- Chimera-users - RBVI Mailing Lists

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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Coloring model by b-factor
by 师扬 07 Jul '22

07 Jul '22

Dear developer, I am trying to color a model by b-facor and used the command like : color by bfactor #4/A palette red:green:blue range 35,45. However, the range setting was not working. So my question is how to color with a user-defined palette and a user-defined range. Best wishes, Yang

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Mask Question in windows Chimera
by Zhang, Ruojing 04 Jul '22

04 Jul '22

To whom it may concern, Hello, this may sound like a silly question. May I ask how to use Mask in Volume? For some unknown reasons, I could not find the Mask button in Volume Viewer and neither in the tool taskbar. The input files are pdb and mrc file. I used Fit in Map to align structure and map. Then I selected the whole structure. When I went back to mask the map, I could not find the Mask button in Volume Viewer. When I tried to run in the command line (mask), it shows "missing required arguments: Volume, SurfaceSpec". Could you please help? Thank you Jing

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ChimeraX Version 1.4 on CentOS/RHEL 7
by Long Gui 01 Jul '22

01 Jul '22

Dear Chimera community, We are interested in the new version of the ChimeraX/1.4 but we could not find the installation file of ChimeraX/1.4 on our CentOS/RHEL 7 system. Only ChimeraX/1.3 supports CentOS/RHEL 7. So we would like to ask if there is a way to install ChimeraX/1.4 on our CentOS/RHEL 7 system? In addition, our computational source would prefer to install the program using docker. Currently I only find this docker file supports ChimeraX/1.3 https://github.com/maduprey/chimerax-docker/ ? Have anyone tried it for ChimeraX/1.4 yet? Thanks! Long Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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AutoDock Vina error on Chimera
by Utkarsh Narsaria 30 Jun '22

30 Jun '22

Dear Team, I am using chimera for a typical protein-ligand docking study. The ligands were prepared in chimera itself using the dockprep options using gasteiger charges and amber ff14SB force field. While docking the same using AutoDock Vina function in Chimera , we encountered few errors for some of the ligands. The errors are explained as follows : 1. "" Ho" is not a valid dock type AutoDock atom types are case-sensitive." 2. Autodock Vina Error on Chimera: "ValueError: Could not find an atomic number for Hc Hc" Any inputs regarding these will be helpful in resolving the issues. Regards, Utkarsh

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Save trajectory file to PDB
by Yan Yi Li 24 Jun '22

24 Jun '22

Hello, I have a question about saving specific frame from trajectory file to PDB. Instead of using MD movie, is there any module/command available so that I can convert the file format directly with python script? Regards

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How to show hydrophobic interactions
by Kenji MATSUI 17 Jun '22

17 Jun '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 have shown hydrophobic interactions between ligands and amino acid residues, how should I display them? I refer to these methods. But, I did not know where to find Examine residues. Therefore, could you please tell me the location of Examine residues? If possible, we would appreciate it if you could attach a diagram after the operation so that we can confirm the operating procedure. *A:Find hydrophobic interactions* Select >> Residue(s) (either in entire structure or within a selected set (see above $ or %)) >> Amino acid category >> hydrophobic >> Action >> Atoms/Bonds >> Show >> Examine residues >> Mouse over atoms or Left click on them to identify them --------------------------------------------------------------------------- 松井健治東京農工大学大学院工学府産業技術専攻修士 2年〒184-8588 東京都小金井市中町2-24-16 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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New residues for swap commands
by Rodrigo Galindo-Murillo 15 Jun '22

15 Jun '22

Hello! Is it possible to add new amino acids to the swapaa and new nucleotides for the swapna commands? Thank you! Rodrigo.

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Discrepancies Between Running Python Script From Terminal and GUI
by Rafi Brent 06 Jun '22

06 Jun '22

To whom it may concern, I have a set of about 20,000 pdb files to which I would like to add Hydrogens, add partial charges, and convert to the mol2 format. I have written a python script to perform these tasks, which it does without issue when opened from the GUI using the "open" option in the top left corner. However, as soon as the script start srunning, I become unable to interact with the Chimera GUI and my computer warns that the application is not responding. While it continues to iterate through the pdb files and convert them to mol2 files, this process slows down drastically over time, from one file per second to over 30 seconds between files, a rate that is prohibitively slow. It is not clear to me why these issues are occurring, as there is nothing about the way my script is written that should increase the computational load over time. Based on the unresponsiveness of the Chimera application, I assumed that the slowdown might have something to do with the GUI, so I instead ran my script from the terminal, using chimera -- nogui python_script.py . This resulted in a rate of file conversion that was much faster than the GUI even before its slowdown, but it raised an error that was never a problem in the GUI: Cannot properly run "/Applications/Chimera.app/Contents/Resources/bin/amber18/bin/sqm -O -i sqm.in -o sqm.out". This only occurred on nonstandard amino acid residues, but the error was not solely determined by the residue's identity, as many carboxylated lysine residues were processed properly before the system encountered one particular file whose KCX residue caused it to crash. However, the error is consistent, meaning that the same KCX residue on that particular file always causes the program to crash. I have had no luck searching for the error online, but I am happy to include the entire error message in context if that would be helpful. More generally, I don't understand why running the exact same python script through the GUI and through the terminal window gives such different results. I'm happy to do it either way as long as the operation can be completed successfully within a day or two, and I would be very thankful for any advice you may have. Sincerely, Rafi Brent

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Downloading Trouble
by Harman Thind 02 Jun '22

02 Jun '22

To whom it may concern, I have a problem opening up Chimera. Every time I run the app the error message found in the image shows up. I have tried reinstalling the app and restarting my laptop... however, that hasn't accomplished much. What steps should I take next? Thank you for your time. - Harman T. [image: image.png]

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Fatal error during Energy minimization
by Saousen Diaf 02 Jun '22

02 Jun '22

Dear all, I am using structure minimize tool in UCSF Chimera to minimize a glycosylated structure, but I get a fatal error: *Failure running ANTECHAMBER for residue BMA+MAN+NAG+MAN+NAG+PHE+MAN+ASN* *Check reply log for details* *any idea on how to resolve the issue.* *Thank you in advance for your help.* *Best* *Saousen*

