- Chimera-dev - RBVI Mailing Lists

[UNIGE] Chimera Request
by RENZULLI Giuseppe 04 Apr '25

04 Apr '25

Good Morning, I'm a cloud engineer for Sopra Steria, and I would like to know more about your software Chimera. We are distributing your software through Intune, but we are having problems with the install and uninstall strings, possibly even for a silent mode. Thank you very much in advance, Have a nice day Giuseppe RENZULLI Senior Cloud Consultant [Sopra Steria] Via Camporeale - 83031 Ariano Irpino (AV) giuseppe.renzulli(a)soprasteria.com<mailto:giuseppe.renzulli@soprasteria.com> - www.soprasteria.it LinkedIn<https://www.linkedin.com/company/soprasteria> | X<https://twitter.com/SoprasteriaIT> | Facebook<https://www.facebook.com/soprasteriaitalia> | Instagram<https://www.instagram.com/soprasteriaitalia/?hl=it> [cid:image002.png@01DBA54A.FB151F30]<https://www.bestworkplaces.it/aziende/soprasteria/> Questo messaggio può contenere informazioni riservate, la cui divulgazione è rigorosamente vietata senza l'esplicita autorizzazione del mittente. Qualora questo messaggio sia stato ricevuto per errore, si prega di rinviarlo al mittente e di distruggerne ogni copia. Gli allegati a questa e-mail sono stati oggetto di un controllo antivirus. Tuttavia, non ci assumiamo alcuna responsabilità per danni causati da eventuali virus. P Please consider the environment - Do you really need to print this email? C2 - Uso Limitato

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Bundle development for chimeraX - svg onClick event to run command from QWebEngineView
by Lou Holland 18 Feb '25

18 Feb '25

Hello, I am currently working on a privateer bundle for carbohydrate validation in chimeraX. At present, I have it so that the privateer tool will display SNFGs of glycans present in the structure using svgs displayed in a QWebEngineView(). I would like, if possible, on clicking elements of the svg to run a chimeraX command (view /chainID:resID) to centre the view window on the residue in question. At present, I can implement an onClick event to display the command that should be run, but haven't managed to figure out how to just run the command from within that QWebEngineView. Is there a mechanism already in place for doing something like this that I could take advantage of? I'd considered using the "log html" to display the svgs in the log instead of the WebEngineView() so that I could take advantage of the href="cxcmd" functionality, but the svgs are long, with semicolons and new-line characters which interfere with this. Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

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Chimera 1.X PDB downloads are broken
by Jeremy Henry 12 Feb '25

12 Feb '25

Hello Chimera team, FYI, this morning we switched the backend file serving at RCSB Protein Data Bank to a newer service. In viewing our logs we have noticed that Chimera 1.X is using http/1.0 POST to pull the files, which is now broken due to more restrictive policies we have in place compared to our previous service. Using GET should still work with http/1.0. I'm not sure what ChimeraX uses, but that seems to be working fine. Shall I direct our support team to recommend users switch to ChimeraX if we get asked? Thanks and regards, Jeremy Henry DevOps Engineer RCSB Protein Data Bank UC San Diego

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Command to "reinstall" a plugin?
by Rocco Moretti 10 Feb '25

10 Feb '25

Hello, The instructions at https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/introduction.html#bu… talk about how to build and install a bundle plugin (with the "devel build" and "devel install" commands). However, I notice that executing these commands doesn't necessarily reflect the changes I'm making to the plugin I'm actively developing. (The changes I make to the source code don't take effect in ChimeraX.) -- I've figured out that to make the changes show up, I need to execute `toolshed uninstall` first, prior to `devel install`. (I've also noticed that it seems like a separate `devel build` step isn't needed if you are running `devel install`, which is not clear from the documentation.) Is there something like a `devel reinstall` command which will do this for me in a single command? That would make doing things like iterative debugging a bit easier. -- Or am I potentially doing something wrong with how I'm running the install command. Thanks, Rocco

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Thread_safe REST Api call
by Simon Dürr 09 Oct '24

