- Chimera-users - RBVI Mailing Lists

Utilizing Chimera in Web-Based Workflows
by Rafi Brent 27 Apr '23

27 Apr '23

To whom it may concern, I'm wondering if there's any way to access Chimera without having the GUI downloaded on a local computer. Specifically, I'd like to run chimera as part of a public Google Colab (.ipynb) notebook, which would allow users to access the chimera functionality through either installing a PyPi package or calls to a web-accessible API. Do you know of any tool like this, or have any other ideas for how Chimera could be used in Colab notebook? Thanks so much for any advice you may have. Sincerely, Rafi Brent

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Can't open a cif file
by Steven Frey 26 Apr '23

26 Apr '23

Dear Chimera Team, I’m unable to open the CIF file for a structure that we had done in 2018 and am getting the error shown on the attached jpeg. I am also attaching the CIF file downloaded from CCSD which comes from our original paper: Steven T. Frey, Hillary A. Ramirez*, Manpreet Kauer, and Jerry P. Jasinski. “Crystal structure of a seven-coordinate manganese(II) complex with tris(pyridin-2-ylmethyl)amine (TMPA),” Acta Crystallographica, 2018, E74, 1075-1078. https://doi.org/10.1107/S2056989018009611. I’d like to be able to open the file in Chimera so that I can produce an ORTEP drawing for another paper. Can you help me figure out what the problem is? Thanks, Steve Frey ~~~~~~~~~~~~~~~~~~~~~~~ Steven T. Frey Associate Professor Skidmore College Department of Chemistry 815 North Broadway Saratoga Springs, NY 12866 Phone: 518-580-5124 Email: sfrey(a)skidmore.edu<mailto:sfrey@skidmore.edu>

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Chimera 1.17.1 release
by Eric Pettersen 20 Apr '23

20 Apr '23

Hi again, As it turns out, the changes to web services in the 1.17 release only worked correctly on Mac. Therefore we have made a 1.17.1 release to fix web services on Linux and Windows. If you downloaded the 1.17 release on Mac there is no need to upgrade, but if you downloaded it on Linux or Windows you should upgrade to the 1.17.1 release. Sorry for the inconvenience. --Eric Eric Pettersen UCSF Computer Graphics Lab

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deleting alternate locations
by Elaine Meng 18 Apr '23

18 Apr '23

> On Apr 18, 2023, at 3:07 AM, Yu GUO 郭宇 <guoyu60(a)westlake.edu.cn> wrote: > > Dear, > > I am using Chimera/ChimeraX. I have 2 questions: > > I cannot open ChimeraX (win10 version) recently. Is there any problem in the server? > > I have a PDB file with two structural populations. In Chimera, how to delete the part with fewer population (say 40%)? I rememer it can be realized in the command line, but I forgot. > > Best wishes > Dear Sir, In the future, please use the following addresses (CC'd here) for general questions about the programs: chimerax-users(a)cgl.ucsf.edu for ChimeraX questions chimera-users(a)cgl.ucsf.edu for Chimera questions (where you sent this question is for commercial licensing questions -- thanks) (1) after you download the program, it does not depend on our servers to start. The issue is something with your own setup. The most likely problem is that you need to update your graphics driver but we would need more information from you to say anything else. (2) if you mean atomic occupancy, - in Chimera you can use Dock Prep (menu: Tools... Structure Editing... Dock Prep) and turn on the option "If alternate locations, keep only highest occupancy". You can turn off all the other options if you want. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockpre…> - in ChimeraX, it is not currently in the Dock Prep GUI, but you can use the "altlocs clean" command which would delete all the altlocs that are not currently used. By default, the highest-occupancy ones are the ones that are used, so this would delete the lower-occupancy ones (e.g. your 40%). You can change which altlocs are used with "altlocs change" and show a list of them with "altlocs list" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/altlocs.html#clean> If you need a PDB file then you can save PDB in a separate step, e.g. using File menu or a command. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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determine angle of rotation among two states
by Sen, Anindito 18 Apr '23

18 Apr '23

Dear All, How can I determine the angle of rotation between 2 states of an atomic model, with one state being somewhat skewed from the other. Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

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Doubt regarding the analysis of covalent bonds between the ligand and protein
by Krishna Priya K R 17 Apr '23

17 Apr '23

I am a MSC student working on docking . By using UCSF chimera 1.14 I tried to analyse the H bonds and covalent bonds. Even after following every step for H bond analysis it shows 0 bond and i am not able to find the option to analyse the covalent bond between the protein and ligand. Hope you will help me to rectify my problem. My contact details : 8848890240 Email id : krishnapriyaifs1999(a)gmail.com

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Issues with Chimera
by Bella Carnahan 17 Apr '23

17 Apr '23

Hi! My name is Bella Carnahan and I am a graduate student at the University of Delaware. I am trying to model a small peptide in Chimera 1.17 and keep getting an error message telling me I have a missing file. I have redownloaded the software twice now and have not been able to fix the problem. I have attached a screenshot of the error/any relevant windows. -Bella Carnahan

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Chimera 1.17 release
by Eric Pettersen 14 Apr '23

14 Apr '23

Hello everybody, A new production release of UCSF Chimera (version 1.17) is available: https://www.rbvi.ucsf.edu/chimera/download.html <https://www.rbvi.ucsf.edu/chimera/download.html> Updating to 1.17 is required to continue to use the following tools: BLAST protein, Modeller comparative and loop modeling, and multiple sequence alignment with Clustal Omega and MUSCLE. Due to imminent changes in web services, these tools will soon stop working in older versions of Chimera. Version 1.17 can also fetch UniProt sequences (previously broken by UniProt website changes). Alternatively or in addition, you may want to consider switching to UCSF ChimeraX instead, as it also has tools to run these web services, as well as many new features and enhancements. https://www.rbvi.ucsf.edu/chimerax/index.html <https://www.rbvi.ucsf.edu/chimerax/index.html> Note that Chimera 1.17 includes an export-to-ChimeraX feature, as detailed in the release notes: https://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.17.html <https://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.17.html> Enjoy!

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Chimera cannot read multi-molecules .xyz files in
by Francois Berenger 09 Apr '23

09 Apr '23

Dear list, I can read one molecule fine in .xyz format using chimera. However, if my .xyz file has several molecules (like a MD trajectory), chimera fails to read it in. Is there planned support for MD trajectories given as .xyz file? I have chimera-1.16. I shall test with ChimeraX very soon. Regards, F.

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Aligning homdimers
by James Nettles 04 Apr '23

04 Apr '23

I’m asking a question that has been asked and answered before in 2009 - but not with exact solution that I would like. I have a relatively small homo dimer( <200 residue) and would like to fit with a homo dimer of the almost same sequence but slightly different conformations. I would like to fit the dimers as a pair (A/B to A/B) rather than A to A and B to B separately. In other word, I’m wanting to spread the deviation across both monomer units of the dimer in a single step rather than fitting separately and then recombining. I know Chimera isn’t formally supported any more, but I’m running this on an old machine with an old OS , so ChimeraX isn’t an option here. Thanks so much in advance - this group has always bee fabulous over the years. Best regards, Jim

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