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Blast not working
by Antonio Díaz Quintana 02 Jun '22

02 Jun '22

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Re: [Chimera-users] Blast not working
by Tom Goddard 01 Jun '22

01 Jun '22

Hi Antonio, Glad to hear the new Chimera 1.16 version is working. Tom > On Jun 1, 2022, at 3:25 AM, Antonio Díaz Quintana <antonio.diaz(a)iiq.csic.es> wrote: > > Hello Tom, > > Thankyou. It worked. > > Best, > > Antonio > > El 01/06/2022 a las 07:07, Tom Goddard escribió: >> Hi Antonio, >> >> The error "ImportError: No module named replyobj" means Chimera cannot find its message logging module called "replyobj". That suggests that your Chimera installation is broken, and does not appear to be a problem specifically with BLAST. I would suggest installing the current Chimera version 1.16. >> >> If that does not fix it, use the Report a Bug... button that should appear when this error message is shown. Or if that button does not appear use Chimera menu entry Help / Report a Bug.... >> >> Tom >> >> >>> On May 31, 2022, at 8:05 AM, Antonio Díaz Quintana via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >>> >>> Dear all, >>> >>> Recently, I stopped being able to perform a BLAST search from the SEQUENCE tool in UCSF Chimera. Is there anything I could do to fix this? >>> >>> Log message follows: >>> >>> Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr or pdb for sequences similar to the given protein sequence >>> Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service <http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service> >>> Opal job URL: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1654009255276130143… <http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1654009255276130143…> >>> Traceback (most recent call last): >>> File "C:\Program Files\Chimera 1.15rc\share\chimera\tasks.py", line 179, in runStatusCB >>> task.statusCBList[0]() >>> File "C:\Program Files\Chimera 1.15rc\share\blastpdb\ParserBlastP.py", line 434, in _statusCB >>> self.finishCB(self.params, output) >>> File "C:\Program Files\Chimera 1.15rc\share\blastpdb\gui.py", line 424, in _finish >>> self.fetchColumnValues() >>> File "C:\Program Files\Chimera 1.15rc\share\blastpdb\gui.py", line 449, in fetchColumnValues >>> info = fetch_pdb_info(pdb_ids) >>> File "C:\Program Files\Chimera 1.15rc\share\blastpdb\pdbinfo.py", line 151, in fetch_pdb_info >>> import replyobj >>> ImportError: No module named replyobj >>> >>> Best, >>> >>> Antonio >>> >>> -- >>> Dr. Antonio J. Díaz Quintana >>> Instituto de Investigaciones Químicas >>> Universidad de Sevilla - CSIC >>> Avda. Americo Vespucio 49 >>> 41092 Sevilla >>> Spain >>> >>> Phone: +34 954 48 9631 >>> _______________________________________________ >>> 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> >> > -- > Dr. Antonio J. Díaz Quintana > Instituto de Investigaciones Químicas > Universidad de Sevilla - CSIC > Avda. Americo Vespucio 49 > 41092 Sevilla > Spain > > Phone: +34 954 48 9631

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Re: [Chimera-users] HBONDS comparing GROMACS and CHIMERA
by Elaine Meng 31 May '22

31 May '22

----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco Forwarding to the list so that somebody who knows more about the code can answer... > On May 30, 2022, at 1:23 AM, Sourpis, Anastasios <asourpis(a)uni-mainz.de> wrote: > > Dear Elaine, > > I would like to ask you if > CHIMERA is openned source. > > And if yes how can I have access to the Hbonds > class/funtion to understand better how it works? > > Kind regards, > Tasos > > > > On May 25, 2022, at 11:32 AM, Elaine Meng via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > > > > > Dear Tasos Sourpis, > > > It is not surprising that different programs give (partially) different results, because each program uses somewhat different methods and/or parameters to identify H-bonds. There is no universally accepted exact method. However, my guess is that they would agree in the majority of cases. > > > > > > The method used by Chimera is described in the help page: > > > <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhb…> > > > > > > To summarize, there are several different distance and angle cutoffs depending on the atom types (element and hybridization state) of both the donor and acceptor. The diagram of how the angle is defined would also depend on both of those types. > > > > > > So probably what you are interested in are the exact diagrams for the different donor-acceptor pair types and the cutoff values for distances and angles. These are in the figures and tables of the paper cited in the link above, namely > > > > > > Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22. > > > > > > Then Chimera allows adding tolerance values to the cutoffs of distances and angles from the paper, because they were defined on very high-resolution crystal structures, but used on structures that may not be so precise. > > > > > > I hope this helps, > > > Elaine > > > ----- > > > Elaine C. Meng, Ph.D. > > > UCSF Chimera(X) team > > > Department of Pharmaceutical Chemistry > > > University of California, San Francisco > > > > > > > > >> On May 25, 2022, at 2:57 AM, Sourpis, Anastasios via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > >> > > >> Dear All, > > >> > > >> I would like to ask about the hydrogen bonds' built-in configuration > > >> of CHIMERA. > > >> > > >> Can I possibly have some insight into how it works? > > >> > > >> Regarding the distance and angle constraints do you have any > > >> graphical representation of the conditions. > > >> > > >> I would like to attach a figure and ask if this is the correct > > >> applying configuration regarding the distance and the angle > > >> (hbonds_lst.pdf). > > >> > > >> > > >> Also, I would like to share with you the output > > >> when I compare gmx hbond using GROMACS and > > >> chimera. > > >> > > >> ATTENTION: using gmx hbond I have the connected atoms > > >> via hydrogen, but the two configurations are essentially > > >> different (chimera_(molecules).tga and gromacs_atomonly.tga). > > >> > > >> Thank you in advance. > > >> Kind regards, > > >> Tasos Sourpis > > > > > > > > > _______________________________________________ > > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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how to solve the problem of topology
by Kenji MATSUI 31 May '22

31 May '22

Dear Chimera Thank you for your support the other day. I also apologize for contacting you outside of business hours due to the time difference. Excuse me, I have a question about the issue of ligand topology for the docking study. ligand: 25-hydroxy cholesterol The topology did not match when I used this ligand for the docking study. Could you tell me how to solve this problem? The thing I tried 1. I tried to add hydrogen atoms on UCSF Chimera by following the URL below, but it did not work Reference: https://www.swissparam.ch/SwissParam_gromacs_tutorial.html 2. I tried to change the conformation of the C23-24 part, but the situation won't be changed. Reference:< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.… > --------------------------------------------------------------------------- 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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Drawing a set of spheres describing a pocket in a protein
by svle＠tiscali.it 30 May '22

30 May '22

Hi all, I would like to draw a set of colored and transparent spheres that describes a pocket knowing the coordinates of the center and the radius for each of these shapes. For example: radius: 0.7777, y: 18.333, x: -23.99, z: -64.765 and so on. Can you suggest me a way to do this. Thanks. Saverio Voucher MISE per P.IVA e PMI: fino a 2500€ per la Banda Ultralarga. https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busi…..