09 Oct '24

Hi, I'm currently developing a chimerax extension that makes a REST Api call using the gradio_client library: Here is a minimal working example (using gradio_client==1.4.0) from gradio_client import Client from chimerax.core.commands import run def print_result(self, results): results[1] is a path to a local file run(self.session, f"open {results[1]}") client = Client("https://mlsb-demo-plinder-smina.hf.space/") result = client.submit( input_sequence="", input_ligand="COc1ccc(cc1)n2c3c(c(n2)C(=O)N)CCN(C3=O)c4ccc(cc4)N5CCCCC5=O", input_protein=handle_file('https://huggingface.co/spaces/MLSB/demo_plinder_smina/raw/main/input_test.p…'), exhaustiveness=1, api_name="/predict", result_callbacks=[print_result] ) However, when I try to open the loaded file in ChimeraX after the prediction is finished and the callback is run I get the following error: RuntimeError: Attempted to make OpenGL context current in wrong thread (26408, context thread 21820). I presume I need to use a Task like here to run the chimerax.core.commands.run in the same thread as the ui. https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/core/tasks.html Are there any minimal examples how to do this or other suggestions how to make this work? Thanks, Simon Dürr https://simonduerr.eu<https://simonduerr.eu/>

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Example Bundle links broken
by Simon Dürr 11 Sep '24

11 Sep '24

Dear Chimera Developers, it seems the example source code download links are broken in the documentation: https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_tool_qt.html All links have the format as below and don't work http://www.rbvi.ucsf.edu/chimerax/cgi-bin/bundle_tutorial.zip?name=tut_tool… Could you fix this or point me to the correct location for the download? Thank you Simon Dürr

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chimera stereo anaglyph implementation
by Jonas Hiltmann 12 Jun '24

12 Jun '24

Dear madam, dear sir, I am trying to write a bundle for ChimeraX that includes the possibility to apply an anaglyph (red-cyan) filter to a model. It has come to my attention that this function had already been featured in chimera but not in chimerax. I have been trying to find how it has been implemented in the chimera sourcecode but have not been successful. I found the method declaration in the include/_chimera/stereo.h file but not the code that defines the logic. If you could help me find it I would greatly appreciate it. This is in the context of a research project of the Hochschule Bonn-Rhein-Sieg. Yours sincerefuly, Jonas Hiltmann

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Finding Coordinates of Maps
by Maximilian Julian Pokutta 04 Mar '24

04 Mar '24

Dear Chimera Dev Team, I have a chimera session with the ~500 maps overlayed onto a tomogram saved, and I would like to get their coordinates in relation to the tomogram on which they are overlayed. I am unsure how to get started on this and wanted to know if you had any pointers as to where to start. Best, Max

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Seeking Assistance with PyCharm Debugging Configuration
by himalgodage2759＠gmail.com 19 Feb '24

19 Feb '24

Dear ChimeraX Dev Team, I'm Himal Godage, and I am currently in the process of developing a bundle for ChimeraX software. I have been thoroughly following the provided documentation, successfully completing the steps related to setting up a ChimeraX development environment, obtaining the code, and compiling ChimeraX. However, I have encountered a challenge in the IDEs, Debugging, and Profiling section, specifically within PyCharm. Following the provided steps, I am instructed to: 1. Create a new Run/Debug Configuration. 2. Set the script path field to point at a module. 3. Set the module to “chimerax.core”. 4. Set the Python interpreter to ChimeraX’s internal Python. 5. Uncheck “Add content roots to PYTHONPATH”. 6. Uncheck “Add source roots to PYTHONPATH”. While attempting to follow these instructions, I encountered difficulty in locating the "chimerax.core" module. Unfortunately, the provided directory structure or module seems to be difficult to find in my current project. However there is a module named core in the following path. ChimeraX > src > bundles > core I am reaching out to seek your guidance on resolving this issue. Could you please provide insights on how I can locate or create the necessary "chimerax.core" module or suggest an alternative approach to address this problem? Thank you in advance for your time and support. Best regards, Himal Godage himalgodage2759(a)gmail.com

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Using Chimera in teaching
by Simon Wheeler 01 Feb '24

