- Chimera-users - RBVI Mailing Lists

Running the Modify Structure tool using command line in UCSF Chimera
by Prathvi Singh 03 Nov '22

03 Nov '22

Hi Elaine, Is there a way to run the *Modify Structure *tool in UCSF Chimera using command line? I want to substitute a S-atom with O-atom in more than 100 structures and doing it for each structure using the GUI looks very time consuming. Please help. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Jagged edges in chimera X
by Prathvi Singh 03 Nov '22

03 Nov '22

Hello Elaine, Is there a way to smoothen the jagged edges seen around ribbons and sheets in ChimeraX? The jagged edges can be removed in UCSF chimera by setting the *subdivision *value to 20 and enabling multisampling but I do not see these features in chimeraX. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Doubt regarding Copyright for the use of UCSF Chimera free software in research paper
by aiswarya tressa chacko 03 Nov '22

03 Nov '22

Sir/Madam, I am a post graduate student who is working on a research article which involves molecular docking and analysis. I am using the free software of UCSF Chimera (version 1.16) for obtaining results and analysing them. I am wondering whether using these results and images that I acquired from Chimera in my research study, will subject me to Copyright Issues. Kindly address my doubt as soon as possible.

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xyz axis indicator
by Xiang Zhang 01 Nov '22

01 Nov '22

Hi all, I was wondering how I could hide the xyz indicator in the center of window when I was viewing the X-ray density from mtz file? It only appears in crystal unit view mode but disappears in EM projection side view. Best, Xiang

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AlphaFold Modeling
by S.M. RAIHAN RAHMAN 31 Oct '22

31 Oct '22

Hi! Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models? Please let me know. Thank you. Regards, Raihan

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How to invert a map values in UCSF Chimera
by Junha Song BA 31 Oct '22

31 Oct '22

Dear RBVI, I am currently looking into the ways to invert a map in UCSF Chimera so that I can flip the histogram of a map, but I cannot find a volume operation command that does the job. What command in UCSF Chimera allows creating a map with inverted map values? I thought it was vop but I cannot find a parameter that allows assigning negative value operation that would invert the map in UCSF Chimera command line documentation. Best, Junha Song.

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Question regarding protein-protein interactions in ChimeraX
by Lake, Camille (NIH/NIAID) [C] 31 Oct '22

31 Oct '22

Hello, My name is Camille Lake and I have used ChimeraX to model proteins. I was wondering - if I load two completely separate proteins from PDB, what is the nature of their interaction as shown by ChimeraX? The two proteins I'm interested in, TIM-3 (5f71) and CEACAM1 (5dzl), are predicted to interact in the literature, but if I load them separately into ChimeraX, is this predicted interaction what displays automatically? It seems that they are, but I can't find anywhere on the web whether this is automatically done in ChimeraX. Other proteins I randomly add in generally keep far away from each other in space. Thank you, Camille Camille Lake, PhD Emerging Leaders in Data Science (ORISE) Fellow National Institute of Allergy and Infectious Diseases (NIAID) - Office of Data Science and Emerging Technologies (ODSET) National Institutes of Health (NIH) 5601 Fishers Lane, 6C5 Rockville, MD 20871 camille.lake(a)nih.gov 301-761-7976 ---------------------------------------------- The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender’s own and not expressly made on behalf of the NIAID by one of its representatives.

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Need guidance
by Naima syed 30 Oct '22

30 Oct '22

Hello I am trying to find the RMSD between docked ligand and original ligand but I am not able to do it. When i tried the command "match" it showed the error atom spec missing. Can you please tell me how to fix this problem? Thank you

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Question about use of Chimera to view data from SALIGN program
by Edmund Marinelli 26 Oct '22

