- Chimera-users - RBVI Mailing Lists

fit into map global
by Dieter Blaas 12 Oct '22

12 Oct '22

Hi, I am struggling to fit a model of a single protomer into a viral cryo-EM map. I usually succeed after a very long process of manually positioning the model approximately and then running 'fit into map' that arranges it in the best way. I filtered the map to low resolution and used the option to generate a density map of the pdb file which makes it easier but it is still complicated. However, I believe that there is a routine to globally fit that does not require the very cumbersome first manual fitting. Can anybody please give me a hint? Thanks a lot, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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how to find size of a molecule using Chimera
by Aditi Laddha 10 Oct '22

10 Oct '22

Hi Elaine, I wanted to find the size of a molecule which acts as a substrate (consisting of multiple elements) for my protein, I want to know the diameter of the molecule. But I am unable to find a way to do it. Can you please guide me through the process of determining the size of a molecule? -- Regards, Aditi Laddha PhD Scholar Indian Institute of Technology, Kanpur, Uttar Pradesh 208016

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Enquiry about the ligand library generation by scripts in Chimera
by Zhenjiao Du 07 Oct '22

07 Oct '22

Good morning, Dear Professor, My name is Zhenjiao Du, from Kansas State University. I am employing molecular docking for peptide screening and need to build peptide ligands for docking screening. I used to generate ligand by VMD and then energy minimized by molecular dynamics simulation, but the final conformation is not that matchable to the crystallography results. Chimera generated ligands perform a better job. I find Chimera provides amazing ligand energy minimization protocols, but there is no any resource for the scripts based ligand generation and minimization since I might need to generate thousands of peptide ligands for virtual screening. I find Chimera also supports python programming. Could you please provide me some information for the ligand generation by Chimera based on python scripts? I really appreciate it. I am looking forward to your reply. Sincerely, Zhenjiao Du Vice president of CAFS Student Committee Ph.D. student, Cereal Chemistry Grain Science & Industry, Kansas State University 150A Waters Hall, Manhattan, KS 66502 Pronouns: He/His

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Unit cell for dcd
by Huang, Caleb 05 Oct '22

05 Oct '22

Hello, I'm trying to make a psf+dcd movie with periodic boundaries on. The feature I'm looking for I believe is "Unit Cell", but it seems to only work for pdb files. Is there a way to create repeating cells using psf+dcd files? Thanks for any help! -Caleb

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Molecular Dynamics Simulation RMSD for only spesific atoms
by Barış KURT 27 Sep '22

27 Sep '22

Hello, my intention is to plot RMSD chart for only Pd,Cl,Cl,C atoms (their numbers are 1,2,3,4). But I couldn't find a way to do it.Also II want to plot dihedral RMSD for all atoms except C,H,Cl,P atoms.How can I do that? Thank you

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save map
by Wu, Weimin /US 27 Sep '22

27 Sep '22

Hi, Does Chimera have a built-in function to save the map after it is fit into another map? The current save map could not save the new orientation and new location. Thanks, Weimin

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chimeraのダウンロードについて
by 加藤　玲佳 27 Sep '22

27 Sep '22

初めまして、私は日本の大学に通う加藤玲佳と申します。この度、大学の授業でUCSF chimeraを用いることになったのですが、「accept」ボタンを何回もクリックしてもダウンロードができません。何が原因なのかを教えていただけると幸いです。ちなみに私が普段使っているパソコンはWindows10です。よろしくお願いいたします。加藤玲佳 reika.0204(a)outlook.jp<mailto:reika.0204@outlook.jp>

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Website downtime starting Tuesday, Sep 27
by Elaine Meng 26 Sep '22

26 Sep '22

Dear users, The RBVI website (Chimera, ChimeraX, etc.) and RBVI-hosted web services will be down for maintenance from Tuesday, Sep 27 9pm PDT, through Wednesday, and possibly extending to Thursday, Sep 29 5pm PDT. PDT = Pacific Daylight Time. RBVI-hosted web services called from Chimera and ChimeraX include Blast Protein, Modeller, and multiple sequence alignment with Clustal Omega or MUSCLE. Sorry for the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Website downtime starting Tuesday, Sep 27
by Elaine Meng 23 Sep '22

23 Sep '22

The RBVI website (Chimera, ChimeraX, etc.) and RBVI-hosted web services will be down for maintenance from Tue, Sep 27 9pm PDT, through Wed, possibly extending to Thu, Sep 29 5pm PDT. RBVI-hosted web services called from Chimera and ChimeraX include Blast Protein, Modeller, and multiple sequence alignment with Clustal Omega or MUSCLE. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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help
by Carlos Alberto Lira Júnior 22 Sep '22

22 Sep '22

Hello, I'm trying to open a file through tools>MD/Ensemble>MD movie. Then I add the path of the file but several errors appear, as shown in the images below. Therefore, I ask for help to solve this problem. I point out that the files were opening normally [image: image.png] [image: image.png] [image: image.png] [image: image.png] -- *"Não te deixes vencer pelo mal, mas vence o mal com o bem”* (Romanos 12:21) Prof. Carlos Alberto Lira Junior (98) 9 988298677 Lattes <http://lattes.cnpq.br/3535248767494263> *AVISO DE CONFIDENCIALIDADE*: Esta mensagem, e qualquer conteúdo anexo, pode conter informações confidenciais e/ou sensíveis, destinadas exclusivamente aos seus destinatários. Se você recebeu esta mensagem e qualquer conteúdo anexo por erro, qualquer reenvio, disseminação, distribuição ou cópia é proibida por lei. Por favor notifique o remetente imediatamente e destrua a mensagem e todo o conteúdo anexo. *CONFIDENTIALITY NOTICE*: This message and any attachment(s) may contain confidential and / or sensitive information and is for the sole use of its intended recipient. If you receive this transmittal and any attachment(s) in error, any review, dissemination, distribution or copying is prohibited by law. Please notify the sender and immediately destroy the message and all its attachments. Thank you for your co-operation. -- *Missão Institucional:* Promover educação profissional, científica e tecnológica, por meio da integração do ensino, pesquisa e extensão com foco na formação do cidadão e no desenvolvimento socioeconômico sustentável.*__*

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