May 2023 - Chimera-users - RBVI Mailing Lists

Chimera interface to Modeller
by Vonderviszt Ferenc 03 Sep '24

03 Sep '24

Hello, I have been using the Chimera interface to Modeller via a web service. This service has been down for a few days. It always stops with the following error message: Service 'opal:Modeller9v8Service' is unavailable What should I do? Please help me. Thanks, Feri

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Finding SASA for individual residues
by Prathvi Singh 29 Aug '24

29 Aug '24

Hi Elaine, Can I use chimera or chimeraX to know the solvent accessible surface area (SASA) for selected residues? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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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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REMINDER: Chimera website downtime
by Elaine Meng 13 Jun '23

13 Jun '23

REMINDER: Due to a scheduled power outage at UCSF followed by server upgrades, the Chimera website and web services will be unavailable -- the estimated downtime is from Tuesday May 16 8pm PDT through Wednesday May 17 8pm PDT. 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. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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chimera-users mailing should be working
by Greg Couch 24 May '23

24 May '23

But the web interface to look at old messages will take some time to get to work. -- Greg

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chimera-users mailing list will be down temporarily
by Greg Couch 23 May '23

23 May '23

We're upgrading the mailing software. Should be back "soon".

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question regarding relative rotation
by Jannick Cornelius Snel-Prentø 21 May '23

21 May '23

Dear Chimera team, I would like to rotate a protein chain with respect to an axis that I define, but I cannot seem to find any way to do that. I have defined the axis, but the turn command will not allow me to use this as the center of rotation. I have also tried constrained motion, but this does not seem to have the parameters needed to do this. Is there a command or a menu that permits rotating a chain or structure around an axis you define yourself? Kr, Jannick

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Making a rotation matrix file by UCSF Chimera or indexing the position
by Dmitry A. Semchonok 19 May '23

19 May '23

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3D_printing
by Francois-Hugues Poree 18 May '23

18 May '23

Dear Chimera Team, first of all, I would like to thank you for providing a sotfware solution to molecular visualization and by the way 3D- printing. I send you this message concerning the UCSF Chimera X version. We usually are preparing our 3D-printing files from data collected from the pdb and to ensure the rigidity of the system, we thick the ribbon size and also add some H-bonds (mainly for helices). However, we are not able to find the way to do it in this version. In the previous version (1.17), the command line was : Tools-depiction-ribbon style editor Could you explain us the new procedure to make this ? We also noticed that the opportunity to save the file in a stl extension was not allowed in the 1.17 version. This option is running in the X version. Thank you very much for your reply Best regards. fhporee François-Hugues Porée Professeur de Chimie Thérapeutique Institut des Sciences Chimiques de Rennes UMR CNRS 6226 Faculté de Pharmacie - Université de Rennes 2 Avenue du Pr Léon Bernard F-35043 Rennes France Tel.02 23 23 41 87

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error
by Athithi Prakash 17 May '23

17 May '23

Hello, I have been trying for a while to build the structure using the SMILES ID, and every time, this error pops up and I am not sure what to do.

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UCSF Chimera Molecular Dynamics: CPU vs GPU
by Alan Carbajo 07 May '23

07 May '23

Good morning, I'm running a molecular dynamics simulation in Chimera, and it seems that the program is only using my cpu for the calculations. Why is this? Is it possible to switch it to use my GPU? Thank you, Alan

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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 04 May '23

04 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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