- Chimera-users - RBVI Mailing Lists

How to show certain hydrogen bonds and hide others
by Karjalainen, Mikael 29 Aug '23

29 Aug '23

Hi! I am having problems to show certain hydrogen bonds and hide others. For example, I would like to hide some completely. Then others should be shown always. Even when atoms are not shown and only ribbon is. I couldn't find how to do this by googling or for example reading how to use hbonds command. I am using Chimera 1.16. I know that there is ChimeraX, but now I need to modify old project. Regards, Mikael

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Atlocs
by Hernando J Sosa 28 Aug '23

28 Aug '23

Dear ChimeraX, I have an atomic model with several chains that have residues with alternate locations A and B. I noticed that while Chimera by default displays alternate locations A. ChimeraX for some chains display alternate locations A and for other chains alternate locations B. Why is this behavior different in Chimera and ChimeraX? Is this a novel feature of ChimeraX? I this is the case how ChimeraX decides which of the two alternate locations A or B to display? Thanks Hernando ___________________________________ Hernando Sosa, PhD. Dept. of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 emai: hernando.sosa@einsteinmed.<mailto:hernando.sosa@einsteinmed.org>edu ___________________________________

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Saving the resolution of structure to a file
by Prathvi Singh 22 Aug '23

22 Aug '23

Hi Elaine, Is there a way to save the resolution of a protein structure to a file using command line, either in chimeraX or chimera? Thanks -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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dms from command line
by Guido Leoni 21 Aug '23

21 Aug '23

Dear list Is there an option to write dms from command line? I' m able to launch the command line interface with a pdb loaded within . Then I estimate the surface with this command surface #0 now I would write a dms ... Please do you have any tips that can help me? Thank you Guido

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non-integral charge warning
by Chris Ellis 21 Aug '23

21 Aug '23

Hi, After running the dock prep, I get the following warning in the reply log. Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log How can I fix this warning? Do I need to fix this? Thank you for any help you can provide. I truly appreciate it. Chris

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San Jacinto College Software Intake Form Chimera
by Yates, Michael 18 Aug '23

18 Aug '23

Greetings. I am the Supervisor of Desktop Support Services for San Jacinto College. Information Technology Services (ITS) has been asked to evaluate Chimera to ensure that the San Jacinto College computing environment meets the requirements for the service as well as to ensure that the service offering complies with our requirements. As part of our standard process we reach out to software vendors to request the completion of the attached form after the requestor has completed section 1. At this time we request that you complete section 2 or 3 of the attached form and return it to us by August 21st so that we may complete our evaluations and grant purchase eligibility if the service qualifies. Additional questions may follow. In addition to what is in the form, please include (if applicable) any information / documentation that you have available regarding the options below and please indicate if there are any additional charges for the implementation of such: * Azure AD Single Sign On capability * Office 365 Integration features * Ellucian Banner Integration features [Description: Description: cid:image001.png@01CEC8EF.F2E97C50] Michael Yates San Jacinto College Supervisor of Desktop Support Services 4624 Fairmont Pkwy, Pasadena, TX 77504 Direct: (281) 998-6150 X7325 | Technical Support: (281) 998-6137 Web<http://blogs.sanjac.edu/its> | Facebook<http://www.facebook.com/sanjacits> | ITS Twitter<http://www.twitter.com/sanjacits>

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Moving atoms of a protein
by Abril Gijsbers 18 Aug '23

18 Aug '23

Hi Elaine, I have this alphafold structure (see picture) that is basically a huge string/thread and then a folded domain. I wanted to stretch the string to make its length more obvious. Is it possible to pull the residues without messing with the connections (peptide bond)? I am using chimeraX and I saw that you can "move atoms" but when you pull one you don't pull the others. If chimera cannot do this, do you know if another program will allow me to do it? Thank you in advance for your help, Best regards, Abril Gijsbers [image: image.png]

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Re: ChimeraX license and download
by Elaine Meng 17 Aug '23

17 Aug '23

Please disregard and delete the previous message. I messed up and accidentally CC'd the chimera users list instead of the licensing address. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2023, at 12:56 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > [...] > Thank you for licensing the commercial version of ChimeraX, the next-generation molecular visualization and analysis program from our research lab. ChimeraX is under active development, with version 1.6.1 released in May 2023. As new features are added, daily development builds are also available for download. Daily builds are not tested as thoroughly as production releases, but in practice are highly usable. > [...]