26 Oct '22

Helllo: I used SALIGN to obtain alignment / superposition of peptides. On the SALIGN webpage there is a link for Launch Chimera. When I click this I get a download of a file named "show.chimerax". Then nothing happens. The file contents appear to be directing ChimeraX to the data on the web and are as follows: <?xml version="1.0"?> <ChimeraPuppet type="std_webdata"> <web_files> <file name="alignment.pir" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/str-str_out.…" /> <file name="model1_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model1_fit.p…" /> <file name="model2_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model2_fit.p…" /> <file name="model3_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model3_fit.p…" /> <file name="model4_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model4_fit.p…" /> </web_files> <commands> <py_cmd>chimera.processNewMolecules(chimera.openModels.list(modelTypes=[chimera.Molecule]))</py_cmd> <py_cmd>import MultAlignViewer</py_cmd> <py_cmd>mols = chimera.openModels.list()</py_cmd> <py_cmd> m=chimera.extension.manager for i in m.instances: if isinstance(i, MultAlignViewer.MAViewer.MAViewer): mav = i </py_cmd> <py_cmd> for m in mols: if not m in mav.associations.keys(): mav.associate([m]) mav.match(mols[0], mols[1:], iterate=True)</py_cmd> </commands> </ChimeraPuppet> What am I supposed to do with this file. ChimeraX does not have a file extension .ChimeraX hence I do not know how to proceed next. Can anyone help? Thanks in advance.

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Set a reference coordinate for a viral structure?
by Feng, Y. 20 Oct '22

20 Oct '22

Hi there, I am a fresh new user of Chimera and have literally no experience in it. So I was wondering how to perform the process as mentioned in the Figure S4 of the following article: DOI: 10.1021/acs.jpcb.6b10131. My questions would be: In Chimera, 1. How to make an appointed atom in a viral structure with coordinates of (0,0,1)? 2. How to rotate the target point to the coordinates (0,0,1) and read out the original coordinates of the target point? What I want to do in Chimera is exactly the same as mentioned in the above article. But I don't have much experience with Chimera. So if you could explain how to do that step by step, that would be very much helpful. Sincerely appreciate! With best regards, Yuzhen Feng

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Set a reference coordinate and rotate target point to the reference coordinate?
by Feng, Y. 18 Oct '22

18 Oct '22

Hi there, I am a fresh new user of Chimera and have literally no experience in it. So I was wondering how to perform the process as mentioned in the *Figure S4* of the following article: DOI: 10.1021/acs.jpcb.6b10131. My questions would be: In Chimera, 1. How to make an appointed atom in a viral structure with coordinates of (0,0,1)? 2. How to rotate the target point to the coordinates (0,0,1) and read out the original coordinates of the target point? What I want to do in Chimera is exactly the same as mentioned in the above article. But I don't have much experience with Chimera. So if you could explain how to do that step by step, that would be very much helpful. Sincerely appreciate! With best regards, Yuzhen Feng

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Question: Why hydrogen bonds are not displayed?
by Kenji MATSUI 16 Oct '22

16 Oct '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. I am now looking at protein-ligand interactions. We found in the paper that His 421 interacted with another ligand. Therefore, the interaction between His-421 and the ligand. Problem :However, no hydrogen bonds were displayed.(first figure) I would like you to ask why this is caused. ---------------------------------------------------------- <detail> This is because the distance between the His-421 and OH oxygen atoms was 3.7 Å. A ligand with a structure similar to this one in the paper formed a hydrogen bond with His-421 at 3.8 Å. The thing I tried The Relax H-bond constraints section was adjusted from 3.0 to 5.0. [image: image.png] you can show this figure when you open the attached file Wheat: Ligand the other color:protein [image: image.png] H-bond parameter [image: image.png] --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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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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Geometric objects
by Reza Khayat 18 Aug '22

18 Aug '22

Hi, Can the size of geometric objects be changed? For example, can I make the ellipsoid drawn by command "measure inertia #0:167-285.A" smaller? Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Question regarding RMSD
by ALI, MUNIRA (PGT) 16 Aug '22

16 Aug '22

Good morning, I have conducted a superposition between two of the same protein where one was obtained by X ray and the other was predicted by alphafold. I wanted to use the RMSD value of the alignment rather then just have qualitative results but I am unsure of how to interpret the values given by chimera. When I get the output of for example: RMSD between 189 pruned atom pairs is 1.164 angstroms; (across all 553 pairs: 10.750), what exactly do these two outputs mean, which one should I be using and how exactly do I interpret this? Kind regards, Munira

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Trouble generating surface
by Heilman, Destin 12 Aug '22

