- Chimera-users - RBVI Mailing Lists

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 12 Jun '23

12 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 12 Jun '23

12 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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question regarding relative rotation
by Jannick Cornelius Snel-Prentø 21 May '23

21 May '23

Dear Chimera team, I would like to rotate a protein chain with respect to an axis that I define, but I cannot seem to find any way to do that. I have defined the axis, but the turn command will not allow me to use this as the center of rotation. I have also tried constrained motion, but this does not seem to have the parameters needed to do this. Is there a command or a menu that permits rotating a chain or structure around an axis you define yourself? Kr, Jannick

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Making a rotation matrix file by UCSF Chimera or indexing the position
by Dmitry A. Semchonok 19 May '23

19 May '23

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3D_printing
by Francois-Hugues Poree 18 May '23

18 May '23

Dear Chimera Team, first of all, I would like to thank you for providing a sotfware solution to molecular visualization and by the way 3D- printing. I send you this message concerning the UCSF Chimera X version. We usually are preparing our 3D-printing files from data collected from the pdb and to ensure the rigidity of the system, we thick the ribbon size and also add some H-bonds (mainly for helices). However, we are not able to find the way to do it in this version. In the previous version (1.17), the command line was : Tools-depiction-ribbon style editor Could you explain us the new procedure to make this ? We also noticed that the opportunity to save the file in a stl extension was not allowed in the 1.17 version. This option is running in the X version. Thank you very much for your reply Best regards. fhporee François-Hugues Porée Professeur de Chimie Thérapeutique Institut des Sciences Chimiques de Rennes UMR CNRS 6226 Faculté de Pharmacie - Université de Rennes 2 Avenue du Pr Léon Bernard F-35043 Rennes France Tel.02 23 23 41 87

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error
by Athithi Prakash 16 May '23

16 May '23

Hello, I have been trying for a while to build the structure using the SMILES ID, and every time, this error pops up and I am not sure what to do.

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UCSF Chimera Molecular Dynamics: CPU vs GPU
by Alan Carbajo 07 May '23

07 May '23

Good morning, I'm running a molecular dynamics simulation in Chimera, and it seems that the program is only using my cpu for the calculations. Why is this? Is it possible to switch it to use my GPU? Thank you, Alan

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Web site downtime
by Eric Pettersen 04 May '23

04 May '23

Hi all, Due to a scheduled power outage at UCSF followed by server upgrades, the Chimera website and web services will be unavailable from Tuesday May 16 through most of Wednesday May 17. 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. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [Chimera-users] use with iPads
by Levy,Hazel C 04 May '23

04 May '23

Hello. I'm looking to use chimera on iPads to introduce High School and Middle School students to structural biology. Do you offer a discount for education licenses? Can Chimera be used on an ipad, even if not to its full capacity? Kind regards, Hazel C. Levy, M.Sc., Ph.D. Associate Director – UF Center for Precollegiate Education and Training (CPET) Adjunct Assistant Instructional Professor – Department of Biology | College of Liberal Arts and Sciences Doctoral Student – Higher Education Administration and Policy | College of Education ______________________________________________ Office: 339 Yon Hall | Box 112010 | Gainesville, FL 32611-2010 Phone: (352) 392-7683 Fax: (352) 392-2344 www.cpet.ufl.edu<http://www.cpet.ufl.edu/> [Image result for uf logo] ________________________________ From: Levy,Hazel C <hclevy(a)ufl.edu> Sent: Thursday, May 4, 2023 10:08 AM To: chimera(a)cgl.ucsf.edu <chimera(a)cgl.ucsf.edu> Cc: Desai,Ayan D <ayan.desai(a)ufl.edu>; Anthony, Michael S. <anthonym(a)cpet.ufl.edu> Subject: use with iPads Hello. I'm looking to use chimeraX on iPads to introduce High School and Middle School students to structural biology. Do you offer a discount for education licenses? Can Chimera be used on an ipad, even if not to its full capacity? Kind regards, Hazel C. Levy, M.Sc., Ph.D. Associate Director – UF Center for Precollegiate Education and Training (CPET) Adjunct Assistant Instructional Professor – Department of Biology | College of Liberal Arts and Sciences Doctoral Student – Higher Education Administration and Policy | College of Education ______________________________________________ Office: 339 Yon Hall | Box 112010 | Gainesville, FL 32611-2010 Phone: (352) 392-7683 Fax: (352) 392-2344 www.cpet.ufl.edu<http://www.cpet.ufl.edu/> [Image result for uf logo]

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Midas Error- reg
by Johnson Paul 03 May '23

03 May '23

Dear Sir, I am J Johnson Paul, I have recently used your software for my study and research purposes after usage of your software in the area of peptide build structure area I have got an error like MidasError: Dunbrack rotamer library does not support ASX File "C:\Program Files\Chimera 1.17.1\share\Rotamers\__init__.py", line 680, in useBestRotamers raise MidasError("%s rotamer library does not support %s" %(lib, rType)) This type of error is soon to me,So please kindly reply to my mail to solve the problem as soon as possible *With Regards,* *J Johnson Paul.*

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Looking Glass
by tolung.bio＠gmail.com 29 Apr '23

29 Apr '23

Hello, � When I try the look on command as instructed on this page: � � I receive the message � “Did not find LookingGlass screen name LKG-P14191, found \\.\DISPLAY2 <file://./DISPLAY2> , \\.\DISPLAY1 <file://./DISPLAY1> , \\.\DISPLAY3 <file://./DISPLAY3> , \\.\DISPLAY4 <file://./DISPLAY4> ” � Then the quilt window opens but in the main display where the main ChimeraX window is, instead of on the LookingGlass Portrait. � When I tried the option “deviceNumber 2”, since my Looking Glass in display #2, the same happens. � Do you have any suggestions to try for getting this to work? � Looks like Looking Glass might have changed how the device is named, and may that be the reason why ChimeraX is failing to detect it correctly? If that’s the case, will there be an updated version with a fix for this? � Thanks, Gökhan �

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Utilizing Chimera in Web-Based Workflows
by Rafi Brent 27 Apr '23

27 Apr '23

To whom it may concern, I'm wondering if there's any way to access Chimera without having the GUI downloaded on a local computer. Specifically, I'd like to run chimera as part of a public Google Colab (.ipynb) notebook, which would allow users to access the chimera functionality through either installing a PyPi package or calls to a web-accessible API. Do you know of any tool like this, or have any other ideas for how Chimera could be used in Colab notebook? Thanks so much for any advice you may have. Sincerely, Rafi Brent

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Can't open a cif file
by Steven Frey 26 Apr '23