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Requesting protocol to find protein configuration units
by Panapakam, Jyotheeswaran 17 Aug '23

17 Aug '23

Dear Officail, This is Jyo writing from UNT biological sciences at Denton, TX, USA. I have been using your software for my research project for about an year. I was looking for a help/instructions about how to find out the configuration change in the protein after docking with a ligand. I have heard about RMSD docking value, that will be given in Amstrong units, could you kindly instruct me the process to perform it. It would be more glad if you are able to answer me withing a week from now : ) Sincerely, Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas. Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas.

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Re: [chimerax-users] re error with Movie recorder utility
by Elaine Meng 17 Aug '23

17 Aug '23

Hi Anna, This chimerax-users email address is for questions about ChimeraX, but it sounds like you are using the Chimera program instead, since only Chimera has a Movie Recorder tool. So I am CC-ing the chimera-users email address on this reply, and you do not need to re-send your question. There is no separate "freeware version" -- Chimera is free for academic use and the download is the same for academically or commercially licensed users. (This is also the case for ChimeraX). The Command Line is always for entering one command at a time, i.e. that is the normal situation, not a problem or bug. If you have just a few commands you can enter them as one line with semicolons between them. However, if you mean that you have a script that contains many Chimera commands, you do not enter them one at a time into the command line. Instead you use some text-editing program (outside of Chimera) to create a plain text command file containing those commands, then you open that file using either the Chimera menu File... Open, or the Chimera "open" command. Normally command files are named with the filename extension ".com" or ".cmd" so that Chimera knows what kind of file you are trying to open. See Chimera help pages and tutorials on making movies, namely: Making movies: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html> Movie Recorder help page (you can just click the Help button on the tool, or see the copy of the same thing at our website here): <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorde…> Chimera movie-making tutorials: <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies09/moviemaking.html> <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.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 Aug 16, 2023, at 6:31 PM, Anna Lohning via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi > I have the freeware version installed and trying to make a movie using the Tools/Utilities/Movie recorder window. > At this stage, I seem to only have the command line available for commands one at a time. > Anyway, under the Tools/Utilities, the only options there currently are > Register > Updates > > Be grateful for some clarification as I cant seem to find anyone having this issue. > Many thanks > Kind regards > > Anna > Dr Anna Elizabeth Lohning > Associate Professor - Biochemistry > Faculty of Health Science & Medicine > Bond University > ROBINA 4229 > (07) 5595 4779 > alohning(a)bond.edu.au >

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.msi chimera
by Yanni Goudetsidis (Staff) 11 Aug '23

11 Aug '23

Good morning Is there a .msi installer for chimera I could download, please? Thank you

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making composite map using vop maximum command
by ytakagi＠iu.edu 10 Aug '23

10 Aug '23

Hi I want to make a composite map using two locally refined maps. I tried Phenix but did not work well. So, I like to do it by Chimera. Apparently, a composite map can be made using Chimera's vop maximum command. But I could not find the instruction of how to do it. Can you tell me how to do it? Thanks

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San Jacinto College Security Evaluation
by Melendez, Aaron 09 Aug '23

