- Chimera-users - RBVI Mailing Lists

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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Centering icosahedron and capsid in the same place in Chimera
by Elaine Meng 15 Sep '22

15 Sep '22

Hi Heather, Maybe your other capsid coordinates just happened to be centered on the default location for centering the icosahedron, but this one has offset coordinates. Still you could just move one or the other (capsid or icosahedron) so that they are centered in the same place. In Chimera (not ChimeraX) you can deactivate/activate models for motion so that only the active ones move with the mouse. I.e. uncheck the model number in the "Active models" list under the command line so that only the other one moves with the mouse. Other ways described here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> I cc'd Chimera-users because the details in this message are about Chimera rather than ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 14, 2022, at 7:06 PM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hello, > > Hi Elaine and Tom. I appreciate your help on the inner volume from before both methods with blob and shape, I think I have been able to tailor it for my usage. I also have been using the icosahedron surface in Chimera, and have not had any issues until this capsid, why is it not forming inside the capsid? Did I do something? Thanks in advance. > icos_why.py > > Thank you, > > Heather Noriega > PhD-Pharmaceutical Science student > Howard University > heather.noriega(a)bison.howard.edu > 520-203-1883 > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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Chimera problem
by Eleni Pontiki 09 Sep '22

09 Sep '22

Dear Sir, I am trying to use chimera for windows for docking, but it does not work (photos attached). I have downloaded: https://github.com/ccsb-scripps/AutoDock-Vina/releases/tag/v1.2.3 and put the correct location but still having problems. Could you possible help me? I have followed all the steps described here. Thank you in advance for your help. Best regards, Eleni Pontiki Eleni Pontiki, Assistant Professor, Guest Editor "Molecules" Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki Greece. tel. +302310997671 fax. +302310997612

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Pdb saved in Chimera not displaying upon opening
by Magdalena Riad 09 Sep '22

09 Sep '22

Hi, I have opened a pdb structure of a ribosome, hidden parts of it and then saved a new pdb of the displayed atoms through “File->Save pdb” ticking “save displayed atoms only”. When I try to open this saved pdb file, Chimera states “Opened ….pdb”, however, it does not display. The model panel is empty etc. Checking the pdb file in textedit, it does contain the secondary structure information and all the amino acids but it seems to lack coordinate information, see pictures below of parts of it. I’ve also tried to save the pdb through “Actions-> write pdb”. Do you know how I can solve this issue? Is it a saving issue or a displaying issue? Thanks, Magdalena [cid:image001.png@01D8C371.3C765B60][cid:image002.png@01D8C371.3C765B60] 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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How to caluculate buried surface area
by Kenji MATSUI 07 Sep '22

07 Sep '22

Dear Chimera I am sorry to interrupt your busy schedule. My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day. We are investigating the buried surface area to see the magnitude of the interaction between protein and ligand. For this purpose, I calculated the solvent accessible area of the ligand. However, the value is 9955, which shows the entire surface area of the protein. What should I do? I am not in a hurry for answers , so I would appreciate a reply when you have the time. In this case, the ligand was in the binding pocket of the protein, so I would like to calculate the ligand's solvent contact area = buried surface area. I tried to check and tried , but it did not work. 1.See https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html 2.Try to use measure blob using chimera X. Reference: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea However, I didn't know how to solve this command. Command ;ui mousemode right "pick blobs Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan

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