November 2022 - Chimera-users - RBVI Mailing Lists

How to insert a nucleotide to a pdb
by Magdalena Riad 18 Nov '22

18 Nov '22

Hi, I have a pdb-file of the ribosome and would like to insert two nucleotides to one of the rRNA-chains. How do I do that? I’ve found the addaa command for amino acids, is there a similar one for nucleotides? Best regards, Magdalena När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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Query regarding the Zone tool in UCSF chimera
by Prathvi Singh 18 Nov '22

18 Nov '22

Elaine, In UCSF Chimera, when I try to find all the atoms within 4A of a selected residue using the *Zone* tool, it selects several atoms around that residue. However, I am not able to understand which atom of the selected residue was taken as the reference point for calculating the distances. Please help. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Information regarding double bonds
by Naima syed 18 Nov '22

18 Nov '22

Hello, I have one concern, before docking there is a double bond which i can check in pymol but after docking that double bond was lost. Can you please tell me how to fix this problem. Thank you

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No MMTK name for atom "H" in standard residue "GLY"
by Marco Sette 15 Nov '22

15 Nov '22

Dear all, i'm trying to minimize a peptide (Tools, Structure editing, Minimize Structure) but I obtain this error message: No MMTK name for atom "H" in standard residue "GLY". I have a Gly in position 1, does this depends on the NH protonation? Also, I fixed most of the residues, including Gly 1, trying to minimize a small region (Fixed Atoms: selected, in minimize panel) but still have the same errors. How can I solve it? Thanks for your help, Best Marco -- Dr Marco Sette, PhD. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 -- Questa email è stata esaminata alla ricerca di virus dal software antivirus Avast. www.avast.com

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combining two models into single model with two chains
by Elaine Meng 13 Nov '22

13 Nov '22

Hi Ali, I don't know what you mean by "sub-branches of that chain" -- if they are listed as two separate things in the Model Panel (e.g. #0.1 and #0.2), then it means they are two separate models. You can show Model Panel from the Favorites menu. If so, then you want to put them together into one model with two different chains. For that, see the "copy/combine" function in the Model Panel (in the menu under Favorites) or the "combine" command. Details in the User Guide: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> If they are really only one model with one chain, then you can only change the ID of part of the chain if the two parts are really disconnected. See Tools... Structure Editing... Change Chain IDs: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changech…> If they are NOT disconnected, you would have to manually edit the PDB file in some text editor first to add a TER between the parts. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.h…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. for general questions the better address is chimera-users(a)cgl.ucsf.edu CC'd here. The chimera-dev address is for programming questions. > On Nov 12, 2022, at 5:56 AM, Ali Doostmohammadi via Chimera-dev <chimera-dev(a)cgl.ucsf.edu> wrote: > > 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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NHR Atomistic Simulation Center Online Symposium 2022, Nov 28-29
by Harald Lanig 11 Nov '22

11 Nov '22

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MD simulation movie in chimeraX
by Shivam Gupta 09 Nov '22

09 Nov '22

Hello Support Team, I am a commercial license user of chimeraX. I have .trr and .tpr files from the Gromacs MD simulation. I am not getting any option to create an MD movie. I know how to do it in chimera but couldn't find a similar GUI/option in chimeraX. Literature/tutorial of chimeraX didn't help me much. Please help me out by guiding me to generate MD movies. Please reply to this email inline. I am Looking forward to hearing from you. Thanks -- With Regards Gupta Shivam グプタシヴァム E-mail: *shivam-gupta(a)pharmafoods.co.jp <a-higashiyama(a)pharmafoods.co.jp>* Biomedical Department Pharma Foods International, Kyoto Japan 株式会社ファーマフーズ〒615-8245 京都市西京区御陵大原1-49 TEL:075-748-9811 FAX:075-948-9818 URL: http://www.pharmafoods.co.jp/

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EULA modification request
by Smith, Lua J. 08 Nov '22

08 Nov '22

Hello UCSF Chimera creators, Our Chemistry department of Missouri University of Science and Technology would like to use your software. Our attorney reviewed the non-commercial software license agreement, and is requesting the legal jurisdiction be struck from the license agreement as well as other modifications. Due to the University being an instrumentality of the state of Missouri and having sovereign immunity under Missouri and federal law, we are not authorized to waive our legal jurisdiction (See Fowler v. Board of Regents, 637 S.W.2d 352 (Mo.App. 1982)). Would you please review the attached requested license agreement modifications, and initial if acceptable? Thank you! Lua Lua Smith Software Support, Information Technology 800 University Drive ljhqn8(a)mst.edu<mailto:ljhqn8@mst.edu> | 573-341-7990<tel:573-341-7990> | it.mst.edu<https://it.mst.edu> [Missouri S&T - 150 Years]<https://www.mst.edu/>

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Finding disulphide bonds
by Prathvi Singh 08 Nov '22

08 Nov '22

Hi Elaine, I have found out a way to select the disulphide bonded CYS residues in UCSF chimera using the command: *select disulphide*. However, is there a way to count the number of disulphide bridges in a protein and save in a variable? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Question regarding 2dlabels in Chimera
by leonard.maurer＠uni-bonn.de 07 Nov '22

07 Nov '22

Hi, I am using Chimera for several years now and I really enjoy it, but there is one issue I could not solve until now: Is it possible to have subscript/superscript for the 2D labels? For example something like "subunit A\_{1}" and "subunit A\^{1}" that I can type either in the 2d labels GUI text part or with the 2dlabels command, which gives me the raised and lowered versions of the "1"? I am confident that this feature might be already implemented given Chimera's impressive amount of tools, but I was not able to find it in the documentation so far. Thanks in advance! Best regards, Leonard

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