09 Aug '23

Good afternoon, San Jacinto College, as part of its new application/vendor procurement process, is evaluating the security posture of Chimera and would like to ask for your help in procuring documentation that proves the security controls in place for the company. If you have any Information Security documentation you can share with us, it would be greatly appreciated. If an NDA needs to be signed, we would be happy to provide that to you. Documents that help: * HECVAT (one will be attached that can be filled out) * SJC Vendor Questionnaire (one will be attached that can be filled out) * Information security policies and procedures * Datacenters or Hosting Providers used. * Incident response plan * Disaster recovery plan * Business continuity plan * System and network architecture diagrams * Penetration testing reports * Vulnerability scan reports If you can provide the Data Centers that are used and the Hosting Providers, it will also help our evaluation process. Thank you in advance for your help. Please reach out if you have any questions. Regards, e Aaron C. Melendez Third-Party Risk Analyst The Office of Cybersecurity Cell: (281) 635-2940 (Please call x 2 or Text) San Jacinto Community College 4624 Fairmont Pkwy, Pasadena, TX 77504 Technical Support: Get help at SanJac ITS<https://www.sanjacits.org/> | call (281) 998-6137 www.sanjac.edu<https://www.sanjac.edu/> | www.facebook.com/sanjacintocollege<http://www.facebook.com/sanjacintocollege> | @SanJacCollege [2z5cr1lnO9iMtMLfMHSAYwzcMySsBwfq8SYpRxc6xBeRPF2c+m+YTgIc8IdrhL4f1IjMkJpGrM5AAAAAElFTkSuQmCC] “Under pressure, you don’t rise to the occasion, you sink to the level of your training.”

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Secondary structure editing of molecules
by GABRIELLE LUPETI DE CENA 08 Aug '23

08 Aug '23

Good morning! I have doubts about how to turn the peptide structures of the four images below (A), (B), (C), and (D) into a cartoon model like figure (E). I've tried, but I'm not succeeding. Thank you very much. -- ---- É obrigatória a utilização do e-mail @unifesp em todas as correspondências oficiais, institucionais e no acesso aos equipamentos e sistemas da Universidade Federal de São Paulo, conforme a portaria Reitoria n. 1182/2022 <https://sti.unifesp.br/documentos/termos-de-uso-do-email> que define a Política de e-mail institucional da Unifesp. <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=pub…>

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Saving phi psi values to a text file
by Prathvi Singh 06 Aug '23

06 Aug '23

Hi Elaine, Is there a command to save the phi and psi angle values of each residue of a PDB file in a text file using UCSF chimera? I know we can do this in chimeraX using the command: save C:\myphi.defattr attrName phi format defattr model #1 Also, can we use chimeraX to save the phi and psi values in a single file? Thanks in advance -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Query regarding selection
by Prathvi Singh 04 Aug '23

04 Aug '23

Hi Elaine, I want to select all the atoms except the backbone oxygen and nitrogen atom of residues 100.A to 120.A . Is there a command to do this in either chimera or chimeraX? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Re: [EXTERNAL] Chimera-users Digest, Vol 243, Issue 22
by Reza Khayat 01 Aug '23

01 Aug '23

Hi Elaine, Thanks for the help. This will speed things up quite a bit. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________________ From: chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Tuesday, August 1, 2023 3:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: [EXTERNAL] Chimera-users Digest, Vol 243, Issue 22 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Measure rotation without writing PDB (Reza Khayat) 2. Re: Measure rotation without writing PDB (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 1 Aug 2023 18:23:19 +0000 From: Reza Khayat <rkhayat(a)ccny.cuny.edu> Subject: [Chimera-users] Measure rotation without writing PDB To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Message-ID: <1690914198332.72284(a)ccny.cuny.edu> Content-Type: multipart/alternative; boundary="_000_169091419833272284ccnycunyedu_" Hi, I'm trying to measure the movement of a domain between two structures of the same protein. Here are the conditions: 1. There are two domains in each structure 2. I want to overlay the first domain and measure the rotation of the second domain 3. There are lots of structures, so I want to minimise the number of steps 4. I'd like to do this with a script and the --no_gui option on headless Chimera Here is my current script for the routine: open pdb1 open pdb2 match #1:1-50 #0:1-50 write format pdb relative #1 #0 t.pdb delete #1 open t.pdb match #1:55-80 #0:55-80 measure rotation #1 #0 delete #1 open pdb3 ... Is it possible to not have to write, delete, and open #1 after the first match step? If I don't do this, then the measure rotation #1 #0 will measure rotation of the initial match rather than the second match. Thanks for the help. 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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Measure rotation without writing PDB
by Reza Khayat 01 Aug '23