12 Aug '22

Hi, I’m trying to generate a square surface between 4 markers to trace an atomic plane. I’ve created a marker file (attached) with the positions of the 4 atoms and when I select all markers and use the Volume Tracer tool to generate the surface, I see it show up in the Model Panel but it is not visible (see screen shot - I’m trying this in a random PDB file to test). The Volume Tracer tool also says “No surface” despite the Traced surface showing up in the Model Panel. I notice that there is no color next to the traced surface as well. It’s likely something silly I’m missing but I would appreciate help with this. Thanks. DH Destin Heilman, Ph.D (he/him/his) Professor of Chemistry and Biochemistry Chair, Undergraduate Studies Director, UMass MQP Project Center Department of Chemistry and Biochemistry Worcester Polytechnic Institute 100 Institute Road, Worcester MA 01609-2280 Goddard Hall 103B Office: 508-831-5396 Lab: 508-831-5386 [cid:787efcd6-e2fa-4b91-a11d-7b66c303cbed@prod.exchangelabs.com]

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ASKING FOR HELP WITH INTERPRETATION OF RR DISTANCE MAPS
by Ernest Matambo 08 Aug '22

08 Aug '22

Dear Sir/Madam, I am using Chimera 1.16 to compare two protein structures: one with mutations and a reference. I would like to calculate residue-residue distance of the substitute amino acids to the reference. I have used chimera to come up with a graph of the difference but I am struggling to interpret it. Any help will be greatly appreciated. Regards, Ernest

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Fwd: Making Fusion Proteins using Chimera
by Eric Pettersen 04 Aug '22

04 Aug '22

> Begin forwarded message: > > From: Milad Mapar <milad.mapar(a)yahoo.com> > Subject: Making Fusion Proteins using Chimera > Date: August 4, 2022 at 6:26:46 AM PDT > To: "pett(a)cgl.ucsf.edu" <pett(a)cgl.ucsf.edu> > > Dear Eric > > Hello > > With thanks to your support on Chimera, could you please help me to make a Fusion Protein using Chimera 1.16 > > Any links to tutorials or hints would be appreciated > > Many thanks > > Pharmaceutical Biotechnology PhD Student > Milad

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Help Coordinating Metal Atom to an Amino Acid (Cysteine)
by Sydney Marchi 01 Aug '22

01 Aug '22

Hello Chimera Software Developers, I am having a lot of trouble coordinating a metal atom (using Zinc in place of Cr) to the nitrogen, oxygen, and potentially sulfur atom on cysteine. The two main problems that I am having are getting the geometry I need, which is octahedral, where the metal is also coordinated to two-three water molecules as well as eventually the N-7 of guanine. I am trying to build and minimize the Zn-Cysteine model first though before incorporating it into a DNA oligo. I can't seem to get the geometry I need but beside from that, I have tried to minimize the structure using Amber with an undesired geometry just to test if it will run, and it doesn't let me. I have read the reply log and I believe this is due to the atom labeling on cysteine being the issue. But changing the atoms names is a coding problem, and I don't know anything about coding. I tried building cysteine on my own as a potential fix in place of using the prebuilt model but ran into the same problem where it would not minimize my structure. I need this model for my dissertation, so any help would be greatly appreciated. I can attach any files that you may need, set up a zoom meeting, whatever is easiest for you. I know this is probably not the most conventional use for this software, but I really need to figure this out, and I don't have enough knowledge to tinker with it on my own anymore. Thank you for any feedback. Best Regards, Sydney Marchi PhD Candidate, Chemistry Office: Shelby Hall, 3043 University of Alabama

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Question about equivalent command in Chimera
by Thu Nguyen 28 Jul '22

28 Jul '22

Good afternoon, I want to ask if we have any command in Chimera that is similar to the command "volume cover" in ChimaraX. My goal is to create a map and pdb file of individual chains from the whole structure. For example: > open 12554 from emdb > open 7ns0 > volume cover #1 atomBox #2/A1 pad 1.0 > save 12554_A1.mrc models #3 Could you tell me how I can do this using Chimera commands? Thank you very much. Best regards, Thu

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Re: [Chimera-users] How to show hydrophobility clearly
by Elaine Meng 27 Jul '22

