- Chimera-dev - RBVI Mailing Lists

Request UCSF Chimera source code
by Juan Sebastian Rey Lancheros 22 Dec '22

22 Dec '22

Hello! I'm Juan Rey, a PhD student at University of Delaware. I am interested in reading chimera's methods for resamling EM density maps. I tried downloading the source code from https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html But the download hyperlink ends in a 404 code. If possible could you please send me the source code? Thank you in advance! Best, -- Juan Rey

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https://www.cgl.ucsf.edu/chimerax/docs are down?
by Gong, Zhen 22 Dec '22

22 Dec '22

Dear Chimera and ChimeraX developers, I was not able to open any webpage of https://www.cgl.ucsf.edu/chimerax/docs and getting this error message: [cid:image001.png@01D915F8.4C0EA080] I switched to Chrome and still had the same problem. I am wondering if there is a problem with the UCSF server? Many thanks to your help and happy holidays. Best, Zhen

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Help
by Ali Doostmohammadi 13 Nov '22

13 Nov '22

Hi! I gave my protein to ClusPro for docking and it gave me the PDB file. For the next step, I need to upload to Prodigy, which requires me to separate the ligand chain and receptor chain to perform the analysis. But in the PDB file that I open in Chimera, there is only one chain, and ligand and receptor are divided as sub-branches of that chain, and Prodigy algorithm does not accept it. I wanted to know how to divide the protein and its receptor into two different chains? Best regards!

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Application Security Questions for Chimera
by Hart, Michael 25 Oct '22

25 Oct '22

I've been asked to approve installation of Chimera in one of our labs, and I was hoping that you might have documentation on your development processes and policies such that I can feel comfortable installing your app in our environment. I have searched but not found documentation related to OWASP or other dev standards, or any assessments that may have been run. Would you have information available? Thank you in advance, Mike Hart | Chief Information Security Officer (CISO) Metropolitan State University of Denver Information Technology Services Campus Box 96, P.O. Box 173362, Denver, CO 80217-3362 Admin Building - 1201 5th Street 480M Denver, CO 80204 303-615-0541 (Office) 303-352-7548 (Help Desk) mhart20(a)msudenver.edu<mailto:mhart20@msudenver.edu> | www.msudenver.edu/technology<http://www.msudenver.edu/technology> [cid:image001.jpg@01D8E848.158CADA0]

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ChimeraX pyhton script
by Jan Hofmann 17 Oct '22

17 Oct '22

To whom it may concern, I want to write a python script to open a pdb file, then load a .xplor file in as well. After one rotation which I also want to do via the script I want to export the output file as a .png file. Could you provide any advice to me on how to write such a script? I am having troubles loading any python script into ChimeraX. Eventually I want to use this script to batch wise output structures including guest adsorption where the guest species is introduced via the .xplor from previous analysis and the structure is provided by a .pdb file. I really would need some advice/tutorial at this stage so I would be more than happy to hear back from you. Many thanks and kind regards, *Jan Hofmann, M.Sc.* *PhD Student, Department of Chemistry* *Chapman Group* Stony Brook University *jan.hofmann(a)stonybrook.edu <andrew.nicoll(a)stonybrook.edu>* Office: Room 563, Chemistry

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Old post edit or deletion?
by Bernard Lieberman 27 Sep '22

27 Sep '22

Hi folks, I'm trying to scrub some of my data from the web and noticed my phone number and website appear at the following page. Can this please be removed or edited? http://plato.cgl.ucsf.edu/pipermail/chimera-dev/2015/001208.html Thanks! Bernard

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popup balloons with custom information for vrml models
by Merce Alemany Chavarria 13 Sep '22

13 Sep '22

<mailto:chimera-dev@cgl.ucsf.edu> Dear Chimera developers, We are developing an extension that renders vrml models using BILD commands. For the moment the vrml models have a name that shows up on Models Panel, but when the mouse is placed on top of them only the number of model is displayed (like '#11'). We would like to add to the models a popup balloon with customized information, in a similar way as information if shown for classical chimera objects (atoms, bonds...). Could you guide us on how to approach it? I will use this e-mail also to let you know that the link to chimera's source code (https://plato.cgl.ucsf.edu/trac/chimera/browser/trunk) found in this page https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html returns a 404 error. Is there an alternative way to check it out? Thank you for your help, Mercè

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Surfnet
by Samo Lešnik 31 Aug '22

31 Aug '22

Dear Madam/Sir, I was wondering if it is possible to run the Surfnet calculation using the command line tool. I wish to automate it for MD trajectory for every frame and this would be useful. Thank you! Samo Dr. Samo Lešnik, mag. farm. / Researcher Univerza v Mariboru / University of Maribor Fakulteta za kemijo in kemijsko tehnolgijo Faculty of Chemistry and Chemical Engineering Smetanova ulica 17, 2000 Maribor, Slovenija T: +386 2 2294 428 E: samo.lesnik(a)um.si<mailto:samo.lesnik@um.si>

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Issue regrading saving the protein-ligand complex
by preetj 02 Aug '22

02 Aug '22

Hello Elaine, I have been trying to save a protein-ligand complex in pdb format with the command line,but i haven't successful doing so. I have tried using write, display, select command but nothing worked. Steps that i followed: Open the NoH.pdb file in chimera With command line: cd /home/Desktop/test/Cmd_Tango_Dock/OUT/1abe.pdb/tmpO9IqaJ viewdock rigid_ranked.mol2 "Dock 4, 5 or 6" combine #0,1.1 111_#name.pdb-I used this command to save my result. If you could tell me what mistake I am making in saving the file. Thank You Regards Preet ------------------------------------------------------------------------------------------------------------ [ C-DAC is on Social-Media too. Kindly follow us at: Facebook: https://www.facebook.com/CDACINDIA & Twitter: @cdacindia ] This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. ------------------------------------------------------------------------------------------------------------

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python script for ligand preparation
by ngayatri 07 Jul '22

07 Jul '22

Dear Chimera Team, I am trying to prepare separate ligand file and saving it in the .mol2 file. So if you could help with script or the approach would be grateful. Thank You Regards Gayatri ------------------------------------------------------------------------------------------------------------ [ C-DAC is on Social-Media too. Kindly follow us at: Facebook: https://www.facebook.com/CDACINDIA & Twitter: @cdacindia ] This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. ------------------------------------------------------------------------------------------------------------

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