3 6

Fwd: [chimerax-users] relative position of a marker
by C.J. 25 May '22

25 May '22

Thank you both Tom and Elaine. I just test the command but it doesn't work. See attached picture. Elaine Meng <meng(a)cgl.ucsf.edu> 于2022年5月25日周三 11:45写道： > Hi Jianhao, > It depends what you mean by relative position. If you mean distance, one > way would be to place a marker at the map center and then measure distance > between it and the marker you already have. > > You can place a marker at map center with "measure center" and the "mark > true" option: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#center> > > ....or at specific coordinates such as 0,0,0 with "marker" and the > "position" keyword to specify a point: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html#create> > > Then you can select the two markers (same as atoms) with Ctrl-click, > Shift-Ctrl-click and then use command "distance sel": > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> > > Or regardless of whether you wanted to measure any distances, you can save > the marker(s) to file and just look at the file with a text-editor to see > what its coordinates are: > <https://rbvi.ucsf.edu/chimerax/docs/user/markers.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On May 25, 2022, at 7:54 AM, C.J. via ChimeraX-users < > chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hi, > > I place a marker in a cryoEM map with "Volume Tracer" tool. How can I > know the relative position of the marker to the origin or center of the > map? Thank you! > > Best, > > Jianhao > >

2 1

HBONDS comparing GROMACS and CHIMERA
by Sourpis, Anastasios 25 May '22

25 May '22

Dear All, I would like to ask about the hydrogen bonds' built-in configuration of CHIMERA. Can I possibly have some insight into how it works? Regarding the distance and angle constraints do you have any graphical representation of the conditions. I would like to attach a figure and ask if this is the correct applying configuration regarding the distance and the angle (hbonds_lst.pdf). Also, I would like to share with you the output when I compare gmx hbond using GROMACS and chimera. ATTENTION: using gmx hbond I have the connected atoms via hydrogen, but the two configurations are essentially different (chimera_(molecules).tga and gromacs_atomonly.tga). Thank you in advance. Kind regards, Tasos Sourpis

2 1

Place Objects output to mrc
by Ricardo Righetto 20 May '22

20 May '22

Hi, Regarding https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-March/018516.html I stumbled upon this thread somewhat late, so here is my approach to do what Pranav asked, just in case: 1. Use the "Place Objects" plugin to map back your particles into the tomogram, using STL files to represent the average 2. Generate an MRC volume made up entirely of "ones", exactly the same size as your tomogram. For example, for a volume that is 928x928x464 voxels one can do this in EMAN using: $ e2proc3d.py :928:928:464:1 ones_bin4.mrc You could obviously use some other program to do the same thing, or Python, MATLAB, etc. 3. Load this "ones" volume in your Chimera session. Make sure all regions are loaded in step 1, e.g. vol #2 style surface step 1 level 0.5 region all (the volume doesn't have to be visible, though) 4. Mask your "ones" volume using the surface of the mapbacks from "Place Object", e.g.: mask #1 #2 fullmap true 5. Save the new, masked volume as an MRC file The result is essentially a binary volume (well, not exactly because of the masking interpolation) where voxels of your mapped-back particles are 1 and the rest is 0. This is quite useful to compose segmentations and mapbacks on tomograms in Chimera or ChimeraX having full control like we do with any MRC volume (unlike e.g. STL or COLLADA objects). Note you may get some artifacts on the edges, so you might have to play a bit with the thresholds both when creating the STL of your subtomogram average and when displaying your new volume "sculpted" by the mapbacks, to minimize those. The results however have been good enough in my experience, working with low-resolution averages :-) Hope this helps! Best wishes, -- Ricardo Diogo Righetto

2 1

Allocating GPUs
by Giono Matteo (PSI) 19 May '22

19 May '22

Dear all, Does anyone know if it’s possible to make Chimera use GPUs instead of CPUs? I have a 2021 Macbook Pro with 12-core GPUs and knowing that all the work is done by the CPU make all these GPUs kind of useless. Best, MG

5 5

USCF CTRL + Left Click
by Luke Kurfman-Student 19 May '22

19 May '22

Hello Sr./Ms., Most everyone in my laboratory has access to UCSF Chimera and can use it with no issues. However, one new person has had trouble selecting atoms. Specifically, neither CTRL + Left Click nor CTRL + SHIFT + Left Click appear to work on selecting atoms in a molecular geometry, even though their computer can run the program. They can translate, rotate, and zoom in-and-out of the geometry, and they can use actions such as "Select All" . However, they cannot deselect individual atoms once the entire geometry is selected, and they can only CTRL + Left Click outside the geometry to deselect the entire geometry. Additionally, drag-clicking does not appear to work. CTRL + Click is a fundamental feature that our group uses, especially since we use Chimera for journal figures. Are there any suggestions on how to troubleshoot the issue with selecting atoms? For reference, their computer runs Windows 10 and operates on a x64 bit system. Any help is appreciated, Luke

2 2

Set scale factors from displayed contours?
by Oliver Clarke 17 May '22

17 May '22

Hi, When combining maps using vop maximum (or volume maximum in chimerax), we often want to adjust the scale factors of the maps such that the overlapping bits of two aligned maps are visually on the same scale. It is possible to calculate the appropriate scale factors from the displayed thresholds, but this becomes a little time consuming when combining many maps. Would it be possible to add a flag, something like "get scalefactor from display thresholds" that would take care of this automatically? Cheers Oli