01 Feb '24

Dear Chimera people, I would like to use Chimera to teach some classes on an MSc course at my university and so would like to install the software on about 40 PCs. I just want to make sure that this is okay, and in particular how I would register the software. Please can you offer some guidance? Thanks very much. Best wishes, Simon Dr Simon Wheeler Lecturer in Pharmaceutical Chemistry, De Montfort University, Leicester, LE1 9BH Chemical Probes for Lysosomal Biology<https://royalsociety.org/science-events-and-lectures/2024/09/lysosomal-prob…> is a two-day conference bringing together lysosomal biologists and analytical chemists who have an interest in making sensors to interrogate the functions of this organelle. Click on the link for more details and to register your interest. [cid:image001.png@01DA54F3.C489C400]

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Web server inquiry
by Paula Jofily De Lima Rangel 26 Oct '23

26 Oct '23

Dear Chimera developers, I am Paula, a second-year PhD student at the University of Waterloo. I have recently developed a python program which performs automatic exhaustive mutagenesis of protein-ligand complexes using Chimera at the backend. My supervisor and I believe that the community could benefit from such a tool, so we intend to publish the code as a free and open source pipeline, with a permissive license. In addition, we believe that making it available as a web server would be especially useful. Therefore, we would like to ask your permission to run UCSF Chimera in a webserver hosted by our University. We will never distribute Chimera itself, and users would be instructed to register their own installation and always cite it whenever they use our server. Thank you for your time and consideration. Kind regards, Paula

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None
by None 26 May '23

26 May '23

Chimera User's Guide, the coloring of the MSMS surface using red, blue and white is described: "The Molecular Surface option allows coloring by electrostatic potential at the molecular surface (as in the figure above). Positive potentials range from white to blue, and negative potentials range from white to red. Potentials at or above the cutoff value are fully blue, and potentials at or below the negative of the cutoff value are fully red. The white area is transparent in MSMS surfaces, opaque in Grasp surfaces." The Chimera help menu has a User's guide entry that will show this stuff in a web browser. As you note, the areas of low potential really look gray, and dark gray not white. This is because they are set to be a very transparent white and the black background of the Chimera window shows through. To see this you can go to Settings/Preferences category Background and change the background color to white. That makes the low potential areas look white, but you probably don't want a white background. Eric Pettersen has added color buttons to the DelphiViewer user interface so you can change the red, blue, and white colors, including the transparency, and this will be in the next release. What you want is probably to make the white less transparent. You can do that in your current Chimera 1602 by editting a file. Look at /usr/local/chimera/share/DelphiViewer/MSMSTexturer.py near line 78 you'll find red = chimera.MaterialColor(1, 0, 0, 0.9, None) white = chimera.MaterialColor(1, 1, 1, 0.1, None) blue = chimera.MaterialColor(0, 0, 1, 0.9, None) This is setting the colors, red, white, blue, and transparency values each on a scale of 0 to 1. For the transparency 0 means completely transparent and 1 means completely opaque. So if you change these lines to red = chimera.MaterialColor(1, 0, 0, 0.9, None) # white = chimera.MaterialColor(1, 1, 1, 0.1, None) white = chimera.MaterialColor(1, 1, 1, 0.9, None) blue = chimera.MaterialColor(0, 0, 1, 0.9, None) and restart Chimera, you'll get white low potential regions. Here the "#" is the comment character in the Python language. I can ask Eric if the unreleased DelphiViewer with the color buttons on the user interface will work in Chimera 1602, and try to get that to you so you don't need to edit the file. Tell me if you want that. You say the MSMS surface looks incomplete. Can you tell me a specific PDB file and atom to look near to see the problem? The MSMS probe radius is set to 1.4A. You can see this by using Controllers/Model Panel, click on the line for the MSMS surface, and press the Attributes button. Normally you can edit the probe radius and press enter and it will automatically update the surface. But when I tried this with Delphi coloring I got an error and had to close the MSMS surface to get the graphics window to display anything again. If I change the probe radius before doing the Delphi coloring the surface is recalculated with no error. Tom > From: "Wade Nasholds" <vesuvius(a)omantel.net.om> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: DelPhi in Chimera > Date: Fri, 14 Feb 2003 21:08:41 +0400 > > Hello Tom, > Thanks for your previous email. Certainly helps. > I got build 1602 of Chimera (thanks) and have tried it with some DelPhi .phi files > that I've generated. > I've been able to render MSMS surfaces showing electrostatic potentials successfully. > This is great news > because that's what I've been aiming to do! The potential extremes are shown in red > & blue but the intermediate > potential shows as shades of light grey to dark grey rather than the expected white > (neutral). Also, the molecular surface seems incomplete > in certain spots. I don't think it is a matter of DelPhi parameter settings, as I've > tried different ones but to no avail. Although it still may > be due to DelPhi settings still unknown to me as I'm still learning how to use it. > Might it be something to do with Chimera? I've altered the kT/e settings in DelPhi > viewer but it hasn't resolved the problem. > > Is the default surface probe (water) set at 1.4A in the MSMS feature of Chimera? > > Thanks again for your time. > Wade