27 Jul '22

Hi Kenji In this latest message, you are using one method that shows the pocket surface only, like in the tutorial. Your image after step 1 of what you tried looks OK to me: But if you are not happy with that, I am guessing you do not want this method. If you want it to look more like this example image with the labeling "hydrophobic pocket" and "allosteric tunnel" ...then you need to use a DIFFERENT method that includes clipping: showing the whole surface of the protein and then using clipping to slice. We already discussed this method, and you were already using this method the first time you asked the question: <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018741.html> <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018746.html> With that method, all you can do is to move and rotate the structure and move the clipping (either global clipping plane with Side View tool or surface-only clipping with Per-Model Clipping, both mentioned in previous replies) to try to get a good view. However, different pockets are different shapes and depending on the shape of your pocket it may not be possible to make an image that clearly shows what you want. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 26, 2022, at 6:40 PM, Kenji MATSUI <s214903z(a)st.go.tuat.ac.jp> wrote: > > 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 am looking at ligand-protein interactions and how they affect binding affinity. > > Therefore, I would like to examine the hydrophobicity and hydrophilicity around the ligand in the figure(third) > > If you know of any, could you please let us know? > > I tried to show what you mentioned in your email.(clip off, mclip) > > I apologize for asking this question so often in your busy schedule, but I would appreciate it if you could confirm it for me. > > <image.png> <image.png> > > The picture I want to show > <image.png> > > Tried thing > 1. clip off +~ribbon > <1edf41f0-9f2e-4921-92fe-19399979fd97.png> > > 2.m clip > <image1.png> > > > > > . > --------------------------------------------------------------------------- > > > Kenji Matsui > Graduate School of Tokyo University of Agriculture and Technology　M2 > 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan > Mail: s214903z(a)st.go.tuat.ac.jp > <Hydrohobility_1P8D_LXR_LBD_mono_24,25-epoxycholesterol.pyc>

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Help with Fetch ID from UNIProt
by Tina Wright 26 Jul '22

26 Jul '22

Hi there, I have worked my way through the majority of the Chimera tutorials and thought I would try to Fetch ID of Human SP-B (P07988) from UNIProt but unlike the tutorials, it will not upload an image. Can you please help? Many thanks Tina Wright

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How to examine the hydrophobicity and hydrophilicity around the ligand
by Kenji MATSUI 21 Jul '22

21 Jul '22

Dear Chimera Thank you for taking the time to answer my question the other day. I also apologize for contacting you outside of business hours due to the time difference. I'm Kenji Matsui, a second-year master's student at a national university in Japan. I am looking at ligand-protein interactions and how they affect binding affinity. Therefore, I would like to examine the hydrophobicity and hydrophilicity around the ligand in the figure below（second photo,）. [image: image10.png] [image: image.png] second photo Methods Tried select→ligand→Focus This method causes some parts of the surface to be difficult to see. As shown in the second photo, it is difficult to see the degree of hydrophobicity around the ligand. [image: image.png] Please confirm. --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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VolumeViewer in python
by Yumeng Yan 20 Jul '22

20 Jul '22

Hi all, I tried to fit some models into a large density map using python script for chimera. Do you know how to set the VolumeViewer module in python script to show all the surface of the density map like command line” volume #1 style surface region all level 0.15 step 1”? Here is my python code: Import chimera import FitMap import VolumeViewer model_list = chimera.openModels.open("test.pdb") em_map = VolumeViewer.open_volume_file("test.mrc")[0] “python code ” for “volume #1 style surface region all level 0.15 step 1” model = chimera.selection.ItemizedSelection([model_list[0]]) listfit = FitMap.fitcmd.fitmap(model, em_map, resolution=5.0, metric="correlation") Thanks and best wishes, Yumeng

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imod
by Aaran Vijayakumaran 13 Jul '22

13 Jul '22

Dear all, I was wondering if it was possible to measure the distance of structures within an IMOD segmentation file. For instance, measuring the length of microtubules lets say? Thank you in advance for any assistance. Bests, Aaran Vijayakumaran PhD Researcher Medical Research Council Toxicology Unit University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR av623(a)cam.ac.uk<mailto:Av623@cam.ac.uk> [A picture containing text, screenshot Description automatically generated] [cid:image001.png@01D84DAF.64335190]

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IOError for non-existing ViewDock_Accelerator.py when executing Chimera
by 夏前程 07 Jul '22

07 Jul '22

Hi, Recently I've received an error message from CLI each time I executed chimera as before. Although it does not affect the normal use of chimera, I am still curious what's the issue and how to get rid of it? The error message is as below: Error executing accelerators file $HOME/Downloads/Chimera/ViewDock_Accelerator.py: IOError: [Errno 2] No such file or directory: '$HOME/Downloads/Chimera/ViewDock_Accelerator.py' File "$HOME/opt/UCSF-Chimera64-1.15rc/share/Accelerators/__init__.py", line 103, in load_accelerators execfile(path, dict) See reply log for Python traceback. With Regards, Qiancheng Xia, 2022/07/07

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