26 Apr '23

Dear Chimera Team, I’m unable to open the CIF file for a structure that we had done in 2018 and am getting the error shown on the attached jpeg. I am also attaching the CIF file downloaded from CCSD which comes from our original paper: Steven T. Frey, Hillary A. Ramirez*, Manpreet Kauer, and Jerry P. Jasinski. “Crystal structure of a seven-coordinate manganese(II) complex with tris(pyridin-2-ylmethyl)amine (TMPA),” Acta Crystallographica, 2018, E74, 1075-1078. https://doi.org/10.1107/S2056989018009611. I’d like to be able to open the file in Chimera so that I can produce an ORTEP drawing for another paper. Can you help me figure out what the problem is? Thanks, Steve Frey ~~~~~~~~~~~~~~~~~~~~~~~ Steven T. Frey Associate Professor Skidmore College Department of Chemistry 815 North Broadway Saratoga Springs, NY 12866 Phone: 518-580-5124 Email: sfrey(a)skidmore.edu<mailto:sfrey@skidmore.edu>

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Chimera 1.17.1 release
by Eric Pettersen 20 Apr '23

20 Apr '23

Hi again, As it turns out, the changes to web services in the 1.17 release only worked correctly on Mac. Therefore we have made a 1.17.1 release to fix web services on Linux and Windows. If you downloaded the 1.17 release on Mac there is no need to upgrade, but if you downloaded it on Linux or Windows you should upgrade to the 1.17.1 release. Sorry for the inconvenience. --Eric Eric Pettersen UCSF Computer Graphics Lab

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deleting alternate locations
by Elaine Meng 18 Apr '23

18 Apr '23

> On Apr 18, 2023, at 3:07 AM, Yu GUO 郭宇 <guoyu60(a)westlake.edu.cn> wrote: > > Dear, > > I am using Chimera/ChimeraX. I have 2 questions: > > I cannot open ChimeraX (win10 version) recently. Is there any problem in the server? > > I have a PDB file with two structural populations. In Chimera, how to delete the part with fewer population (say 40%)? I rememer it can be realized in the command line, but I forgot. > > Best wishes > Dear Sir, In the future, please use the following addresses (CC'd here) for general questions about the programs: chimerax-users(a)cgl.ucsf.edu for ChimeraX questions chimera-users(a)cgl.ucsf.edu for Chimera questions (where you sent this question is for commercial licensing questions -- thanks) (1) after you download the program, it does not depend on our servers to start. The issue is something with your own setup. The most likely problem is that you need to update your graphics driver but we would need more information from you to say anything else. (2) if you mean atomic occupancy, - in Chimera you can use Dock Prep (menu: Tools... Structure Editing... Dock Prep) and turn on the option "If alternate locations, keep only highest occupancy". You can turn off all the other options if you want. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockpre…> - in ChimeraX, it is not currently in the Dock Prep GUI, but you can use the "altlocs clean" command which would delete all the altlocs that are not currently used. By default, the highest-occupancy ones are the ones that are used, so this would delete the lower-occupancy ones (e.g. your 40%). You can change which altlocs are used with "altlocs change" and show a list of them with "altlocs list" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/altlocs.html#clean> If you need a PDB file then you can save PDB in a separate step, e.g. using File menu or a command. 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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determine angle of rotation among two states
by Sen, Anindito 18 Apr '23

18 Apr '23

Dear All, How can I determine the angle of rotation between 2 states of an atomic model, with one state being somewhat skewed from the other. 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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Doubt regarding the analysis of covalent bonds between the ligand and protein
by Krishna Priya K R 17 Apr '23

17 Apr '23

I am a MSC student working on docking . By using UCSF chimera 1.14 I tried to analyse the H bonds and covalent bonds. Even after following every step for H bond analysis it shows 0 bond and i am not able to find the option to analyse the covalent bond between the protein and ligand. Hope you will help me to rectify my problem. My contact details : 8848890240 Email id : krishnapriyaifs1999(a)gmail.com

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Issues with Chimera
by Bella Carnahan 17 Apr '23

17 Apr '23

Hi! My name is Bella Carnahan and I am a graduate student at the University of Delaware. I am trying to model a small peptide in Chimera 1.17 and keep getting an error message telling me I have a missing file. I have redownloaded the software twice now and have not been able to fix the problem. I have attached a screenshot of the error/any relevant windows. -Bella Carnahan

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Chimera 1.17 release
by Eric Pettersen 14 Apr '23

14 Apr '23

Hello everybody, A new production release of UCSF Chimera (version 1.17) is available: https://www.rbvi.ucsf.edu/chimera/download.html <https://www.rbvi.ucsf.edu/chimera/download.html> Updating to 1.17 is required to continue to use the following tools: BLAST protein, Modeller comparative and loop modeling, and multiple sequence alignment with Clustal Omega and MUSCLE. Due to imminent changes in web services, these tools will soon stop working in older versions of Chimera. Version 1.17 can also fetch UniProt sequences (previously broken by UniProt website changes). Alternatively or in addition, you may want to consider switching to UCSF ChimeraX instead, as it also has tools to run these web services, as well as many new features and enhancements. https://www.rbvi.ucsf.edu/chimerax/index.html <https://www.rbvi.ucsf.edu/chimerax/index.html> Note that Chimera 1.17 includes an export-to-ChimeraX feature, as detailed in the release notes: https://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.17.html <https://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.17.html> Enjoy!

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Chimera cannot read multi-molecules .xyz files in
by Francois Berenger 09 Apr '23

09 Apr '23

Dear list, I can read one molecule fine in .xyz format using chimera. However, if my .xyz file has several molecules (like a MD trajectory), chimera fails to read it in. Is there planned support for MD trajectories given as .xyz file? I have chimera-1.16. I shall test with ChimeraX very soon. Regards, F.

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Aligning homdimers
by James Nettles 04 Apr '23

04 Apr '23

I’m asking a question that has been asked and answered before in 2009 - but not with exact solution that I would like. I have a relatively small homo dimer( <200 residue) and would like to fit with a homo dimer of the almost same sequence but slightly different conformations. I would like to fit the dimers as a pair (A/B to A/B) rather than A to A and B to B separately. In other word, I’m wanting to spread the deviation across both monomer units of the dimer in a single step rather than fitting separately and then recombining. I know Chimera isn’t formally supported any more, but I’m running this on an old machine with an old OS , so ChimeraX isn’t an option here. Thanks so much in advance - this group has always bee fabulous over the years. Best regards, Jim

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Chimera when saving as ray
by Shona Hepworth (CHE - Postgraduate Researcher) 30 Mar '23

30 Mar '23

Hello, When I try to save my image by ray tracing it has the following in the reply log. Is this an issue? It is also taking a very long time - I assume this is because I have set surface transparency to 90% but is there anything I can do to speed up the saving as a ray? I tried saving as chimera but the image quality isn't as good. [cid:3D248385-806F-44B1-9B22-478D459DFF1C] Thanks in advance, Shona

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Energy minimization
by Nedra Rached 27 Mar '23

27 Mar '23

Hello; I attempted to do energy minimization on my protein but i get this error message when i try to run it: AttributeError: '_molecule.Atom' object has no attribute 'gaffType' So, could you please help me to resolve this issue Best regards

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Select close residues by name
by Marco Sette 23 Mar '23