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None
by None 26 May '23

26 May '23

"Note: Stereo is only available on Quadro cards, and is not supported in TwinView. Currently, stereo operation may not be completely stable on the original Quadro chip and left-right flipping may be erratic. This issue will be resolved in a future release." So it should work on our lastest Quadro 4 board, but might have problems on the ELSA Gloria IIs we bought. Greg

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Queries about operational command of chimera
by 吴明松 15 May '23

15 May '23

Dear Chimera developer, I would like to perform the same operation on multiple files and I know that this can be done using a loop. However, I am not sure how to write the corresponding command or script. Therefore, could you please help me by writing a script that can perform the following operation? I have installed the 64-bit version of Chimera Headless Linux on my Windows subsystem. Thank you very much for your help! ################################### operation: File-> open -> abc.pdb Select-> structure->ligand Actions-> delete File->save PDB->rec_noH.PDB Actions->Surface->show Tools ->structure editing->write dms->rec.ms Actions->Surface->hide Tools ->structure editing->Dock prep->rec_charged.mol2 ##select the parameter of Unspecified(determined by method)   File-> open -> abc.pdb Select-> structure->ligand Select-> invert (all models) Actions-> delete File->save mol2->ligand_site.mol2 ################################### Sincerely, Mingsong Wu mingsong_wu(a)foxmail.com

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question
by Ouertani Awatef 16 Mar '23

16 Mar '23

Dear all Good morning Please i would like to know : 1) how to make serine and threonine dehydration using chimera 2) how to make a cysteine-cysteine bridge using chimera Many thanks

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Fwd: RBVI web update results
by Eric Pettersen 22 Feb '23

22 Feb '23

For whoever is responsible for the "createPub" script... > Begin forwarded message: > > From: root <root(a)cgl.ucsf.EDU> > Subject: RBVI web update results > Date: February 22, 2023 at 4:04:54 AM PST > To: pett(a)cgl.ucsf.edu > > Traceback (most recent call last): > File "/usr/local/bin/createPub", line 188, in <module> > main() > File "/usr/local/bin/createPub", line 46, in main > htmlList = formatIds(idList, url) > File "/usr/local/bin/createPub", line 99, in formatIds > output.extend(bufferPid(url, idBuffer, flush=True)) > File "/usr/local/bin/createPub", line 109, in bufferPid > data = formatPubmedId(idBuffer, url) > File "/usr/local/bin/createPub", line 124, in formatPubmedId > esr = eSummaryResult.eSummaryResult(data) > File "/usr/local/lib/python2.7/site-packages/ncbi_eutils/eSummaryResult.py", line 43, in __init__ > raise ExpatError > xml.parsers.expat.ExpatError

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How to make script to run chimera command like add H and charged for multiple file
by Broto Santoso 15 Jan '23

15 Jan '23

Dear Chimera Staff, I want to run some chimera commands (such as add hydrogen and add charge) via python script for multiple files and save them as mol2 or pdb. I have read some examples, but still know nothing. Would you like to give me more about the script, how to make it easily? Thank you Best regards, -- *Broto Santoso* Laboratorium Kimia Farmasi Fakultas Farmasi UMS mobile: +6282136414379 (*no call, sms only*) My Youtube Channel <https://www.youtube.com/channel/UCCiJ8VZ1Vd3rVtywWkm4GyQ>

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Request UCSF Chimera source code
by Juan Sebastian Rey Lancheros 22 Dec '22

22 Dec '22

Hello! I'm Juan Rey, a PhD student at University of Delaware. I am interested in reading chimera's methods for resamling EM density maps. I tried downloading the source code from https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html But the download hyperlink ends in a 404 code. If possible could you please send me the source code? Thank you in advance! Best, -- Juan Rey