01 Aug '23

Hi, I'm trying to measure the movement of a domain between two structures of the same protein. Here are the conditions: 1. There are two domains in each structure 2. I want to overlay the first domain and measure the rotation of the second domain 3. There are lots of structures, so I want to minimise the number of steps 4. I'd like to do this with a script and the --no_gui option on headless Chimera Here is my current script for the routine: open pdb1 open pdb2 match #1:1-50 #0:1-50 write format pdb relative #1 #0 t.pdb delete #1 open t.pdb match #1:55-80 #0:55-80 measure rotation #1 #0 delete #1 open pdb3 ... Is it possible to not have to write, delete, and open #1 after the first match step? If I don't do this, then the measure rotation #1 #0 will measure rotation of the initial match rather than the second match. Thanks for the help. 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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Silent install?
by Jim Richard 27 Jul '23

27 Jul '23

Hello, We are using MECM (SCCM) to install Chimera and need to suppress ALL windows. I have tried the /verysilent flag but a command prompt still pops up with what looks to be the compiling portion. Is there a way to have ALL windows silent? -- *Jim Richard* Pronouns: he/him/his Client Systems Administrator

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Saving Animations on Mac OS
by Natalie Walsh 25 Jul '23

25 Jul '23

Hello, I am having troubles saving my animations on my Mac OS. I get this error when I record and save my animation: An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: -1 Error message: Could not find ffmpeg executable —————————————— I googled some solutions regarding “ffmpeg” and I believe I successfully installed it to my terminal, but I am still receiving the same error. Thank you, Natalie Walsh

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Unable to dock
by Panapakam, Jyotheeswaran 20 Jul '23

20 Jul '23

[cid:9962344b-5095-47ba-a1c2-1c6fef113ef2] Dear Official, I was unable to move the green grid, thus, I am unable to dock a compound on the protein target. Could you please help me with this? Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas.

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How do I colour all my hydrogen atoms grey?
by Mazin Nasralla 17 Jul '23

17 Jul '23

Hello, I imported an x,y,z model of water molecules into Chimera. I want to create an image of my water structure so I am setting the background to grey. That works. But I would prefer to set the hydrogen atom colour to light grey. I can't work out how to do that. I can select each individual atom, and then colour edit it but that will take ages. Is there a simple command line solution? Thanks Mazin

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hiding a model slowly
by Sen, Anindito 14 Jul '23

14 Jul '23

Dear Chimera X team, Is there a way I can hide one of the models in a ChimeraX session slowly (like fading it off) while making a movie. typically I use hide #7 model 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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Chimera-X inteprhase of the AlphaFold
by Enrico Martinez 13 Jul '23

13 Jul '23

Dear Chimera-X users! In parallel to the modeller, I am trying to use the Alpha fold interface with the aim to full model starting from the sequence using template. The problem is that I can not define manually which template I would like to use for each prediction so the interphase takes its automatically based on the input sequence and the final prediction is not very precise. Would it be possible rather to specify a specific pdb ID additionally to a given sequence ? Many thanks in advance Enrico

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Modeler interphase in Chimera
by Enrico Martinez 13 Jul '23

13 Jul '23

Dear Chimera Users! I would like to try MODELLER interphase implemented in the Chimera for prediction of the segments missed in input PDB structure having as the input: the pdb structure with missed N and C terminal fragments (everything in one chain), as well as the full sequence of the protein in FASTA. Could you please provide me with a link to the tutorial (or just explain a very basic workflow here .. ), which simply explains how I could predict the model based on the data and save the predicted solutions in pdb format ? Many thanks in advance Cheers Enrico

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Remove me from mailing list
by Saima Sam 10 Jul '23

10 Jul '23

Hi, I am no longer a user of Chimera so please opt me out of these emails. I would truly appreciate it.

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Placing of a hame-ion centre into an AlfaFold structure
by George Tzotzos 10 Jul '23

10 Jul '23

I’d be grateful for any suggestions regarding the following problem/question. Problem Placing of the haem-iron centre in mosquito P450 structure(s) obtained by means of AlfaFold. This is required for follow up docking simulations. There no insect P450 structures deposited in PDB. However, there are numerous mammalian P450 crystal structures some of which are homologous to the mosquito structures I’m dealing with. A distinctive feature of these structures is a haem-iron centre tethered to the protein via a cysteine thiolate ligand. Six regions have been designated as substrate recognition sites (SRS 1-6) based on comparative sequence analysis methods. These SRS are conserved and are thought to participate in the formation of the substrate access channel, and form part of the catalytic site surrounding the haem iron center. My initial approach would be to use Chimera to align the AlfaFold structure against its mammalian homologue PDB structure and assume that the haem-iron centre would be located in the same place. Is there a better way to achieve the same objective?. Your help will be greatly appreciated. Best regards George