23 Mar '23

Dear all, I have a series of pdb files and I would select particular regions that contain specific residues, for example KAYFPG, of which I do not know the exact position in the sequence. Actually I open the sequence window and search for the sequence but this is time consuming if you have multiple pdb. Is there a command to shorten this search? Using the select command seems not possible as I can select all residues of a particular amino acid and not neighbour residues by name. Thanks for your help, Best Marco -- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it e-mail: m77it(a)yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette

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Restoring the original numbering of the amino acids of a chain after a Loop Modeling
by svle＠tiscali.it 20 Mar '23

20 Mar '23

Hi, after a modeling a missing loop in a chain of a protein the amino acid numbering has been shifted by -1 due , I guess , to the "no corresponding structure residue" that I read in the status bar of the panel for Tool --> Sequence --> Sequence in the first position. The catalytic triad of interest now has positions X-1 , Y-1 and Z-1 instead of X,Y and Z. It is possible to restore the original numbering? Thanks. Saverio VOUCHER CONNETTIVITÀ per P.IVA e PMI: internet a canone 0 per 48 mesi. ATTIVA ORA https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busi…..

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ligand
by José Manuel González Hernández 19 Mar '23

19 Mar '23

Hello, Is there a way to change features such as width and height of a ligand instead of the ribbons? Thanks, José

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Re: [Chimera-users] Delete pseudobonds
by Justin Prado 17 Mar '23

17 Mar '23

Good evening, I am emailing on behalf of a message that was responded to in 2018. It involved the deleting of CONECT records from a PDB file. I was wondering if there were instructions on how that was done? I look forward to hearing from you. Thank you Justin Prado

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Chimera Deployment to several MacOS Computers
by Sonny Mei 15 Mar '23

15 Mar '23

Hello, I hope all is well! I am trying to deploy Chimera into several computers and do not want to manually do this. I decided to write a script and was wondering if there is a direct download link? The link I found on your site requires users to accept the license before the dmg file is installed. Thank you, Sonny Mei -- PLEASE NOTE: This message, including any attachments, may include privileged, confidential and/or inside information belonging to IPI. Any distribution or use of this communication by anyone other than the intended recipient(s) is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system. Thank you.

2 1

Creating discs
by Prathvi Singh 14 Mar '23

14 Mar '23

Hi Elaine, Is it possible in chimera or chimeraX to create such planes for membrane proteins which show the plasma membrane boundaries as shown in: https://www.cgl.ucsf.edu/chimera/ImageGallery/framedD3R.html If yes, then kindly tell me how to do it. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 2

Query colors?
by Esser, Lothar (NIH/NCI) [E] 13 Mar '23

13 Mar '23

Hi, in my current project I am reading about 50 pdb files. Chimera does a good job at assigning pleasant colors automatically and I would like to get access to the chosen colors to write 2dlabels with the same color. How do I get access to the molecular (ribbon color) ? It's probably trivial but well, I somehow could not figure this out. Thanks, Lothar Dr. Lothar Esser National Institutes of Health 37 Convent Dr. Rm2122B Bethesda, MD 20892

3 3

Selecting planes using command line
by Prathvi Singh 13 Mar '23

13 Mar '23

Hi Elaine, I see that after defining a plane, it gets listed in the "Axes/Planes/Ellipsoids" section with each plane having a unique ID. However, I am unable to use these IDs to select planes individually via command line. Moreover, when I hover my mouse over a plane, it displays: #0:? How to select the planes using the command line? And, can I move these planes independent of the protein model? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

export stl file
by Yifan Wang 07 Mar '23

07 Mar '23

Hi Chimer team, I have a question about exporting stl files. Because I load one pdb file in chimera and export as a stl file then I load in a CAD based software to compare with another stl file I generated through another software. So the input to generate the stl file are the same, but the results are different. The results show that two different stl files in the same 3D quadrant but it got rotated at different angles. What may cause this issue? Thank you so much! Yifan

3 2

Issue with MD movie
by Enrico Martinez 14 Feb '23

14 Feb '23

Dear Chimera Users ! I am working on visualization of MD trajectory dealing with the multi-model pdb composed of 3000 snapshots. First of all, there are no problems with this file in other software like vmd or even Chimera-X. But when I load it into the Chimera (I use context menu tools ... / MD movie), I get three times more frames (9000 !) and the overall dynamics looks very unnatural when I try to play it as a movie. Any possibilities how could I fix it ? Many thanks in advance Best regards Enrico

2 1

Questions about cartoon visualisation
by Enrico Martinez 14 Feb '23

14 Feb '23

Dear Chimera Users! I have several basic commands related to the visualization of cartoon models: 1) Is it possible to color secondary structure elements (normally integrated in the context menu by means of tools -> depiction) via some command called from command line / script ? 2) how could I change the representation style of the cartoon diagrams e.g. radius of loops or introducing some artistic elements in alpha-helixes / B-sheets ? Is it possible to modify it via commands ? Many thanks in advance Best wishes Enrico

2 2

Hydrogen issue with minimization
by Guillaume Grataloup 08 Feb '23

08 Feb '23

Dear support, I currently trying to perform a minimization on a hERG canal pdb file but I run into an issue I didn't manage to solve: "Residue #0:23.A (GLU/glutamic_acid) should have either atom HB1 or HB3, but not both" Maybe the problem comes from the pdb file, I put it in attachment just in case it can help understand the issue. Also my Chimera version is 1.16 and I'm on Windows Thank you in advance Guillaume Grataloup 5th year bioengineering studient at Polytech Nice Sophia, France

2 1

A question abount "define axis"
by squirrel 07 Feb '23

07 Feb '23

Dear Chimera list, I'm Interested in finding and showing the distance of N-terminal and C-terminal between two proteins. As I can't download GUI so I use "chimera --nogui" to compute them. That's my command: open protein.pdb sel:1.Ln; measure center sel mark True radius 0.3 color cyan modelId 1; sel:1.S2; measure center sel mark True radius 0.3 color cyan modelId 2; sel:390.Lz; measure center sel mark True radius 0.3 color cyan modelId 3; sel:44.LH; measure center sel mark True radius 0.3 color cyan modelId 4; distance #1 #3; define axis name Ln_N_Lz_C #1 #3; distance #1 #4; define axis name Ln_N_LH_C #1 #4; distance #2 #3; define axis name S2_N_Lz_C #2 #3; distance #2 #4; define axis name S2_N_LH_C #2 #4; stop But I found that when I input "distance" and "define axis" the terminal shows that "Must specifiy at least two atoms/centroids to define an axis". I am puzzle because I can see the #1,#2,#3，#4 in the list. Can you give me some guidance? Thanks in advance

4 3

Conference Announcement: 35th MMWS in Erlangen, Germany
by Harald Lanig 07 Feb '23