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https://www.cgl.ucsf.edu/chimerax/docs are down?
by Gong, Zhen 22 Dec '22

22 Dec '22

Dear Chimera and ChimeraX developers, I was not able to open any webpage of https://www.cgl.ucsf.edu/chimerax/docs and getting this error message: [cid:image001.png@01D915F8.4C0EA080] I switched to Chrome and still had the same problem. I am wondering if there is a problem with the UCSF server? Many thanks to your help and happy holidays. Best, Zhen

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Help
by Ali Doostmohammadi 13 Nov '22

13 Nov '22

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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Application Security Questions for Chimera
by Hart, Michael 25 Oct '22

25 Oct '22

I've been asked to approve installation of Chimera in one of our labs, and I was hoping that you might have documentation on your development processes and policies such that I can feel comfortable installing your app in our environment. I have searched but not found documentation related to OWASP or other dev standards, or any assessments that may have been run. Would you have information available? Thank you in advance, Mike Hart | Chief Information Security Officer (CISO) Metropolitan State University of Denver Information Technology Services Campus Box 96, P.O. Box 173362, Denver, CO 80217-3362 Admin Building - 1201 5th Street 480M Denver, CO 80204 303-615-0541 (Office) 303-352-7548 (Help Desk) mhart20(a)msudenver.edu<mailto:mhart20@msudenver.edu> | www.msudenver.edu/technology<http://www.msudenver.edu/technology> [cid:image001.jpg@01D8E848.158CADA0]

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ChimeraX pyhton script
by Jan Hofmann 17 Oct '22

17 Oct '22

To whom it may concern, I want to write a python script to open a pdb file, then load a .xplor file in as well. After one rotation which I also want to do via the script I want to export the output file as a .png file. Could you provide any advice to me on how to write such a script? I am having troubles loading any python script into ChimeraX. Eventually I want to use this script to batch wise output structures including guest adsorption where the guest species is introduced via the .xplor from previous analysis and the structure is provided by a .pdb file. I really would need some advice/tutorial at this stage so I would be more than happy to hear back from you. Many thanks and kind regards, *Jan Hofmann, M.Sc.* *PhD Student, Department of Chemistry* *Chapman Group* Stony Brook University *jan.hofmann(a)stonybrook.edu <andrew.nicoll(a)stonybrook.edu>* Office: Room 563, Chemistry

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Old post edit or deletion?
by Bernard Lieberman 27 Sep '22

27 Sep '22

Hi folks, I'm trying to scrub some of my data from the web and noticed my phone number and website appear at the following page. Can this please be removed or edited? http://plato.cgl.ucsf.edu/pipermail/chimera-dev/2015/001208.html Thanks! Bernard

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popup balloons with custom information for vrml models
by Merce Alemany Chavarria 13 Sep '22

13 Sep '22

<mailto:chimera-dev@cgl.ucsf.edu> Dear Chimera developers, We are developing an extension that renders vrml models using BILD commands. For the moment the vrml models have a name that shows up on Models Panel, but when the mouse is placed on top of them only the number of model is displayed (like '#11'). We would like to add to the models a popup balloon with customized information, in a similar way as information if shown for classical chimera objects (atoms, bonds...). Could you guide us on how to approach it? I will use this e-mail also to let you know that the link to chimera's source code (https://plato.cgl.ucsf.edu/trac/chimera/browser/trunk) found in this page https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html returns a 404 error. Is there an alternative way to check it out? Thank you for your help, Mercè

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Surfnet
by Samo Lešnik 31 Aug '22

31 Aug '22

Dear Madam/Sir, I was wondering if it is possible to run the Surfnet calculation using the command line tool. I wish to automate it for MD trajectory for every frame and this would be useful. Thank you! Samo Dr. Samo Lešnik, mag. farm. / Researcher Univerza v Mariboru / University of Maribor Fakulteta za kemijo in kemijsko tehnolgijo Faculty of Chemistry and Chemical Engineering Smetanova ulica 17, 2000 Maribor, Slovenija T: +386 2 2294 428 E: samo.lesnik(a)um.si<mailto:samo.lesnik@um.si>

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