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Chimera?
by Emma 05 Jul '23

05 Jul '23

Chimera, this is me again

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Opening MTZ files on Mac OS
by Natalie Walsh 04 Jul '23

04 Jul '23

Hello, I am having troubles opening MTZ maps from PDB on ChimeraX 17.1. on Mac OS. I read somewhere that you need to download the Clipper plug-in. I went ahead and installed that (although I am not sure that I was successful) and am still struggling to open these files. Thank you, Natalie Walsh

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Removing lonbond links from pipes-and-planks representation
by philip.robinson＠bbk.ac.uk 02 Jul '23

02 Jul '23

Hi, I'm trying to generate a pipes-and-planks representation of an atomic model that contains gaps. Before generating the pipes-and-planks representation I hid the long bonds to remove the links in the gap regions. However, the gaps are connected again in the pipes-and-planks representation and I cannot find the command to hide them. Any help would be appreciated. Phil

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ChimeraX Question
by Bani Kaur 01 Jul '23

01 Jul '23

Hi, I hope you are doing well! My name is Bani Kaur and I am an active user of ChimeraX for a research project concerning protein modeling, specifically with the CFTR protein. I have been running into issues with showing atoms on my residue, specifically after I change the romater. I am not sure what to do about this as I have downloaded the latest version of ChimeraX. Additionally, I am not able to see clashes for some very reason and am only able to see it when limit by selection is unchecked, but for my research project, we require that it is checked in the clashes settings. Thank you so much for your help! Best, Bani Kaur

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Questions regarding reply log
by Prathvi Singh 28 Jun '23

28 Jun '23

Hi Elaine, Is there a way to clear the Reply Log using the command line? Is there a way to write the contents of the Reply log to a text file? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Supoort for automating superimposition process of multiple pairs of structures using command line
by Vaibhav Anand 28 Jun '23

28 Jun '23

Hello Chimera team, I am seeking your assistance in automating the process of superimposing multiple pairs of structures using the command line. I've performed the MD simulation of the UBA domain (PDB ID - 1OQY), and for analyzing the structural changes, I've extracted the 11 structures from the trajectory at 500ns to 1000ns with steps of 50ns. In total, I've 12 structures [1 reference structure (em.gro - energy minimized structure) and 11 extracted structures]. Now I want to superimpose each extracted structure w.r.t. em.gro and save the image of superimposition with the image name to be (time + rmsd_value). For the RMSD value, I'll have to save the reply log file (or the last 10-15 lines of the reply log) and then copy the rmsd value and save my image file with it. Could you please give me an outline or references on how I can do this task? Thank you for your attention Regards, Vaibhav

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downloading and saving multiple PDB's
by Dmitry Semchonok 26 Jun '23

26 Jun '23

Dear colleagues, Is there a way to 1. download the multiple pdb/mmcif using Chimerax knowing their ID entry? 2. save multiple opened pdbs using their corresponding original names in Chimerax? Thank you in advance. Kind regards, Dmitry

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Regarding issue detected while running chimera
by Suman Dhungel 26 Jun '23

26 Jun '23

Dear concerned one, I have been using UCSF Chimera from another device for the past 10 years. Recently I tried to operate chimera-1.17.1 on my computer. I have been facing a repeated issue that has been reported below. I tried to reinstall however, the issue persisted. I even tried with the new version (Chimera alpha ), similar issue with that as well. [image: chimera error.JPG] [image: my device.JPG] Would you please help... Regards Suman...

