- Chimera-users - RBVI Mailing Lists

Web site downtime
by Eric Pettersen 04 May '23

04 May '23

Hi all, Due to a scheduled power outage at UCSF followed by server upgrades, the Chimera website and web services will be unavailable from Tuesday May 16 through most of Wednesday May 17. This upgrade will remove the Opal web services used by older versions of Chimera. Therefore, to continue using the Chimera tools running BLAST protein, Modeller comparative and loop modeling, and multiple sequence alignment with Clustal Omega and MUSCLE web services, you will need to upgrade to Chimera 1.17 (Mac) and 1.17.1 (Windows/Linux). Please pardon any inconvenience. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [Chimera-users] use with iPads
by Levy,Hazel C 04 May '23

04 May '23

Hello. I'm looking to use chimera on iPads to introduce High School and Middle School students to structural biology. Do you offer a discount for education licenses? Can Chimera be used on an ipad, even if not to its full capacity? Kind regards, Hazel C. Levy, M.Sc., Ph.D. Associate Director – UF Center for Precollegiate Education and Training (CPET) Adjunct Assistant Instructional Professor – Department of Biology | College of Liberal Arts and Sciences Doctoral Student – Higher Education Administration and Policy | College of Education ______________________________________________ Office: 339 Yon Hall | Box 112010 | Gainesville, FL 32611-2010 Phone: (352) 392-7683 Fax: (352) 392-2344 www.cpet.ufl.edu<http://www.cpet.ufl.edu/> [Image result for uf logo] ________________________________ From: Levy,Hazel C <hclevy(a)ufl.edu> Sent: Thursday, May 4, 2023 10:08 AM To: chimera(a)cgl.ucsf.edu <chimera(a)cgl.ucsf.edu> Cc: Desai,Ayan D <ayan.desai(a)ufl.edu>; Anthony, Michael S. <anthonym(a)cpet.ufl.edu> Subject: use with iPads Hello. I'm looking to use chimeraX on iPads to introduce High School and Middle School students to structural biology. Do you offer a discount for education licenses? Can Chimera be used on an ipad, even if not to its full capacity? Kind regards, Hazel C. Levy, M.Sc., Ph.D. Associate Director – UF Center for Precollegiate Education and Training (CPET) Adjunct Assistant Instructional Professor – Department of Biology | College of Liberal Arts and Sciences Doctoral Student – Higher Education Administration and Policy | College of Education ______________________________________________ Office: 339 Yon Hall | Box 112010 | Gainesville, FL 32611-2010 Phone: (352) 392-7683 Fax: (352) 392-2344 www.cpet.ufl.edu<http://www.cpet.ufl.edu/> [Image result for uf logo]

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Midas Error- reg
by Johnson Paul 03 May '23

03 May '23

Dear Sir, I am J Johnson Paul, I have recently used your software for my study and research purposes after usage of your software in the area of peptide build structure area I have got an error like MidasError: Dunbrack rotamer library does not support ASX File "C:\Program Files\Chimera 1.17.1\share\Rotamers\__init__.py", line 680, in useBestRotamers raise MidasError("%s rotamer library does not support %s" %(lib, rType)) This type of error is soon to me,So please kindly reply to my mail to solve the problem as soon as possible *With Regards,* *J Johnson Paul.*

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Looking Glass
by tolung.bio＠gmail.com 29 Apr '23

29 Apr '23

Hello, � When I try the look on command as instructed on this page: � � I receive the message � “Did not find LookingGlass screen name LKG-P14191, found \\.\DISPLAY2 <file://./DISPLAY2> , \\.\DISPLAY1 <file://./DISPLAY1> , \\.\DISPLAY3 <file://./DISPLAY3> , \\.\DISPLAY4 <file://./DISPLAY4> ” � Then the quilt window opens but in the main display where the main ChimeraX window is, instead of on the LookingGlass Portrait. � When I tried the option “deviceNumber 2”, since my Looking Glass in display #2, the same happens. � Do you have any suggestions to try for getting this to work? � Looks like Looking Glass might have changed how the device is named, and may that be the reason why ChimeraX is failing to detect it correctly? If that’s the case, will there be an updated version with a fix for this? � Thanks, Gökhan �

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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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