07 Feb '23

1 0

A question about "Distance Measure"【2】
by squirrel 05 Feb '23

05 Feb '23

Dear Ms/Mr： Thanks to your reply. In the last mail, I ask for your help and I am appreciate your detailed description. This is the content of last mail: "I meet a problem recently. Every proteins have N-terminations and C-terminations, and I want to measure the distance between all proteins at each other's N-C, N-N, and C-C terminals by using UCSF Chimera. But there are too many proteins for me to start.I've read Chimera's tutorials and searched my questions online. But I didn't find the answer I needed.Can you please give me some guidance or tips？" Now I would like to add some new information and have two new questions I would like to consult you. I want to measure the end distances of many proteins within a model. Because there are so many proteins, it is not practical to measure them one by one. So I want to ask if you use the command line method to measure the distance of multiple proteins. In addition, I tried to follow your guidance and found that the measured atoms name showed -1, so I couldn't confirm which atom was the distance between them, and I am puzzled how I should change the name. Looking forward to your reply.♥

2 1

minimization error
by Elaine Meng 03 Feb '23

03 Feb '23

Dear Alaa, Forwarding your question. However, when you get a Chimera error and you think it may be a bug, instead of using e-mail it is usually more helpful to use the Chimera menu: Help... Report a Bug. Also make sure you are using a recent version of Chimera. If you haven't updated in a while, you should try the newest release, then if you still get the error, you could report it. Best, Elaine > Begin forwarded message: > > From: Alaa Nahhas <anahhas(a)kau.edu.sa> > Date: February 3, 2023 at 12:00:13 PM PST > > Dear Chimera team, > I have a peptide and when I minimize its structure, I got the attached message. How can I solve it. > Thanks, > Alaa > > Disclaimer: The information contained in this message is intended for the addressee only and may contain classified information. If you are not the addressee, please delete this message and notify the sender; you should not copy or distribute this message or disclose its contents to anyone. Any views or opinions expressed in this message are those of the individual(s) and not necessarily of the university. No reliance may be placed on this message without written confirmation from an authorized representative of its contents. No guarantee is implied that this message or any attachment is virus free or has not been intercepted and amended. > > إخلاء مسؤليه: ان جميع المعلومات المتضمنة في هذه الرسالة تخص المستلم، وربما تتضمن معلومات سرية، واذا لم تكن انت المستلم فالرجاء الغاء الرسالة واشعار المرسل، كما يمنع نسخ او توزيع هذه الرسالة او افشاء محتوياتها لاخرين. ويجدر بالعلم ان جميع الآراء ووجهات النظر الواردة في هذه الرسالة تعتبر شخصية وليست بالضرورة منسوبة للجامعة. كما لايمكن ان يعتمد على هذه الرسالة ما لم تحصل على موافقة خطية من المسئول عن محتوياتها. كما لايوجد ضمان بان هذه الرسالة أو مرفقاتها خالية من الفيروسات أو انها لم يتم اعتراضها وتعديلها >

4 8

A question about "Distance Measure"
by squirrel 03 Feb '23

03 Feb '23

Dear Ms/Mr： Thanks for your wonderful tool! I meet a problem recently. Every proteins have N-terminations and C-terminations, and I want to measure the distance between all proteins at each other's N-C, N-N, and C-C terminals by using UCSF Chimera. But there are too many proteins for me to start.I've read Chimera's tutorials and searched my questions online. But I didn't find the answer I needed.Can you please give me some guidance or tips？

2 1

Announcement: Release of DOCK 6.10
by Scott Brozell 01 Feb '23

01 Feb '23

We are pleased to announce the release of DOCK 6.10. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.10 is available for download and free for academic users at http://dock.compbio.ucsf.edu/DOCK_6/index.htm This is a release of the new genetic algorithm DOCK_GA: Molecular evolution for ligand design. DOCK_GA evolves molecules through breeding, mutation, fitness pressure, and selection. The method leverages powerful sampling, scoring, and searching routines previously implemented into DOCK 6. For full information on what is new in DOCK 6.10, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.10.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

1 0

Specifier for the z-axis
by Yang Shi 29 Jan '23

29 Jan '23

Dear Chimera-Team, I am wondering if there is a specifier for the z-axis of a map. I would like to measure the angles between defined plains and Z-axis. Best wishes, Yang

2 2

smooth-MD.py script
by Enrico Martinez 26 Jan '23

26 Jan '23

Dear Chimera Users! I am looking for the smooth-MD.py script that I may use with MD trajectories to smooth their visualization. I've already seen it for Chimera-X but it seems that the older version is disappeared ... Many thanks for any info! Yours sincerely Enrico

2 2

Rotation along symmetry axys
by Leonardo Talachia Rosa 25 Jan '23

25 Jan '23

Dear Chimera team, I hope you are well. I am processing a phage dataset which presents D5 pseudossymetry. The C5 axys is aligned to the z axys. I would like to rotate the map 90 degree in the z axys, so that Z axys now separate the molecule in a C2 pseudosymmetry, in order to play with some symmetry relaxation features to refine differences in the two map vortexes. Is there a way in chimera to rotate the map in relation to the xyz axys? The way I see, all rotate commands I know rotate the axys themselves alongside the map. Thank you for your time, Kind wishes, Leonardo -- ************************* Leonardo TALACHIA ROSA, PhD PostDoctoral Researcher Microbiology and Structural Biology Instituto de Química, Universidade de São Paulo - IQ-USP Av. Prof. Lineu Prestes, 748 - Butantã, São Paulo - SP **************************

3 2

Error in energy minimizaion - reg
by SELVA BABU SELVAMANI 24 Jan '23

24 Jan '23

Dear Developers, I did phosphorylation of amino acid in protein, then I was about to do energy minimization using Chimera MINIMIZE STRUCTURE module, but it is throwing the error ( I mentioned below ). **************************************************** Running PARMCHK for PP.pdb Using main parameter file parm10.dat modified by heme-iron.frcmod, frcmod.ff14SB, frcmod.ionsjc_tip3p *Chimera/MMTK cannot minimize structure, probably because there is no parameter for ''No parameters for bond Atom 0.TPO_144__0_0_1_145.N (atom type n) - Atom 0.GLN_143__0_0_1_144.peptide.C (atom type C)''* ********************************************** *Please help me to sort out the issue.* I also tried to do phosphorylate using Chimera, even that structure also getting the same error while doing energy minimization. -- *Have a nice day,* Thanks & Regards, *SELVA BABU S* M.Sc Scholar (Bioinformatics) *TNAU, Coimbatore*

2 3

how to save molmap by command line
by Guido Leoni 23 Jan '23

23 Jan '23

Dear list I would use in programmatic way chimera to elaborate a molmap of a peptide bound in a receptor. I'm able to load the pdb and elaborate the molmap of the peptide "/home/guido/.local/UCSF-Chimera64-1.16/bin/chimera --nogui load <NAMEFILE> molmap :.P 5;" Now I would save the molmap of the peptide to do a fitmap vs another peptide. I tried save test.mrc but the following msg is prompted to me Volume data sets molmap <namefile>.pdb res 5 were not saved in the session. To have them included in the session they must be saved in separate volume files before the session is saved. DO you have any tips? Thank you Guido

