August 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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Unable to run UCSF chimera using
by Prathvi Singh 30 Aug '23

30 Aug '23

Hi, Is it possible to use python to execute commands on the command line of UCSF chimera without actually opening its GUI on the Windows platform? If not, then how to use python to open its GUI and execute the commands? I tried the "subprocess.Popen()" and "os.system()" methods to run its GUI by passing the path of chimera executable (version 1.17.1) to them but chimera is displaying an error with exit code 1 (snapshot attached). However, I am able to launch chimeraX (version 1.6.1) via these methods. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Display of double/tripe bonds
by Ghislain Deslongchamps 29 Aug '23

29 Aug '23

Hi all, I wish to use Chimera for my students to view organic models that I created in MOE. How can Chimera display double/triple bonds? They appear as single bonds in .pdb, .mol, .mol2 formats. Thanks. Cheers, Ghislain GHISLAIN DESLONGCHAMPS Professor Department of Chemistry • Faculty of Science T 506 470-9976 F 506 453-3570 WWW https://www.deslongchamps<https://www.deslongchamps.ca/>.ca<https://www.deslongchamps.ca/> UNB campuses are open with strict adherence to New Brunswick Public Health requirements. Our priority continues to be providing high quality education while ensuring the health and safety of our community. [attachment.jpeg] [attachment.jpeg] /uofnb<https://www.facebook.com/uofnb> [attachment.jpeg] @unb<https://twitter.com/UNB> [attachment.jpeg] @discoverunb<https://instagram.com/discoverunb/> UNB.ca<http://www.unb.ca/> Confidentiality Note: This email and the information contained in it is confidential, may be privileged and is intended for the exclusive use of the addressee(s). Any other person is strictly prohibited from using, disclosing, distributing, or reproducing it. If you have received this communication in error, please reply by email to the sender and delete or destroy all copies of this message.

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How to show certain hydrogen bonds and hide others
by Karjalainen, Mikael 29 Aug '23

29 Aug '23

Hi! I am having problems to show certain hydrogen bonds and hide others. For example, I would like to hide some completely. Then others should be shown always. Even when atoms are not shown and only ribbon is. I couldn't find how to do this by googling or for example reading how to use hbonds command. I am using Chimera 1.16. I know that there is ChimeraX, but now I need to modify old project. Regards, Mikael

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Atlocs
by Hernando J Sosa 28 Aug '23

28 Aug '23

Dear ChimeraX, I have an atomic model with several chains that have residues with alternate locations A and B. I noticed that while Chimera by default displays alternate locations A. ChimeraX for some chains display alternate locations A and for other chains alternate locations B. Why is this behavior different in Chimera and ChimeraX? Is this a novel feature of ChimeraX? I this is the case how ChimeraX decides which of the two alternate locations A or B to display? Thanks Hernando ___________________________________ Hernando Sosa, PhD. Dept. of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 emai: hernando.sosa@einsteinmed.<mailto:hernando.sosa@einsteinmed.org>edu ___________________________________

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Saving the resolution of structure to a file
by Prathvi Singh 22 Aug '23

22 Aug '23

Hi Elaine, Is there a way to save the resolution of a protein structure to a file using command line, either in chimeraX or chimera? Thanks -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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dms from command line
by Guido Leoni 21 Aug '23

21 Aug '23

Dear list Is there an option to write dms from command line? I' m able to launch the command line interface with a pdb loaded within . Then I estimate the surface with this command surface #0 now I would write a dms ... Please do you have any tips that can help me? Thank you Guido

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non-integral charge warning
by Chris Ellis 21 Aug '23

21 Aug '23

Hi, After running the dock prep, I get the following warning in the reply log. Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log How can I fix this warning? Do I need to fix this? Thank you for any help you can provide. I truly appreciate it. Chris

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