- Chimera-users - RBVI Mailing Lists

UCSF Chimera Non-Commercial License Agreement
by Sarah Haar 14 Oct '22

14 Oct '22

Hi, Bowling Green State University would like to use UCSF Chimera Non-Commercial License Agreement. As part of our University review process, all legal Terms need to be examined to assure that we stay in compliance with Ohio law. Please provide all Terms (i.e. Terms and Conditions, Master Service Agreement, EULA, SAAS, etc.) that we need to accept in order to use your product. Because we are a State-owned University there are some Terms that we cannot accept. For example, we cannot indemnify or agree to arbitration. Would you consider Amendment to your Terms if needed? Best regards, Sarah Haar Procurement Specialist Bowling Green State University 1851 N. Research Dr. Bowling Green, OH 43403 Office: 419-372-7926 [cid:image001.jpg@01D8DFDF.BAD37170]

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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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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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Molecular Dynamics Simulation RMSD for only spesific atoms
by Barış KURT 07 Sep '22

07 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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making images of the intermediate steps of morphing
by Sen, Anindito 02 Sep '22

02 Sep '22

Dear Chimera users, How can I generate an image with the intermediate steps in a morphing session (of an atomic structure between its two conformations). The image of intermediate states can appear 'lighter' than the original and final states. Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

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Re: [Chimera-users] How to caluculate molecular volume using UCSF Chimera
by Elaine Meng 31 Aug '22

31 Aug '22

> On Aug 31, 2022, at 2:34 AM, Kenji MATSUI <s214903z(a)st.go.tuat.ac.jp> wrote: > > Dear Elaine > > Thank you for taking the time to answer my question the other day. > > I'm Kenji Matsui, a second-year master's student at a national university in Japan. > > I am trying to find out if the ligand (Attached files) can enter the binding pocket. > > I would like to calculate the volume of the ligand molecule for this purpose, how should I do this in Chimera ? > > What I tried. > I tried the one in the two links below and it did not work. > > Reference > 1.http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005196.html > 2.https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#blob > > Thank you for your time and support. > > --------------------------------------------------------------------------- > Kenji Matsui > Hi Kenji, (1) open ligand structure in Chimera (2) show molecular surface of ligand, e.g. command: surface (3) use menu: Tools.. Volume... Measure Volume and Area. This tool automatically shows the area and volume of the surface. Another way to do the same measurement is with command "measure volume," e.g. if your ligand structure is model #0, command: measure volume #0 The value from the command is shown in Reply Log (menu: Favorites... Reply Log) 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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how to perform minimize structure for enzyme+NADPH complex
by 朱鑫鑫 28 Aug '22

28 Aug '22

Hello everyone I have a question, how to perform minimize structure for enzyme+NADPH complex. Thank you very much. Xinxin Zhu 27/8/2022

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A problem on minmize structure
by 朱鑫鑫 28 Aug '22

28 Aug '22

Hello everyone I want to conduct a minimize structure using a protein complex model, but a error appears during this process. It reminds me to assign the hydrogen geometry info to NADP, and I click these options, but, it next will report a error. And I DONT know how to sovle this problem. I hope some suggestions I will obtain. Thank you very much. Xinxin Zhu 27/8/2022

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POV-RAY rendering and labels
by Francesco Pietra 26 Aug '22

26 Aug '22

Hello In my hands, with CHIMERA (v 1.15 Linux64 X11), POV-RAY rendering does not reproduce labels, only an interrogation mark in their place. Thanks for advice francesco pietra

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Re: [Chimera-users] Chimera ac Im command not working
by Tom Goddard 26 Aug '22