3 4

Assigning nucleotide representation to non-canonical nucleotides
by Jérôme Rihon 16 May '22

16 May '22

Dear I was wondering if there is a way to represent non-canonical (otherwise known as xenobiotic) nucleic acids through UCSF Chimera (specifically, not ChimeraX .. haven't made the jump yet). I've looked through your documentation on the `nucleotides` section but was not able to find something along those lines. My PI told me it was possible, but I can't seem to find it. My apologies if I should be looking for this function elsewhere, but I thought it'd be easier to just ask. Many thanks in advance! Kind regards, Met vriendelijke groeten, Cordialement, ______________________ Rihon Jérôme jerome.rihon(a)kuleuven.be | +32 16 32 53 57 PhD researcher @Rega Institute for Medical Research | Laboratory of Medicinal Chemistry | Computational Research Herestraat 49 - box 1041, 3000 Leuven

3 4

Making a movie from map series while keeping map's colors
by Michal Arie Shmuelov 16 May '22

16 May '22

Hi everyone, I have 20 maps (from 3D variability analysis) that I open as series in chimeraX. I'm coloring the map series using the command "color zone #X near #X distance X" (coloring the map according to pdb model). Next I'm trying to make a movie of this map series while retaining the map colors. For some reason when the morph/ vseries starts to run the colors disappear. Can someone help me to solve this problem? What are the commands that I should write? Thanks, Michal

2 1

question Help
by Firat KURT 16 May '22

16 May '22

*Hi, * *I have several problems regarding running some features of and registration of chimera. * *Firstly, I am not able to do registration. It keeps giving the error message below: * Error reading 1yti: Error during PDB fetch: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host Model 0 (AT4G26590_1_ATOPT5.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 100, in download return sax.parse(string=content) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\sax\parser.py", line 133, in parse sax.parse(source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\xmlreader.py", line 123, in parse self.feed(buffer) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 224, in feed self._err_handler.fatalError(exc) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\handler.py", line 38, in fatalError raise exception SAXParseException: <unknown>:76:2: mismatched tag Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\blastpdb\ParserBlastP.py", line 362, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Blast web service appears to be down. See Reply Log for more details. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 100, in download return sax.parse(string=content) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\sax\parser.py", line 133, in parse sax.parse(source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\xmlreader.py", line 123, in parse self.feed(buffer) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 224, in feed self._err_handler.fatalError(exc) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\handler.py", line 38, in fatalError raise exception SAXParseException: <unknown>:76:2: mismatched tag Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\blastpdb\ParserBlastP.py", line 362, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Blast web service appears to be down. See Reply Log for more details. error Exception in Tk callback Function: <bound method BugReportGUI.Submit of <BugReport.BugReportGUI.BugReportGUI object at 0x000000001A1CAFD0>> (type: <type 'instancemethod'>) Module: <module 'BugReport.BugReportGUI' from 'C:\Program Files\Chimera 1.16\share\BugReport\BugReportGUI.pyc'> (line: 348) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\share\BugReport\BugReportGUI.py", line 426, in Submit BUG_SELECTOR, fields) File "C:\Program Files\Chimera 1.16\share\CGLutil\multipart.py", line 33, in post_multipart_formdata retcode, retmsg, headers = h.getreply() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1196, in getreply response = self._conn.getresponse() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1121, in getresponse response.begin() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 438, in begin version, status, reason = self._read_status() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 394, in _read_status line = self.fp.readline(_MAXLINE + 1) File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) error: [Errno 10054] An existing connection was forcibly closed by the remote host error: [Errno 10054] An existing connection was forcibly closed by the remote host File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) See reply log for Python traceback. IOError Exception in Tk callback Function: <function command at 0x00000000151E8898> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.16\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.16\share\chimera\register.py", line 294, in Register file = urllib.urlopen(regURL, params) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 89, in urlopen return opener.open(url, data) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 215, in open return getattr(self, name)(url, data) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 351, in open_http errcode, errmsg, headers = h.getreply() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1196, in getreply response = self._conn.getresponse() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1121, in getresponse response.begin() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 438, in begin version, status, reason = self._read_status() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 394, in _read_status line = self.fp.readline(_MAXLINE + 1) File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) IOError: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host IOError: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) See reply log for Python traceback. *Secondly, when I try to model a sequence using modeller, I am having error message in first step. When I select "Tools>sequence>sequence>balst protein" and paste the sequence of interest to the respective area, I got the error message below :* Error reading 1yti: Error during PDB fetch: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host Model 0 (AT4G26590_1_ATOPT5.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 100, in download return sax.parse(string=content) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\sax\parser.py", line 133, in parse sax.parse(source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\xmlreader.py", line 123, in parse self.feed(buffer) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 224, in feed self._err_handler.fatalError(exc) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\handler.py", line 38, in fatalError raise exception SAXParseException: <unknown>:76:2: mismatched tag Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\blastpdb\ParserBlastP.py", line 362, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Blast web service appears to be down. See Reply Log for more details. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 100, in download return sax.parse(string=content) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\sax\parser.py", line 133, in parse sax.parse(source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\xmlreader.py", line 123, in parse self.feed(buffer) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 224, in feed self._err_handler.fatalError(exc) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\handler.py", line 38, in fatalError raise exception SAXParseException: <unknown>:76:2: mismatched tag Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\blastpdb\ParserBlastP.py", line 362, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Blast web service appears to be down. See Reply Log for more details. error Exception in Tk callback Function: <bound method BugReportGUI.Submit of <BugReport.BugReportGUI.BugReportGUI object at 0x000000001A1CAFD0>> (type: <type 'instancemethod'>) Module: <module 'BugReport.BugReportGUI' from 'C:\Program Files\Chimera 1.16\share\BugReport\BugReportGUI.pyc'> (line: 348) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\share\BugReport\BugReportGUI.py", line 426, in Submit BUG_SELECTOR, fields) File "C:\Program Files\Chimera 1.16\share\CGLutil\multipart.py", line 33, in post_multipart_formdata retcode, retmsg, headers = h.getreply() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1196, in getreply response = self._conn.getresponse() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1121, in getresponse response.begin() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 438, in begin version, status, reason = self._read_status() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 394, in _read_status line = self.fp.readline(_MAXLINE + 1) File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) error: [Errno 10054] An existing connection was forcibly closed by the remote host error: [Errno 10054] An existing connection was forcibly closed by the remote host File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) See reply log for Python traceback. IOError Exception in Tk callback Function: <function command at 0x00000000151E8898> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.16\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.16\share\chimera\register.py", line 294, in Register file = urllib.urlopen(regURL, params) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 89, in urlopen return opener.open(url, data) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 215, in open return getattr(self, name)(url, data) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 351, in open_http errcode, errmsg, headers = h.getreply() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1196, in getreply response = self._conn.getresponse() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1121, in getresponse response.begin() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 438, in begin version, status, reason = self._read_status() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 394, in _read_status line = self.fp.readline(_MAXLINE + 1) File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) IOError: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host IOError: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) See reply log for Python traceback. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 100, in download return sax.parse(string=content) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\sax\parser.py", line 133, in parse sax.parse(source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\xmlreader.py", line 123, in parse self.feed(buffer) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 224, in feed self._err_handler.fatalError(exc) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\handler.py", line 38, in fatalError raise exception SAXParseException: <unknown>:76:2: mismatched tag Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\blastpdb\ParserBlastP.py", line 362, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Blast web service appears to be down. See Reply Log for more details. *I also attached the image of my input. Would you help me with this please? How can I fix these problems??* *My operating system is Windows 10 64X and chimera version is 1.16* *Regards, * [image: image.png] -- İyi çalışmalar dilerim, Doç. Dr. Fırat Kurt Bitkisel Üretim ve Teknolojileri Bölümü Uygulamalı Bilimler Fakültesi Muş Alparslan Üniversitesi Muş-Türkiye Tel :+90 436 249 10 83 Dahili: 2686 Fax :+90 436 231 22 01 ---------------------------------------------- Fırat Kurt, Ph. D. Associate Prof. of Plant Biotechnology Department of Plant Production and Technologies Faculty of Applied Sciences Mus Alparslan University Mus-Turkey Phone :+90 436 249 10 83 Ext. :2036 Fax :+90 436 231 22 01 www.alparslan.edu.tr