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Error while startup
by Ramanakishore V.S 26 Jun '23

26 Jun '23

Respected sir I have downloaded the Chimera V 1.17.1 on my Laptop. But when I try to open it, I am getting an error code -1073741819. I tried multiple options and sources but couldn't fix it.So can you please look into it. I have attached a image of the error message Thank you

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Re: Seeking help with Chimera regarding superposition of multiple structures
by Elaine Meng 25 Jun '23

25 Jun '23

> On Jun 25, 2023, at 7:21 AM, Vaibhav Anand <dvaibhav(a)iitk.ac.in> wrote: > > Respected Mam, > I hope this email finds you well. I am seeking your assistance in resolving a problem I am currently facing. > > I have performed the Molecular dynamic simulation of the UBA domain (PDB ID - 1OQY), and for analysis, I've extracted the 11 PDB structures at [500ns - 1000ns with steps of 50ns], and I've one reference structure (em.gro - energy minimized structure). > > I want to superimpose 11 structures with respect to my reference structure and compute the RMSD corresponding to helical residues (162-172, 177-187, 192-197). > > I am aware that in Chimera, an in-built tool called Matchmaker can perform the superimposition for multiple structures, but it doesn't have an option for selecting required (helical) residues. > > I've tried using the command line but cannot select the C-alpha atoms of helical residues. I've used the following commands - > > >>mm #0:162-172, 177-187, 192-197@CA #1-11:162-172, 177-187, 192-197@CA (Error - "Invalid atom specifier syntax: '177-187,'") > > >> mm #0:162-172, 177-187@CA #1-11:162-172, 177-187@CA (Error - "Invalid atom specifier syntax: '177-187@CA'") > > However, the following command is running well - > > >>mm #0:162-172@CA #1-11:162-172@CA (Output - "RMSD between 11 pruned atom pairs is 0.607 angstroms; (across all 11 pairs: 0.607)") > > I've also checked the atom specifications from the documentation for further guidance. - Atoms specifications > > I kindly request your assistance in resolving this issue. > Thank you for your attention. > Regards, > Vaibhav Anand Dear Vaibhav Anand, Questions about using Chimera should be sent to chimera-users(a)cgl.ucsf.edu CC'd here. <https://www.rbvi.ucsf.edu/chimera/docs/feedback.html> If you want to specify the exact atoms to use yourself, then the command is "match" (not "matchmaker" or "mm"). See "match" and also the discussion of different superposition methods. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> You are also giving wrong atom specifications. They should not have spaces after the commas. I.e. should be something like the following. match #0:162-172,177-187,192-197@CA #1-11:162-172,177-187,192-197@CA Command-line specification: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic> 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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regarding movie making
by lumbini yadav 22 Jun '23

22 Jun '23

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Support for saving pdb files with 2 models in the same file using command line
by Raquel Cossío Ramírez 20 Jun '23

20 Jun '23

Hello Chimera team, I have been working with docking files obtained from cluspro and I'm working on a set of commands to open the files in chimera, perform a ksdssp and save them in a single individual file. The problem that I have found while doing it was that secondary structure was not well calculated for the second model, so when I run the save (write) command, I only obtain a file with 1 molecule and it does not include the MODEL 1 nor MODEL 2 header, which I need it so I can analyze it later. Here I send the code that I have been running (save_all.py) with the command and a log of the problems it present while running, as well as an example input (model.000.00.pdb) and output file (ch_model.000.00.pdb) that this code produces. Also, an example of the files that I would like to generate is included in ch_model.000.00_manually.pdb The save_all.py runs in the Ubuntu terminal as follows: chimera --nogui save_all.py I believe that the code could be improved by adding an option to "save multiple files in a single file" as the GUI can allow, but using the command line, I could not find that option. I would really appreciate if you had some insight about how it could be solved. Thank you for your attention and I wait for your prompt response. Raquel Cossío Ramírez Corelab Genomics at Tecnológico de Monterrey

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Solvent Accessible Surface Area results
by Abril Gijsbers 15 Jun '23

15 Jun '23

Hi, I calculated the SASA from an AlphaFold model and a homology model with Chimera. Some of the residues got a value of zero and I just wanted to know if that means that those residues are not accessed to the solvent at all or could be a problem in the calculation? Best regards, Abril

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How to tile different models without tiling submodels
by 夏前程 13 Jun '23