2 1

ChiMera: Judith N. Pichel Ford 1999
by Amy Ford 20 Jan '23

20 Jan '23

Hello, I am Amy Ford. My maternal grandmother is Judith N. Pichel Ford (1939-1999). My grandmother was a true fetal ChiMera and her body was studied after her passing in 1999 in the State of New York. I am trying to locate any documents and genetic information that concerns my grandmother so I can understand my health more. I understand that ChiMerism can be passed and filtered through the X Chromosome, I am willing to participate in any future or ongoing studies concerning the nature given my disposition. Please contact me if you have any information of my grandmother, possible trail, or interest in reaching out for a study. Thank you for your time, Amy R. Ford

1 0

problem
by Jianan Li-Harbin Medical University 15 Jan '23

15 Jan '23

Dear Chimera developers： I have a problem in using Chimera！ I want to save a ligand-receptor complex file for further analysis，but I can not save a such PDB file！You can see the figure below！ The target was protein, and the atr_1 was the ligand, all files were saved from the dock results of Swissdock online tool (figure 2)! I hope you can help me, thank you very much! Best wish, Jianan Li Jianan Li-Harbin Medical University 364453372(a)qq.com  

2 2

Sorting through compounds on chimera
by Shinhmar, Sonia (2020) 12 Jan '23

12 Jan '23

Hello, I hope this email finds you well. I'm writing to ask for some help regarding a file that is composed of >15,000 compounds that I would like to separate into 3000 compound groups/ lists. How would I go about doing this? Thank you in advance, Sonia Sonia Shinhmar (She/Her) PhD student Williams Lab Royal Holloway University London This email, its contents and any attachments are intended solely for the addressee and may contain confidential information. In certain circumstances, it may also be subject to legal privilege. Any unauthorised use, disclosure, or copying is not permitted. If you have received this email in error, please notify us and immediately and permanently delete it. Any views or opinions expressed in personal emails are solely those of the author and do not necessarily represent those of Royal Holloway, University of London. It is your responsibility to ensure that this email and any attachments are virus free.

2 1

Question about anomalous Fourier map
by YOSHIWARA Kentaroh 11 Jan '23

11 Jan '23

Dear Developer, I want to have a figure of a zinc atom with the anomalous Fourier map, and I generated the pdb and mtz files from Phenix. refine. Then I converted .mtz into .ccp4 using CCP4i FFT and opened it in UCSF Chimera1.16. While meshes derived from the .ccp4 file were observed, I was not able to regulate the contoured sigma level. Actually, I was able to get a figure with a Fourier map using Pymol. Although the scale of the mesh looks the same between the figures from Chimera and Pymol, the values of the sigma level were completely different. Would you suggest to me how to have a figure of a zinc atom with the anomalous Fourier map? Sincerely, Yoshiwara, K. ------------------------------------------------------------------- Kentaro Yoshiwara Department of Bioscience, Graduate School of Agriculture, Ehime University 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan Mail：i652020m(a)mails.cc.ehime-u.ac.jp

2 3

Re: [Chimera-users] Unable to find the angle between planes
by Elaine Meng 11 Jan '23

11 Jan '23

Hi Prathvi, Please send chimera questions to chimera-users(a)cgl.ucsf.edu instead of my individual address. Otherwise, your question may fall through the cracks and not get any answers. This all works fine for me in Chimera 1.16 release, e.g. commands: open 5fzp define plane :252.B & aromatic ring define plane :261.B & aromatic ring angle p1 p2 ...then the Reply Log contains: 0, chain A: DAIP #0, chain B: DAIP 5fzp opened plane name, ID, center, normal, radius: plane: p1 ( 46.248, 56.206, 31.842) ( 0.547, -0.816, 0.186) 1.399 plane name, ID, center, normal, radius: plane: p2 ( 46.861, 61.257, 27.361) ( 0.280, 0.020, -0.960) 1.403 Angle between p1 and p2 is 87.643 I don't know which part you did wrong. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 7, 2023, at 5:23 AM, Prathvi Singh <prathvi(a)iitk.ac.in> wrote: > > I was using chimera 1.15rc 4 bit but I now installed chimera 1.16 64 bit. I am still getting the mangled atom specifier error. > > On Thu, Jan 5, 2023 at 10:04 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > On Jan 5, 2023, at 12:28 AM, Prathvi Singh <prathvi(a)iitk.ac.in> wrote: > > > > Hi Elaine, > > > > I am defining two separate planes for the aromatic carbon atoms of TYR252.B & TYR261.B in PDB ID:5FZP. > > To find the angle between the two planes, I am using the command: angle p1 p2 > > However, I am getting the error: mangled atom specifier > > > > I followed this thread: https://www.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012404.html > > Here you mentioned that angle between two planes can be found using the same command mentioned above. However, it is not working in my case. Please help. > > -- > > Prathvi Singh, > > Research Fellow, > > Department of Biological Sciences & Bioengineering, > > Indian Institute of Technology, Kanpur-208016 > > Hi Prathvi, > Please clarify which program you are using, or be sure to send Chimera questions to chimera-users(a)cgl.ucsf.edu and ChimeraX questions to chimerax-users(a)cgl.ucsf.edu. If you are using ChimeraX then you cannot specify the plane by something like p1 but instead you need the model number. In Chimera, that command works fine for me. > Best, > Elaine > > > > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016

2 1

Getting position of residues
by Audrey Piraud 11 Jan '23

11 Jan '23

Hello, I'm really sorry to bother you. I'm a student working with Chimera. I'm trying to get the position of the residues in the protein after selecting them with: runCommand("select"+AA_mute+"za<5") ;sel_Res = currentResidues(). I obtain a list of <_molecule.Residue object at 0x1133aa9b8> and I would like to obtain their position in the a.a sequences. I'm waiting for your response, Thanks a a lot, Audrey Piraud

2 3

Question: How to do add charge and minimazation?
by Kenji MATSUI 10 Jan '23

10 Jan '23

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 interactions between protein and ligand. I want to optimize the attached file compound. I want to adjust the charge for this purpose. [image: image.png] Question However, when I press OK in the first photo section, a black screen appears as in the second photo.In you tube and other videos, I was moved to the save etc. screen. Is the charge optimization done correctly here? [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

2 2

Question concerning rotamer choosing
by Noe Robert 09 Jan '23

09 Jan '23

Hi, I'm currently trying to write a python script which automatizes mutageneses on Chimera 1.16, and calculates clashes inducted by the change of amino acid through a local minimization (which explains why I'm using Chimera instead of ChimeraX). I would like to choose which rotamer to use depending on their probability from the rotamer library Dunbrack (for instance, when probability is >0.1), which is visible on the "Rotamers graphical user interface". Is there a way to extract these probability values using a script, in order to run it on a certain number of rotamers ? That way it would be quite automated. On Jul 1, 2015, Eric Pettersen advised to modify the "Python script that uses the functions in the Rotamers module" (here<https://www.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011193.html>), but I don't which one it is. Thank you, Noé Robert, Fifth-year student in bioengineering, minor in Bioinformatics and Modelling, at engineering school Polytech Nice Sophia, France Phone : +33 7 81 00 52 02 "let's limit the use of our resources and lighten our mails"