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Can't open web file
by Emma Belcher 13 May '22

13 May '22

Hi there, I am a complete beginner with Chimera so apologies for the very basic question. I am trying to open a Consurf output which is a .chimerax file. I have downloaded Chimera to do this and have not changed any default settings (running MacOS Monterey 12.2.1). When I try to open the file (either by clicking “Open with Chimera” on the file or opening Chimera and going File > Open… and selecting the file), it comes up with the following error message: Error reading consurf_1652376787.chimerax: Couldn't find url 'https://consurf.tau.ac.il/results/1652376787/msa_file_fasta.aln.clustalw': [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661) I have no idea what this means or how to fix it, so would appreciate any tips! Thank you, Emma Belcher

2 3

Save reply log through chimera command line
by Reeki Emrizal 12 May '22

12 May '22

Hi I working on an automated python script to calculate the rmsd between two molecules using rmsd command. I'm using --nogui when running the script. The standard output did not show the rmsd value. When using the chimera gui, I noticed that the rmsd value is shown in the reply log. Is there a way I could save the content of the reply log through python script? I found previous post with similar issue that use: from chimera.tkgui import saveReplyLog saveReplyLog(path) The solution does not work for me though as the text file is empty even though there is content in the reply log. Kind Regards

2 2

RMSF calculations
by Reza Khayat 12 May '22

12 May '22

Hi, I'm trying to write a script to perform the procedure described here: https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-March/013247.html Can someone help with the command line syntax for associating a structure with a defined sequence? 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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Re: [Chimera-users] [chimerax-users] interface plot
by Elaine Meng 12 May '22

12 May '22

Hi Pranav, If you mean that you wanted a list of the interface residues, you can use the "interfaces" network diagram edge context menu to select the residues, then list them in the Log with "info residues sel" ... and either cut-n-paste from the Log to text file or use "log save" to save it as an HTML file. The "info" command should really allow saving a text file directly, but it doesn't do that yet. I believe we have an open ticket to fix that omission. In the chain-chain network diagram, e.g. when the mouse cursor is over the edge representing the chain B-C interface, context-menu choices include Select Contact Residues of B and C Select Contact Residues of B with C Select Contact Residues of C with B <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#diagram> Or if you get a new daily build, another way to select the residues is to use menu: Select... Contacts, the Chains section of the resulting dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> Then use "info residues sel" and possibly "log save" as mentioned above. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save> Alternatively, you could use "measure buriedarea" specifying the two chains and "list true", which also reports each residue's buried area. (thus avoiding having to select and use "info") <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> Example: measure buriedarea (/A&protein) with (/B&protein) list true I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 12, 2022, at 9:06 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Indeed! Although, as a suggestion, would it be possible to highlight > in the description that in order for the plot to inherit residue > colors, one needs to invoke the plot _after_ the residues have been > identified and colored? Also, could I save the output of the analysis > to a text file? > Best, > Pranav > -- > Pranav Shah > Postdoctoral Research Fellow. > > Division of Structural Biology, > Wellcome Trust Centre for Human Genetics, > University of Oxford, > Roosevelt Drive, Oxford OX3 7BN, > UK > > On Thu, May 12, 2022 at 4:53 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> haha, glad you like it!! >> >> Best, >> Elaine >> >>> On May 12, 2022, at 8:27 AM, Pranav Shah via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> <3 >>> <3 >>> <3 >>> <3 >>> <3 >>> >>> Best, >>> Pranav >>> -- >>> Pranav Shah >>> Postdoctoral Research Fellow. >>> >>> Division of Structural Biology, >>> Wellcome Trust Centre for Human Genetics, >>> University of Oxford, >>> Roosevelt Drive, Oxford OX3 7BN, >>> UK >>> <image.png>_______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>