13 Jun '23

Hi, I want to use chimera to depict two conformation ensembles. Each conformation ensemble is a model, and each conformation in that ensemble is the submodel within that One of the possible way I've found to do that is to use tile command (tile #1-2.*). However, that command will consider each submodel (each molecule) instead of each model (each cluster) as a whole. So I am wondering if there is any solution or suggestion? With Regards, Qiancheng Xia National Institute of Biological Sciences Beijing, China 2023/6/13

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Re: Server problem ??
by Eric Pettersen 13 Jun '23

13 Jun '23

It seems you are in fact using Chimera 1.16. Web services only work with 1.17.1 on Windows. --Eric > > I just got the following error trying to run a python script that includes sequence alignments: within Chimera (1.17) > > TransportError: HTTP Error 404: Not Found > > 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. > > Ix this a problem with the server used to run the alignment ?? > > > Thanks > > Hernando > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>: To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> > Manage subscription:

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REMINDER: Chimera website downtime
by Elaine Meng 13 Jun '23

13 Jun '23

REMINDER: Due to a scheduled power outage at UCSF followed by server upgrades, the Chimera website and web services will be unavailable -- the estimated downtime is from Tuesday May 16 8pm PDT through Wednesday May 17 8pm PDT. This upgrade will remove the Opal web services used by older versions of Chimera. Therefore, to continue using the Chimera tools running BLAST protein, Modeller comparative and loop modeling, and multiple sequence alignment with Clustal Omega and MUSCLE web services, you will need to upgrade to Chimera 1.17 (Mac) and 1.17.1 (Windows/Linux). Please pardon any inconvenience. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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getcrd command
by Yanhe Zhao 09 Jun '23

09 Jun '23

Greeting there, I am trying to get coordinate for fulcrum selection in cryoSPARC. I use volume tracer place a marker on the position of map density I wanted, with the maker selected, I use getcrd command report the coordinate in xyz in Angstroms, when I divide the values by the pixel size, the xyz in voxels are make no sense, as they are larger than my volume size. Like my volume size is 1024^3, got coordinates in Angstroms 2100,2100,2000, my pixel size is 1.475. Could you please anyone help me out? Do I did something wrong? Thanks and best, Yanhe

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Loading Trajectory Files from Command Line
by Shubham Devesh Ramgoolam 09 Jun '23

09 Jun '23

Hi all, Is it possible to load trajectory files directly from the command line in Chimera? In ChimeraX, it would be done as follows: open myfile.psf coords myfile.dcd I was wondering if there was a chimera version for this command. Regards, Shubham

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symmetrisation of the monomer - statistics issue
by Dmitry A. Semchonok 07 Jun '23

07 Jun '23

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missing bonds when visualizing in Chimera
by Aditi Laddha 01 Jun '23

01 Jun '23

Hello Elaine, I am facing some difficulties visualizing my structure in Chimera; whenever I open the .pdb file containing the sucrose molecule, the bond between glucose and fructose is missing (glycosidic bond). But all bonds are visible when I open the same file in other programs. I want to know about its hydrogen bond interaction with my protein and visualize them in Chimera. Please help me with this issue. -- Regards, Aditi Laddha PhD Scholar Indian Institute of Technology, Kanpur, Uttar Pradesh 208016

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Re: permission denied (Chimera file saving)
by Elaine Meng 01 Jun '23

01 Jun '23

Hello Dr. Sarkar, For questions about Chimera, please use the chimera-users(a)cgl.ucsf.edu address CC'd here. The problem is most likely that you are trying to save the file in a location (folder) where you do not have permission to write files. You need to choose a location on your computer in which you have permission to write files. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > From: Dr Sankar P <sankarp1(a)gmail.com> > Sent: Thursday, June 1, 2023 12:53 AM > Subject: permission denied > > Dear sir I am faculty in the dept of ECE. and I was curious and downloaded your software and tried to use it. But i faced a problem that I cannot save any ligand file as mol2IT says permission denied how do I solve this problem? Please clarify. Awaiting your reply > regards > -- > Dr SANKAR . P

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chimera-users mailing should be working
by Greg Couch 24 May '23

24 May '23

But the web interface to look at old messages will take some time to get to work. -- Greg

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chimera-users mailing list will be down temporarily
by Greg Couch 23 May '23

23 May '23

We're upgrading the mailing software. Should be back "soon".

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