3 10

Save cut open model for 3Dprinting
by Haselbach,David 03 Jan '23

03 Jan '23

Hi, I wanted to build a cut open model of a cryoEM map which I achieved through clipping in Chimera. But I am failing to apply the clipping in a way that I can save the cut open mesh as poligone file for 3D printing. Is this possible? All the best, David

3 2

Is there an option to open pdbqt as PDB format smoothly?
by 夏前程 27 Dec '22

27 Dec '22

Hi Chimera team, I'm wondering if there is any chance that I can open a .pdbqt file smoothly (just like open a .pdb file ) through some strategies (for example, maybe modifying some source codes?). Since AutoDock (and vina) always gives a .pdbqt format file but not .pdb format, however the content of which is somewhat like pdb and we always want to open it in pdb format. This is not an important issue. But if so, the experience will be much better at least for me (Now, I have to choose the PDB format or rename the file suffix into .pdb). With Regards Qiancheng Xia 2022/12/23

2 2

Chimera startup error: "Display misconfiguration" (Debian GNU/Linux)
by Powell, William A. 25 Dec '22

25 Dec '22

Hi, Chimera community. I have seen similar problems addressed, and the solution is always to update drivers and make sure there is only on OpenGL renderer. I am unable to resolve my problem this way. When Chimera is launched using my dedicated NVIDIA 3060 Mobile graphics card, there are mixed results. If launched from a terminal instance an by the NVIDIA card, it produces the error below. Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions. Using primusrun, it succesfully launches on the dedicated card. Unfortunately, the nvidia-primus and bumblebee-nvidia packages seem to conflict with the NVIDIA drivers. The only way Chimera works reliably is by launching it through an instance of Steam ran on the NVIDIA card. The Steam client opens ~/.local/bin/chimera, the same file opened through the terminal. I am not sure what is so special about launching an application through Steam. Thanks! W. Andy Powell, B.S., A.S., Graduate Teaching Assistant The University of Oklahoma Singh Lab, INPART Department of Chemistry and Biochemistry Dodge Family College of Arts and Science w.a.powell(a)ou.edu

2 1

Re: [Chimera-users] Is there an option to open pdbqt as PDB format smoothly?
by 夏前程 23 Dec '22

23 Dec '22

Hi Sette and again Chimera team,I know what you said. But what I really want to ask is that if there is any way to open .pdbqt smoothly just like .pdb (without the format-choosing step). Just imagine the suituation of mine: I have to open like 10 .pdbqt file in a chimera session. If I didn't rename the suffix from .pdbqt to .pdb, I have to choose format for 10 times. That should be a bit annoying for me. So I ask the question here to find some smart solutions...With regardsQiancheng Xia2022/12/24> Hi Qiancheng, > > as far I know the File-Open allows to open a .pdbqt file. > simply > choose pdb in the list of possible formats. > > Best > > Marco > > Il 23/12/2022 14:20, ??? via Chimera-users ha scritto: > > > > Hi Chimera team, > > > > I'm wondering if there is any chance that I can open a .> pdbqt file > > smoothly (just like open a .pdb file ) through some > strategies (for > > example, maybe modifying some source codes?). > > > > Since AutoDock (and vina) always gives a .pdbqt format file > but not > > .pdb format, however the content of which?is somewhat like > pdb and > > we always want?to open it in pdb format. > > > > This is not an?important issue. But if so, the experience > will be > > much better at least for me (Now, I have to choose the PDB > format or > > rename the file suffix into .pdb). > > > > > > With Regards > > > > Qiancheng Xia > > > > 2022/12/23 > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list:Chimera-users@cgl.ucsf.edu > > Manage subscription:https://www.rbvi.ucsf.edu/mailman/> listinfo/chimera-users -- > Dr Marco Sette, PhD. > Department of Chemical Sciences and Technology > University of Rome, "Tor Vergata" > via della Ricerca Scientifica, 00133, Rome, Italy > e-mail:sette@uniroma2.it > Tel.: +39-0672594424

1 0

Re: [Chimera-users] Is there an option to open pdbqt as PDB format smoothly?
by sette＠uniroma2.it 23 Dec '22

23 Dec '22

Hi Qiancheng, as far I know the File-Open allows to open a .pdbqt file. simply choose pdb in the list of possible formats. Best Marco Il 23/12/2022 14:20, 夏前程 via Chimera-users ha scritto: > > Hi Chimera team, > > I'm wondering if there is any chance that I can open a .pdbqt file > smoothly (just like open a .pdb file ) through some strategies (for > example, maybe modifying some source codes?). > > Since AutoDock (and vina) always gives a .pdbqt format file but not > .pdb format, however the content of which is somewhat like pdb and > we always want to open it in pdb format. > > This is not an important issue. But if so, the experience will be > much better at least for me (Now, I have to choose the PDB format or > rename the file suffix into .pdb). > > > With Regards > > Qiancheng Xia > > 2022/12/23 > > > > > _______________________________________________ > Chimera-users mailing list:Chimera-users@cgl.ucsf.edu > Manage subscription:https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users -- Dr Marco Sette, PhD. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail:sette@uniroma2.it Tel.: +39-0672594424

1 0

Question about Labeling Beta Sheet
by Yifan Wang 22 Dec '22

22 Dec '22

Hi Chimera team, I have a question for labeling beta sheet. After I get secondary structure, when I look at the 3D structure, It is very clear to see coli, helix and beta-strands. But how can I label and tell the beta strands are in same sheet or not? Does chimera contain the information for beta sheet? Thank you so much! Yifan

2 1

AttributeError of "Model Panel" when using nogui mode to save session
by 夏前程 20 Dec '22

20 Dec '22

Hi, I've tried to use chimera nogui mode to save chimera sessions for a large number of tasks (one session for each task). However, an error message was returned and without the wanted output.py being written. The command I used is chimera --nogui --silent run.cmd. ( followed this https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-October/006863.html) The content of run.cmd ------------------------------------- background solid white set silhouette open rec.crg.pdb xtal-lig.pdb sel #1-2 zone sel 5 ~sel #1-2 sel up ~rib ~ sel color white sel color byhet sel rlabel sel color black ,lr dis sel ~dis HC open rec.crg.pdb save output.py stop ------------------------------------- The error message returned ------------------------------------- Starting extension 'Model Panel' failed Error processing trigger "save session": AttributeError: 'ModelPanel' object has no attribute '_updateHandler' File "/home/xiaqc/.local/UCSF-Chimera64-1.16/share/ModelPanel/base.py", line 1301, in _saveGroups if _mp._updateHandler: See reply log for Python traceback. Error while processing run.cmd: AttributeError: 'ModelPanel' object has no attribute '_updateHandler' File "/home/xiaqc/.local/UCSF-Chimera64-1.16/share/ModelPanel/base.py", line 1301, in _saveGroups if _mp._updateHandler: See reply log for Python traceback. -------------------------------------- I've tested 1.16 (build 42360) and 1.15 (build 42233). Both of them failed.

