- Chimera-users - RBVI Mailing Lists

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.

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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

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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

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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

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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

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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

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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

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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

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