning "Ignoted bad PDB record on line xxx" and it's all for atom # > 9,999. As a result, when I try to open the .nc file along with the pdb file, the # of atoms don't match anymore. Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Re: [Chimera-users] Chimera scripting
by Elaine Meng 06 May '24

06 May '24

Hello Flip, (1) we would generally recommend using ChimeraX over Chimera for many reasons: performance, enhanced features, current development and support. The rest of this answer applies to ChimeraX so I'm putting it on the chimerax-users list. (2) you can create a blank cubic grid first with "volume new" and then refer to that in the "molmap" command "onGrid" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#new> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> (3) I do not understand what you mean by losing secondary structure information when saving a map. Only atomic structures (not maps) have secondary structure information, i.e. helix and strand assignments. Can you clarify? I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 6, 2024, at 10:40 AM, Flip Jansen via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Chimera dev team, > > I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps. > > One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map. > > Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC? > > Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information? > > Any help is highly appreciated, I would also be happy to come by an talk in person. > > Best, > Flip Jansen

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session files question
by Krishnan Raman 06 May '24

06 May '24

I have two large session files (1-2 GB). Is there any way to combine them ? thanks Krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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