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Chimera
by Добромир Калчевски 19 Dec '22

19 Dec '22

Hello, I would like to suggest an improvement in the GUI: when a data set of multiple files is opened (for example multiple .cube files) the Volume Viewer displays options (including hide / show) for only 3 of them. There is no scroll up or down. Resizing the window does not change the number of loaded files to manipulate for visualization. Let's say I want to browse a set of 12 molecular orbitals - I have to manually click on each one in the "Data set list", then click the hide (eye) icon in the detailed options list below and do this for all molecular orbitals / .cube files, otherwise Chimera visualized all of them at the same time. It is simply not convinient to hide and show them if I want to view more than 3 files in the Volume Viewer. In ChimeraX that issue does not exist, yet it lacks working linux binaries (too many dependencies to cover outside of distros like debian ot red hat, especially if the dependencies are not explicitly mentioned and the distro does not provide them with a package manager). Best Regards, Dobromir

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Chromophore missing
by Marco Sette 16 Dec '22

16 Dec '22

Dear all, When I fetch a protein with a chromophore (PDB code 2h5q), the chromophore, not a standard one, is missing, and not present in the Select-Residue menu. Is there any way to obtain it? Thanks, Marco -- Questa email è stata esaminata alla ricerca di virus dal software antivirus Avast. www.avast.com

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Question about Model Loops Option in Chimera
by Ecem Güngör 14 Dec '22

14 Dec '22

Hello, I have a protein crystal structure where some regions are not resolved in the crystal. Therefore, I want to predict and fill these regions, without touching the rest, by using the Model Loops/Refine Structure option of Modeller in Chimera. When I select the non-terminal missing structure as a model and standard as a loop modeling protocol, some atoms in the rest of the structure are shifted from the original positions. However, I want to keep them as they are. Here I would like to ask what standard loop modeling protocol corresponds to. Does it also refine or optimize the structure as a whole? What does it actually correspond to? Any help would be appreciated. Thanks. Ece

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Issues with software in complex building
by Kumar Pratyush 07 Dec '22

07 Dec '22

Hello Sir/Mam, I am not able to save complex of docked output.pdbqt and protein.pdbqt as save button is not getting active. I used to do the same protocol earlier with ease but now not able to execute. I tried by uninstalling and re-installing but still things are not working smoothly. Please help. Thanks & Regards Kumar Pratyush (Dr.) Assistant Professor, Department of Pharmaceutical Chemistry, Contact :- +91-7709714926 Email-<mailto:Email-aherkiran22@gmail.com> kumar.pratyush(a)svkm.ac.in Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Survey No. 499, Plot No- 03, Behind Gurudwara, Mumbai – Agra National Hwy, Dhule, Maharashtra 424001 Phone : 02562-297802 https://svkm-iop.ac.in/ Vision of Institute: To pursue excellence in pharmaceutical education and research to develop competent professionals

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Question: How to find the area of hydrophobic interaction?
by Kenji MATSUI 06 Dec '22

06 Dec '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 hydrophobic interactions between protein and ligand. ,but how can I display the following? distance between faces:show how many Å2 are within Å of each other. I found a hydrophobic contact, but does it work well in my case? https://www.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007236.html 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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Missing bonds
by Naima syed 06 Dec '22

06 Dec '22

Hello, I have one question that when i checked the hydrogen bonds of my original and docked (control) file, 2 bonds are missing. When I checked the distance between them, it is less than 3.40 angstroms. Can you please tell me the reason why these bonds are not showing in the Chimera. Thank you.

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Issue while importing Chimera's runCommand module
by Noe Robert 06 Dec '22

06 Dec '22

Good morning, I'm trying to use a python script for ChimeraX version 1.5, to automate mutageneses on a specific protein. As a first try, it looks like this : from chimera import runCommand as rc rc("open " + "hERGts_compiled.pdb") rc("color red") rc("surf"); So it refers to the chimera module for the runCommand. I tried to install it on Python through the command pip but it failed : ################################# Example of my shell while trying to install chimera module ####################### PS C:> python3 -m pip install chimera Collecting chimera Using cached chimera-0.4.7.tar.gz (355 kB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error �� python setup.py egg_info did not run successfully. �� exit code: 1 �t��> [9 lines of output] Traceback (most recent call last): File "<string>", line 2, in <module> File "<pip-setuptools-caller>", line 34, in <module> File "C:\Users\CE PC\AppData\Local\Temp\pip-install-cfq97mii\chimera_bd7187074876462a9782eded8cb3a816\setup.py", line 1, in <module> import ez_setup File "C:\Users\CE PC\AppData\Local\Temp\pip-install-cfq97mii\chimera_bd7187074876462a9782eded8cb3a816\ez_setup.py", line 170 print "Setuptools version",version,"or greater has been installed." ^ [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed �� Encountered error while generating package metadata. �t��> See above for output. note: This is an issue with the package mentioned above, not pip. hint: See above for details. ###################################################################################################### So it looks like the temporary file generated has an error that doesn't allow the installation of the module, and so I cannot use any command from my script as runCommand is not recognized. There seem to be no mention of this issue in the mail archive but one colleague encountered the same problem, which I find strange. Do you have an idea on how to solve this issue ? Thank you and have a great day, No�� Robert, Fifth-year student in bioengineering, minor in Bioinformatics and Modelling, at engineering school Polytech Nice Sophia, France Phone : +33 7 81 00 52 02 "let's limit the use of our resources and lighten our mails"

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Robbon colouring
by F.Xavier Gomis-Rüth 30 Nov '22

30 Nov '22

Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier --

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Writesel command in chimeraX
by Prathvi Singh 27 Nov '22

27 Nov '22

Hi Elaine, Is the writesel command available in chimeraX because I could not find it in the Actions menu? If not, then is any equivalent available apart from the command which saves selection as a new PDB file? Thanks once again in advance -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Visualizing negative volume as in CastP
by Neelen, Christopher 24 Nov '22

24 Nov '22

Hello everyone, I am trying to visualize cavities from a protein I am currently working on. Therefore I calculated the cavities volume using CastP. I then import the obtained files into chimera. Unfortunately CastP visualizes the cavities as a negative volume of the solvent accessible area. Chimera on the other hand only shows the surface. So is there a way to also visualize the negative volume in Chimara just like in CastP ? Thanks in advance! All the best, Chris

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Query regarding depth cueing
by Prathvi Singh 22 Nov '22

22 Nov '22

Hi Elaine, Is there a way to change the depth cueing gradually using command line in either chimera or chimeraX? If possible, then it would be a great way to emphasize on a specific part of the protein while making a chimera movie. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Alphafold
by Kornelius Zeth 20 Nov '22