26 Aug '22

Hi Wayne, Chimera crashes usually are caused by graphics driver bugs or running out of memory. How large is your map? By the way, we stopped developing Chimera more than 6 years ago and you would be better off using ChimeraX which is the modern version of Chimera which we actively develop. Tom > On Aug 26, 2022, at 4:51 AM, Wayne Lim <wayne.lim(a)student.manchester.ac.uk> wrote: > > Dear Tom, > > I just tried this and over multiple times chimera 1.6 crashed and returned this error message: > > chimera exited abnormally, the exit code was: -1073741819 > > Not sure why it's doing that, any ideas as to what that code means? > > BW, > > Wayne > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, August 25, 2022 11:50 PM > To: Wayne Lim <wayne.lim(a)student.manchester.ac.uk> > Cc: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Chimera ac Im command not working > > Hi Wayne, > > I guess you mean you tried the current Chimera version 1.16. To change the sign of the map values use command > > vop scale #0 factor -1 > > I don't know what is wrong if the graphics is black after that, but I would start looking at the histogram in the Volume Viewer window and see if the yellow brightness curve is in the right place. Below is an image with Chimera 1.16 and map EMDB 1273 showing the histograms for the original and inverted map and it displays correctly on my Mac. > > Tom > > <invertmap.png> >> On Aug 25, 2022, at 8:39 AM, Wayne Lim via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >> >> Dear Chimera team, >> >> I am using Chimera to view the surface pane of my TEM images in attempts to see the features of the image in 3D. Since I stained it positively, I have to invert the map values so I can properly view it under “surface”. However, when I do so in Chimera 1.5, it displays an “unexpected python error”. When tried in Chimera 1.6, the result is simply a black screen. I am stumped as to how to solve this issue. A colleague of mine done it and I followed the same procedure he has done, but to no avail. >> >> Best, >> >> Wayne >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Query Regarding processing protein in Chimera
by asetiya 26 Aug '22

26 Aug '22

Sir/Ma'am, I have query regarding chimera, through command line I want to select a particular residue and delete the remaining protein and save in the .mol2 file for further processing for my project.I used the following command to select the residue: select :30 for selecting the desired residue. Can you give me an insight as to how to delete the remaining protein and save in the .mol2 format. That will be very helpful. Thanks & Regards Anjali Setiya ------------------------------------------------------------------------------------------------------------ [ 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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Chimera ac Im command not working
by Wayne Lim 25 Aug '22

25 Aug '22

Dear Chimera team, I am using Chimera to view the surface pane of my TEM images in attempts to see the features of the image in 3D. Since I stained it positively, I have to invert the map values so I can properly view it under “surface”. However, when I do so in Chimera 1.5, it displays an “unexpected python error”. When tried in Chimera 1.6, the result is simply a black screen. I am stumped as to how to solve this issue. A colleague of mine done it and I followed the same procedure he has done, but to no avail. Best, Wayne

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Fwd: How to display hydrohobic area
by Elaine Meng 23 Aug '22

23 Aug '22

> > From: Kenji MATSUI <s214903z(a)st.go.tuat.ac.jp> > Subject: How to display hydrohobic area > Date: August 22, 2022 at 9:17:37 PM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > > Dear Chimera > Thank you for taking the time to answer my question the other day. > I'm Kenji Matsui, a second-year master's student at a national university in Japan. > > I would like to display the hydrophobicity of the protein around the ligand like the first picture, but I couldn't do it. > How can I do this? > When I actually did it, it turned out to be the second picture. > > I apologize for asking this question so often in your busy schedule, but I would appreciate it if you could confirm it for me. > > First photo > > > Second photo > > Hi Kenji, If I understand correctly, you want to show the amino acid hydrophobicity coloring on the ribbon and sticks, not the molecular surface. When you open the structure, it may already be displayed as ribbon and sticks. Do not show the surface. (Or, if you already are showing the surface, you can hide it with menu: Select... Clear Selection, menu: Actions... Surface... hide) Then you can use the "rangecolor" command to color protein ribbons/sticks by hydrophobicity: rangecolor kdHydrophobicity min dodger blue 0 white max orange red See rangecolor help <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> That command is part of the tutorial for surface coloring: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#h…> However, when the surface is not shown, you can see that this comand also colors the other representations (ribbons and sticks). 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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