1 1

use of the program UCSF Chimera
by GABRIELLE LUPETI DE CENA 12 May '22

12 May '22

Goodnight! My name is Gabrielle, I am a Master's student at UNIFESP (Federal University of São Paulo), SP, Brazil. I'm using UCSF Chimera to analyze the secondary structure of some peptides that I'm studying. When I load the .pdb file in the program, it generates a different structure than the one desired. In the examples below, we have two structures alpha helix and random coil, but the images generated are different and I don't understand why. Could you help me, explaining what is happening, or what I should do to have the image as in the first figure (NATTP_05 chimera). Thanks -- ---- A Universidade Federal de São Paulo segue a política de e-mail Institucional disponível em https://sti.unifesp.br/documentos/termos-de-uso-do-email <https://sti.unifesp.br/documentos/termos-de-uso-do-email> <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=pub…>

2 2

crystal contacts
by Meital Bachar 12 May '22

12 May '22

Hello, my name is Meital and I am a Ph.D. student at the school of chemistry at Tel-Aviv university. i am trying to identify the crystal contacts of a protein that I am studying. and I was wondering if it is possible to get an output for the calculated crystal contacts in a way that the actual residues are listed. appreciate a lot your response. Meital

2 2

Get rotation between two views?
by Oliver Clarke 11 May '22

11 May '22

Hi, In either Chimera or X, is there a way to obtain the orientational relationship between two views? E.g. if I have two views saved, I would like to be able to say "view 1 is related to view 2 by a 45deg rotation about X and a 25deg rotation about Y" - this would be very useful for figure making/writing purposes. Does this exist? Cheers Oli

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Re: [Chimera-users] Get rotation between two views?
by Elaine Meng 10 May '22

10 May '22

Hi Zhen, Are you using Chimera or ChimeraX? Remember they are two different programs with many differences from each other. Chimera only has a "viewdock" command (no "view" series, but I'm not sure what you mean by that anyway). Also if you are having a problem like your window freezing, instead of sending a message to me or the list, it is better to report it by using menu: Help... Report a Bug (both Chimera and ChimeraX have this) and filling out the dialog. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2022, at 10:31 AM, Gong, Zhen <zg2234(a)cumc.columbia.edu> wrote: > > Hi Elaine, > > Thank you very much for your reply. I was trying to use the “view” series command in chimera 1.13 but always get complaint like “no such file” or “unknow view Dockfile type”. Is that these commands could only be used in ChimeraX but not Chimera? > > By the way, I also had problems using chimera 1.16 on my mac (MacOs Montery version 12.2). The window will just freeze once I clicked on the “command line interface” icon and it will take about half minute to come back. Do you know how to solve this problem? > > Many thanks in advance! > > Best, > Zhen

2 1

Move model with associated map?
by Oliver Clarke 10 May '22

10 May '22

Hi all, Is there any way to apply the same transformation used by matchmaker for alignment to a map? I have two structures (map+atomic model) in different frames of reference. I would like to align one structure on the other, but also move the associated map in the same way. Is this possible? Cheers Oli

2 2

ValueError: can't normalize zero length array
by jyoti vishwakarma 04 May '22

04 May '22

ValueError Exception in Tk callback Function:<function<lambda> at 0x000000000EF38DD8> (type:<type 'function'>) Module:<module 'Tkinter' from 'C:\Program Files\Chimera 1.16\bin\lib\lib-tk\Tkinter.pyc'> (line: 590) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\bin\lib\lib-tk\Tkinter.py", line 592, in callit func(*args) File "C:\Program Files\Chimera 1.16\share\chimera\tkgui.py", line 3025, in<lambda> lambda s=self, e=event: s.showLabelBalloon(e)) File "C:\Program Files\Chimera 1.16\share\chimera\tkgui.py", line 3030, in showLabelBalloon objs = self.viewer.pick(event.x, event.y) ValueError: can't normalize zero length array ―――――――――――――――――――― -- Regards, Jyoti Vishwakarma UGC-SRF c/o Dr. R. Ravishankar Biochemistry & Structural Biology Division CSIR-Central Drug Research Institute Lucknow-226031

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Web service issue?
by LaLone, Carlie 03 May '22

03 May '22

Hello, Could you provide advise on how to remedy the issue below? You are now running Chimera version 1.16 (build 42360). Your previous version was 1.15 (build 42258). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) #0, chain X: fatty acid-binding protein, liver Model 1 (m1_Fruit_fly+3stm+X.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 92, in download fp = self.options.transport.open(Request(url)) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 62, in open return HttpTransport.open(self, request) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 67, in open return self.u2open(u2request) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 132, in u2open return url.open(u2request, timeout=tm) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 435, in open response = meth(req, response) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 548, in http_response 'http', request, response, code, msg, hdrs) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 467, in error result = self._call_chain(*args) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 407, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 654, in http_error_302 return self.parent.open(new, timeout=req.timeout) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 429, in open response = self._open(req, data) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 447, in _open '_open', req) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 407, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 1241, in https_open context=self._context) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 1198, in do_open raise URLError(err) URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)> Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from web application request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:ClustalOmegaService' is unavailable. See Reply Log for more details. Thank you, Carlie Carlie A. LaLone, Ph.D. Research Bioinformatician Great Lakes Toxicology and Ecology Division Office of Research and Development U.S. Environmental Protection Agency 6201 Congdon Blvd. Duluth, MN, 55804 Work: (218)529-5038 BIG NEWS…SeqAPASSv6.0 is now available!!!!! Try the Sequence Alignment to Predict Across Species Susceptibility<https://seqapass.epa.gov/seqapass/> (SeqAPASS) tool and predict chemical susceptibility to hundreds to thousands of species Publications 1. International Consortium to Advance Cross‐Species Extrapolation of the Effects of Chemicals in Regulatory Toxicology<https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.5214> 2. Integrative Computational Approaches to Inform Relative Bioaccumulation Potential of Per-and Polyfluoroalkyl Substances Across Species<https://academic.oup.com/toxsci/article-abstract/180/2/212/6112015> 3. Evidence for Cross Species Extrapolation of Mammalian-Based High-Throughput Screening Assay Results<https://pubs.acs.org/doi/abs/10.1021/acs.est.8b04587> 4. In Silico Site-Directed Mutagenesis Informs Species-Specific Predictions of Chemical Susceptibility<https://academic.oup.com/toxsci/article/166/1/131/5060571> 5. Evaluation of the scientific underpinnings for identifying estrogenic chemicals in nonmammalian taxa <https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.3456> 6. SeqAPASS: A Web-Based Tool for Addressing the Challenges of Cross-Species Extrapolation <https://academic.oup.com/toxsci/article/153/2/228/2578709> 7. Molecular target sequence similarity as a basis for species extrapolation to assess the ecological risk<https://www.sciencedirect.com/science/article/pii/S0166445X13002312>