20 Nov '22

Dear all - I'm using Alphafold in Chimera and I have a problem to run this properly on Colab. The people from Colab say that the error messages I get since recently are related to Alphafold developers having installed a new version. Could you please let me know what I could do to get the program running again? Thanks and have a nice day Kornelius

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Using Chimera and Autodock Vina on Catalina OS
by Rao, Mallika 18 Nov '22

18 Nov '22

Hello, I was wondering if anyone had been able to find a workaround in order to use the autodock vina add-on in Chimera for a mac that is running Catalina OS. Thanks in advance, Mallika

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Saving omega angles to file
by Prathvi Singh 18 Nov '22

18 Nov '22

Hello Elaine, Is there a way to save the omega angle of residues to a file using either chimera or chimeraX? I am able to save the phi, psi, chi angles using the *Render by attribute *tool in chimera but I could not find a way to save the omega angle. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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How to insert a nucleotide to a pdb
by Magdalena Riad 18 Nov '22

18 Nov '22

Hi, I have a pdb-file of the ribosome and would like to insert two nucleotides to one of the rRNA-chains. How do I do that? I’ve found the addaa command for amino acids, is there a similar one for nucleotides? Best regards, Magdalena 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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Query regarding the Zone tool in UCSF chimera
by Prathvi Singh 18 Nov '22

18 Nov '22

Elaine, In UCSF Chimera, when I try to find all the atoms within 4A of a selected residue using the *Zone* tool, it selects several atoms around that residue. However, I am not able to understand which atom of the selected residue was taken as the reference point for calculating the distances. Please help. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Information regarding double bonds
by Naima syed 18 Nov '22

18 Nov '22

Hello, I have one concern, before docking there is a double bond which i can check in pymol but after docking that double bond was lost. Can you please tell me how to fix this problem. Thank you

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No MMTK name for atom "H" in standard residue "GLY"
by Marco Sette 15 Nov '22

15 Nov '22

Dear all, i'm trying to minimize a peptide (Tools, Structure editing, Minimize Structure) but I obtain this error message: No MMTK name for atom "H" in standard residue "GLY". I have a Gly in position 1, does this depends on the NH protonation? Also, I fixed most of the residues, including Gly 1, trying to minimize a small region (Fixed Atoms: selected, in minimize panel) but still have the same errors. How can I solve it? Thanks for your help, Best Marco -- Dr Marco Sette, PhD. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 -- Questa email è stata esaminata alla ricerca di virus dal software antivirus Avast. www.avast.com

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combining two models into single model with two chains
by Elaine Meng 13 Nov '22

13 Nov '22

Hi Ali, I don't know what you mean by "sub-branches of that chain" -- if they are listed as two separate things in the Model Panel (e.g. #0.1 and #0.2), then it means they are two separate models. You can show Model Panel from the Favorites menu. If so, then you want to put them together into one model with two different chains. For that, see the "copy/combine" function in the Model Panel (in the menu under Favorites) or the "combine" command. Details in the User Guide: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> If they are really only one model with one chain, then you can only change the ID of part of the chain if the two parts are really disconnected. See Tools... Structure Editing... Change Chain IDs: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changech…> If they are NOT disconnected, you would have to manually edit the PDB file in some text editor first to add a TER between the parts. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.h…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. for general questions the better address is chimera-users(a)cgl.ucsf.edu CC'd here. The chimera-dev address is for programming questions. > On Nov 12, 2022, at 5:56 AM, Ali Doostmohammadi via Chimera-dev <chimera-dev(a)cgl.ucsf.edu> wrote: > > Hi! > I gave my protein to ClusPro for docking and it gave me the PDB file. For the next step, I need to upload to Prodigy, which requires me to separate the ligand chain and receptor chain to perform the analysis. But in the PDB file that I open in Chimera, there is only one chain, and ligand and receptor are divided as sub-branches of that chain, and Prodigy algorithm does not accept it. > I wanted to know how to divide the protein and its receptor into two different chains? > > Best regards!

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NHR Atomistic Simulation Center Online Symposium 2022, Nov 28-29
by Harald Lanig 11 Nov '22

11 Nov '22

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MD simulation movie in chimeraX
by Shivam Gupta 09 Nov '22

09 Nov '22

Hello Support Team, I am a commercial license user of chimeraX. I have .trr and .tpr files from the Gromacs MD simulation. I am not getting any option to create an MD movie. I know how to do it in chimera but couldn't find a similar GUI/option in chimeraX. Literature/tutorial of chimeraX didn't help me much. Please help me out by guiding me to generate MD movies. Please reply to this email inline. I am Looking forward to hearing from you. Thanks -- With Regards Gupta Shivam グプタシヴァム E-mail: *shivam-gupta(a)pharmafoods.co.jp <a-higashiyama(a)pharmafoods.co.jp>* Biomedical Department Pharma Foods International, Kyoto Japan 株式会社ファーマフーズ〒615-8245 京都市西京区御陵大原1-49 TEL:075-748-9811 FAX:075-948-9818 URL: http://www.pharmafoods.co.jp/

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EULA modification request
by Smith, Lua J. 08 Nov '22

08 Nov '22

Hello UCSF Chimera creators, Our Chemistry department of Missouri University of Science and Technology would like to use your software. Our attorney reviewed the non-commercial software license agreement, and is requesting the legal jurisdiction be struck from the license agreement as well as other modifications. Due to the University being an instrumentality of the state of Missouri and having sovereign immunity under Missouri and federal law, we are not authorized to waive our legal jurisdiction (See Fowler v. Board of Regents, 637 S.W.2d 352 (Mo.App. 1982)). Would you please review the attached requested license agreement modifications, and initial if acceptable? Thank you! Lua Lua Smith Software Support, Information Technology 800 University Drive ljhqn8(a)mst.edu<mailto:ljhqn8@mst.edu> | 573-341-7990<tel:573-341-7990> | it.mst.edu<https://it.mst.edu> [Missouri S&T - 150 Years]<https://www.mst.edu/>

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Finding disulphide bonds
by Prathvi Singh 08 Nov '22

08 Nov '22

Hi Elaine, I have found out a way to select the disulphide bonded CYS residues in UCSF chimera using the command: *select disulphide*. However, is there a way to count the number of disulphide bridges in a protein and save in a variable? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Question regarding 2dlabels in Chimera
by leonard.maurer＠uni-bonn.de 07 Nov '22

07 Nov '22

Hi, I am using Chimera for several years now and I really enjoy it, but there is one issue I could not solve until now: Is it possible to have subscript/superscript for the 2D labels? For example something like "subunit A\_{1}" and "subunit A\^{1}" that I can type either in the 2d labels GUI text part or with the 2dlabels command, which gives me the raised and lowered versions of the "1"? I am confident that this feature might be already implemented given Chimera's impressive amount of tools, but I was not able to find it in the documentation so far. Thanks in advance! Best regards, Leonard

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

03 Nov '22

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

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