- Chimera-users - RBVI Mailing Lists

Showbox
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 03 Nov '21

03 Nov '21

Hi, I know that the program showbox is related to Dock, but I can't find a mailing list still active for Dock users... Maybe someone could help me here. I don't understand if ligands that are docked inside the binding site can exit in part from the box the user defines for grid calculation. I think that maybe if sphere centers are very near the boundaries of the box, it could be possible, but I'm not sure. Does anyone know it? Thanks and regards.

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Counting the number of water molecules
by Prathvi Singh 02 Nov '21

02 Nov '21

Hi, Is there a command in UCSF chimera to count the total no. of water molecules in a PDB file? Can we also count, say the total number of alanine residues in a PDB file or any other other residue for that matter? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Bug Report: Chimera exit abnormally: code 1073741819
by Jyoti Singh 01 Nov '21

01 Nov '21

Dear Sir, I have installed Chimera 1.15 successfully.When I try to open it, a window pops-up and gives an exit code: 1073741819 and it never opens for analysis. Below I have shared the start information and please find the attachment. *Cannot execute 'gzip': no automatic decompression of .Z filesinitializing general preferencesloading Tixinitializing graphicsReturn code: -1073741819Press return or enter to to exit* Kindly do needful. Regards. *Jyoti SinghPh.D. Scholar [UGC-SRF]"Molecular Biology and Biotechnology lab"CPMB DIVISION, GARDEN BLOCK.CSIR - National Botanical Research Institute, Lucknow [UP], 226001, 'INDIA'*

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(no subject)
by Thirumurugan Prakasam 30 Oct '21

30 Oct '21

Hi, I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues. Looking forward to hearing from you, Many thanks, Thiru [image: image.png] -- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358

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Postdoc positions to explore the world of molecules!
by Marc 29 Oct '21

29 Oct '21

Seeking 2 post-doctoral fellows with experience related to Biology/Bioinformatics, Unity3D, Virtual Reality or computer graphics to come to Paris. View this email in your browser (https://mailchi.mp/8702ad4a4ddd/postdoc-positions-to-explore-the-world-of-m…) Dear Colleague , I hope you are well. My apologies for contributing to filling your inbox. I am urgently looking for two new people to join my team and I am depending on your help. The positions I am looking to fill are very good positions in France, described below. They deal with immersive scientific visualization of membrane proteins, their assembly and omic data. Could you please forward this email to anyone you know who might be considered for this position? I would be very grateful for it. Please let me know if you have any questions. With best wishes, Marc ** Come explore the world of molecules! ------------------------------------------------------------ https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id… I am seeking two post-doctoral fellows to start immediately in my lab. My lab is focused on the development of novel approaches for interactive visualization of molecular structures, including using UnityMol to create 3D user interfaces and Virtual Reality applications. The positions will involve the development of novel software components for high throughput molecular visualization, as well as challenging biological applications. We are looking for someone that is passionate about Molecular Biology who also has skills in computer programming and graphics design. See more details at the following links: * immersive scientific visualization of membrane proteins and their assemblies (https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id…) (PDF version) (https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id…) * immersive scientific visualization of omic data (https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id…) (PDF version) (https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id…) More information about the institute and work environment is described through a series of short videos with testimonials and overviews (https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id…) . I hope you will be interested in joining our team! Sincerely, Marc Baaden LBT lab . 13 rue Pierre et Marie Curie . CNRS UPR 9080 / IBPC . Paris 75005 . France You are receiving this email as part of my professional network. Want to change how you receive these emails? You can update your preferences (https://ibpc.us4.list-manage.com/profile?u=1a86fc891fac34d890ad5fe30&id=b29…) or unsubscribe (https://ibpc.us4.list-manage.com/unsubscribe?u=1a86fc891fac34d890ad5fe30&id…) Email Marketing Powered by Mailchimp http://www.mailchimp.com/email-referral/?utm_source=freemium_newsletter&utm…

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Re: [Chimera-users] [Chimera] Different bond width in the same model
by Elaine Meng 29 Oct '21

29 Oct '21

On Oct 28, 2021, at 4:56 AM, Konstantin Richter <konstantin.richter(a)bbz.uni-leipzig.de> wrote: > > Dear Elaine, > I am currently trying to create molecular figures with the old Chimera (not ChimeraX). I would like to represent different bonds in the same model in different bond widths: in my case, a disulfide bond should be represented thicker than the bonds of a nearby ligand. > > I already learned that the bond width is the product of the stick scale (which is a model attribute) multiplied by the bond radius (which is an atom attribute, if I got it right): https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-November/009289.html > > So changing the bond radius for only the ligand atoms but not the disulfide atoms would do the job for me, right? Unfortunately I have no idea how to change the bond radius in the command line. Is there any command for that? > > Thanks in advance for your help! > > best wishes > Konstantin Richter Dear Konstantin, You can change the bond radius in the Selection Inspector (e.g. select the part you want to change, then click the green magnifying glass in the lower right). In the Selection Inspector, inspect: Bond, and then change the bond radius value for the current selection. If you hold the mouse over the "radius" part of that dialog, a popup balloon says that the name of this bond attribute (for using in commands) is "radius" If you prefer to use commands only, the command to set attribute values is "setattr," e.g. setattr b radius 0.4 .... to change all bonds setattr b radius 0.1 sel ... to change bonds in the current selection (and you can use any other atomspec, not just "sel", e.g. model numbers, residue names or numbers, etc.) The general explanation of this and how to change it is <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#repre…> Selection Inspector <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html#bondprop"> setattr command <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> 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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Assistance
by Priyanka Abeyrathne 28 Oct '21

28 Oct '21

Hi, Could you please assist me in how to remove the text after measuring distance (ex: text distance 2.0 A) in the Chimera session. Thank you. Kind regards, Priyanka

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RR Distance Maps: Exporting St. Dev Map
by Woods, Taariq (NIH/NEI) [F] 27 Oct '21

27 Oct '21

Hello, I am doing some analysis on homology models. I generated the RR Distance Map for 5 structures. I wanted to export the standard deviations map only so that I can see the numerical values, but every time I click export in only gives me the option of exporting a map of the distances. I was just wondering if I could have some help with this if I am missing something. Regards, Taariq

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Chimera can't be launched
by salar moniri 25 Oct '21

25 Oct '21

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Fwd: video card for chimera?
by Elaine Meng 22 Oct '21

22 Oct '21

> Begin forwarded message: > > From: "Sergei I. Sukharev" <sukharev(a)umd.edu> > Subject: video card for chimera? > Date: October 22, 2021 at 8:37:27 AM PDT > > Colleagues, > I am upgrading my PC and I would take your recommendations about the best video cards that would work with Chimera and Phenix. > Thanks, > sergei sukharev, umd Hi Sergei, We recommend taking a look at using ChimeraX instead of Chimera. We are actively developing ChimeraX (but not Chimera) and in the future it may have features specifically for working with Phenix. I have to leave the video card question for others, but encourage responses about what works well with ChimeraX. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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