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Error in using the "align chain sequences" tool in chimera
by Chara Spanou 02 May '22

02 May '22

Dear all, After performing the structure comparison of 2 structures using the "MatchMaker" tool of the chimera software,I need to run an alignment of the structure sequences using the "align chain sequences" tool of the chimera. Unfortunately, I am getting the following error message in the reply log that persists for weeks: Traceback from web service request (connection setup):Traceback (most recent call last): File "C:\Program Files\Chimera 1.12\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.12\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 92, in download fp = self.options.transport.open(Request(url)) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 62, in open return HttpTransport.open(self, request) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 67, in open return self.u2open(u2request) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 132, in u2open return url.open(u2request, timeout=tm) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 437, in open response = meth(req, response) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 550, in http_response 'http', request, response, code, msg, hdrs) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 469, in error result = self._call_chain(*args) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 409, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 656, in http_error_302 return self.parent.open(new, timeout=req.timeout) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 431, in open response = self._open(req, data) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 449, in _open '_open', req) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 409, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 1240, in https_open context=self._context) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 1197, in do_open raise URLError(err)URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590)> Typically, if you get a TypeError, it's a problem on the remote serverand it should be fixed shortly. If you get a different error orget TypeError consistently for more than a day, please report theproblem using the Report a Bug... entry in the Help menu. Pleaseinclude the traceback printed above as part of the problem description.Traceback from web application request:Traceback (most recent call last): File "C:\Program Files\Chimera 1.12\share\WebServices\appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "C:\Program Files\Chimera 1.12\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears "NonChimeraError: Web service appears to be down. See Reply Log for more details.Service 'opal:ClustalOmegaService' is unavailable. See Reply Log for more details. Can you please help? Thanks a lot for your time,Chara

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Questions in ChimeraX comparing with Chimera
by Long Gui 27 Apr '22

27 Apr '22

Dear Chimera users, I have been recently transferring to ChimeraX from the conventional Chimera and I am currently struggling with two features existing in Chimera but not in ChimeraX. 1. How could I combine two or several different ChimeraX files? I have been doing in Chimera as I was opening new chimera files by "Files...Open...", this is a window pop-up as the following and if I click "No", the new Chimera will be added to the cold Chimera as the old one was not closed. However, when I performed the similar operation in ChimeraX, there is no such window and the new ChimeraX would REPLACE the old one. I wonder if there is a way (probably using command to open? but I did not find the correct open options.) to open the new ChimeraX without closing the old one? [cid:23bcde4a-3b02-4fc4-9b5e-7b034cd22a9f] 1. I am also working with tomogram slices and cellular segmentation. Previously, in Chimera I can set this Transparency value to 0 and the Plane of the tomogram will be totally opaque. Now in ChimeraX I have used the command "transparency #2 0" (#2 is the tomogram files) but it still look quite different from my previous images in Chimera. Is there a way to set it up in ChimeraX so it could look similar as before? [cid:1e2eb72a-f2e5-4c83-b4e4-81b881b9dc67] Thanks again and I am very grateful if any advice or help could be provided. Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Re: [Chimera-users] Help and guidance on using chimera
by Tom Goddard 27 Apr '22

27 Apr '22

Hi Tommy, Sure those things can be easily be done. I'd encourage you to use ChimeraX instead of the old Chimera program. Also best to email questions to the Chimera mailing list (chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>) or ChimeraX mailing list (chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>). To delete a domain of a protein in ChimeraX that is say residues 151 to 375 of chain B delete /B:151-375 The command syntax would be different in Chimera. To add short linkers is more difficult and I will leave that question to Elaine to advise on the mailing list -- I am not the most knowledgable about how to do that. Tom > On Apr 26, 2022, at 4:45 PM, Tommy Tong <ttong(a)SDBRI.ORG> wrote: > > Dear Thomas, > Good afternoon. How are you? My name is Tommy from San Diego Biomedical Research Institute, CA. I am new to Chimera software and my level of usage has been at the basic level, eg selecting chains and to color label the specific region on the protein. > > May I ask if there is a way to selectively deleting a specific domain on a protein from a pdb file? I want to show graphically how the structure of the molecule will look like without the domain(s). In addition, is it possible to add short amino acid sequence, such as short linkers (eg GSGS) after a domain has been deleted from the protein structure? > > I am currently using UCSF Chimera version 1.16. > > Your help and advice are greatly appreciated. > Thank you for your time. > > Sincerely, > Tommy

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Tomogram display
by Han, Shen 26 Apr '22

26 Apr '22

Hi Elaine, I want to ask some questions regarding displaying tomogram in ChimeraX. is it possible to reveal the density in the tomogram and trace the objects throughout the tomogram (also docking model in the density) in ChimeraX? Best wishes, Shen _________ Dr. Shen Han Postdoctoral Researcher Max Planck Institute for Multidisciplinary Sciences Department of Molecular Biology / Cramer Lab Am Faßberg 11, Göttingen 37077, Germany

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Creating Bonds between Models
by Draven Houser 25 Apr '22

25 Apr '22

Hello, I am trying to build a structure in chimeraX that is a combination of several other known structures. To do this I need to be able to create bonds between different models in the software, but this doesn't seem to be possible for the moment. Can anyone suggest a workaround for this? Thanks! Best regards, Draven Houser

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renumbering sequence with gap
by Haghighijoo, Zahra 25 Apr '22

25 Apr '22

Hi, I am editing a retrieved pdb from homology modeling that has two gaps, is there a way to insert the gaps and renumbering pdb? could you please help me ? Thank you, Zahra

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Open Castp file in Chimera X
by Zhang, Bixia 21 Apr '22

21 Apr '22

Good afternoon, I am trying to open .poc file from CASTP server in Chimera X. And I found this chimeraX recipe https://rbvi.github.io/chimerax-recipes/castp/castp.html. However, when I used the command open<help:user/commands/open.html> read_castp.py, it said No such file/path: read_castp.py. I am working on a Linux unbuntu box and I don't know if this is making any difference. Could you please help with this issue? Thank you so much! Best, Bixia Read CASTP pockets file - ChimeraX Recipes<https://rbvi.github.io/chimerax-recipes/castp/castp.html> We for the ChimeraX atom specifier from chain identifier, residue number and atom name. For example, the above lines are for atoms /A:45@NH2, /B:27@O, /B:27@CG1 in ChimeraX syntax belonging to pockets 2, 1 and 1. rbvi.github.io

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Command for measuring distance between centroids and to show dotted lines depicting the measurement
by Shubham Devesh Ramgoolam 21 Apr '22

21 Apr '22

Hi, I hope you are doing well. Is there a command in chimera that allows us to measure the distance between centroids and also to show dotted lines depicting the measurement? I used the command distance but no lines were shown for centroids. I am considering of using the coordinates of the centroids to place dummy atoms and then, use distance. However, I do not know if there is a command for placing dummy atoms in specified positions. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Upcoming deprecation of Chimera webservices
by Zach Pearson 21 Apr '22

21 Apr '22

Hello Chimera users, In the next 12 to 18 months, some Chimera tools that depend on web services may stop working: BLAST protein (which is also used by Multidomain Assembler), Modeller comparative and loop modeling, multiple sequence alignment with Clustal Omega and MUSCLE, Small-Angle X-Ray Profile, and 2D Chemical Diagram (used by Structure Diagram and ViewDock). The reason is that some necessary upgrades to our internal systems may break these web services. However, ChimeraX uses a different type of web service that will continue to work, and we have already integrated the following into ChimeraX: BLAST protein, Modeller comparative and loop modelling. In progress: multiple sequence alignment with Clustal Omega and MUSCLE. We wanted to make sure that our users would be prepared for the need to switch to ChimeraX for these features. If you have comments on how to prioritize integrating the remaining services (Small-Angle X-Ray Profile, 2D Chemical Diagram) with ChimeraX, please let us know. Thank you!

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Loop through hundreds of files and find HBonds
by Samuel Kyobe 19 Apr '22

19 Apr '22

Dear Chimera (and ChimeraX) team I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation. I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file. Thanks Samuel Dr. Samuel Kyobe Department of Medical Microbiology, 3rd floor, Pathology/Microbiology BLDG, School of Biomedical Sciences College of Health Sciences, Makerere University. Box 7072, Kampala, Uganda. Mob: +256775468605 Skype: samuelkyobe

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Chimera(X) in Centos stream 9
by Antonio Díaz Quintana 19 Apr '22

19 Apr '22

Dear all, I am unable to install Chimerax and Chimera—yes I still use the old one because its great tools—using the rpm package in Centos Stream 9, because lack of LibOSMesa package in this distribution. I tried using dnf, but a mesa-libGL library (21.3.4...) is already installed Similarly, it seems my OS distribution does not contain python Tk, nor I can get suitable python with Tk-devel from repository, so I get the following message. Could I get any help? Meanwhile I got it on my old Win10, 11 years-old laptop. Both programs work well there. Best, Antonio -- Dr. Antonio J. Díaz Quintana Instituto de Investigaciones Químicas Universidad de Sevilla - CSIC Avda. Americo Vespucio 49 41092 Sevilla Spain Phone: +34 954 48 9631

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Command for selecting aromatic ring
by Shubham Devesh Ramgoolam 18 Apr '22

18 Apr '22

Hello, I hope you are doing well. Is there a command on chimera that will allow me to select for the atoms in aromatic rings? I found a workaround by defining the atoms involved in the aromatic rings and then making my selection. However, I would like to use a command (or perhaps combination of commands) from chimera to select the aromatic atoms. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Revised Need Help
by Ali Raza Azeemi 14 Apr '22

14 Apr '22

Hi, hope you are doing well? dear, we have a question about making an animation/movie in chimera. I want to add molecular dynamics(MD) movie to the animation timeline, so I am facing difficulty to add on it. Kindly tell me if an option is available for this?. I will be very thankful to you. Thank you -- *Ali Raza Siddiqui* *Jr. Research Fellow* *Computer-Aided Drug Design (CAAD) unit. P-133, PCMD* H.E.J. Research Institute of Chemistry International Center for Chemical & Biological Sciences University of Karachi, 75270 Karachi- Pakistan.

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Question regarding bond angle
by Prathvi Singh 14 Apr '22

14 Apr '22

Hi again Elaine, Is there a way in chimera or chimeraX to change the angle between three atoms A,B,C where atoms A & B are covalently bonded to each other but neither A nor B is bonded to C ? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Need Help
by Ali Raza Azeemi 14 Apr '22

14 Apr '22

Hi, hope you are doing well? dear, we have a question about making an animation/movie. I want to add molecular dynamics(MD) movie to the animation timeline, so I am facing difficulty to add on it. Kindly tell me if an option is available for this?. I will be very thankful to you. Thank you -- *Ali Raza Siddiqui* *Jr. Research Fellow* *Computer-Aided Drug Design (CAAD) unit. P-133, PCMD* H.E.J. Research Institute of Chemistry International Center for Chemical & Biological Sciences University of Karachi, 75270 Karachi- Pakistan.

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Loop through pbd files (ligand poses) and find hydrogen bonds against one template receptor
by Samuel Kyobe 13 Apr '22

13 Apr '22

Dear Chimera (and ChimeraX) team I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation. I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file. Thanks Samuel Dr. Samuel Kyobe Department of Medical Microbiology, 3rd floor, Pathology/Microbiology BLDG, School of Biomedical Sciences College of Health Sciences, Makerere University. Box 7072, Kampala, Uganda. Mob: +256775468605 Skype: samuelkyobe

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