- ChimeraX-users - RBVI Mailing Lists

Re: [Chimera-users] Questions regarding reply log
by Elaine Meng 28 Jun '23

28 Jun '23

Hi Prathvi, Normally one would *not* include any residue numbers in a mmaker command. You only need model numbers (not chain IDs either, except if you want to make sure that specific chains match specific other chains when each model has more than one chain). Also it is completely useless to include the @ca in a mmaker command because mmaker always only uses @ca for proteins anyway. See the mmaker help for whichever program you are using (Chimera or ChimeraX). Your description does not make sense for Chimera. You must be using ChimeraX. The specifications are different for Chimera and ChimeraX, only ChimeraX uses "/" for chains. In either program, you would simply omit the chain part of the specification if there is no chain ID. To avoid confusing others, make sure to email chimerax-users if you are asking about ChimeraX usage, and chimera-users for Chimera. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 28, 2023, at 1:47 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thank you so much for the info Elaine! > I just have one more question. > Is it possible to run the "mmaker" command without inputting chain IDs of the residues to be superimposed? > I am asking this because I have a few PDB files whose residues lack chain ID information (I know this because when I hover my mouse over one of these residues, it shows something like: "/? PRO 190") > I tried the command: mmaker #0/?:162-172@CA to #1/?:162-172@CA > But it shows the error: No molecules/chains to match specified > > > > On Tue, Jun 27, 2023 at 9:46 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Prathvi, > Both of these things are much easier/better in ChimeraX, since it has commands to do them. We are recommending everybody use ChimeraX if possible (if it has the features that they need). > > In Chimera, the Reply Log has buttons to Clear and to Save, but there are no commands for those functions. If there were commands, it would be mentioned in the Reply Log help. > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/reply.html> > > For saving only (not clearing), there are instructions of how to do it in python at the bottom of this page: > <https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jun 27, 2023, at 4:21 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > > > Hi Elaine, > > Is there a way to clear the Reply Log using the command line? > > Is there a way to write the contents of the Reply log to a text file? > > > > -- > > Prathvi Singh, > > Research Fellow, > > Department of Biological Sciences & Bioengineering, > > Indian Institute of Technology, Kanpur-208016 > > > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016 > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu: To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Manage subscription:

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opening multiple csx files at same time
by stevensb＠ufl.edu 26 Jun '23

26 Jun '23

How can you open 2 or more csx files simultaneously in order to have the all contents of both *.csx files showing and superpositioned. This can be done for opening multiple *.pdb files which then shows all the chains of all the opened files superpositioned on the same page. But when I try to open multiple csx files, the second one completely deletes and replaces the currently open csx file and deletes what was showing from the originally open csx file.

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Re: [Chimera-users] downloading and saving multiple PDB's
by Elaine Meng 26 Jun '23

26 Jun '23

Hi Dmitry, You sent this to the chimera-users list but chimerax-users(a)cgl.ucsf.edu (CC'd here) is the better address for ChimeraX questions. We try not confuse Chimera users with ChimeraX answers and vice versa. Since your text said "Chimerax" I will answer for ChimeraX. Not sure what you mean by "multiple" ... of course you can fetch structures from the PDB using their IDs, e.g. commands: open 1zik open 2gbp 2fw0 1plx 1plz <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> If by "multiple" you mean a huge number that is not practical to put in a single command, that is a different matter. Also, a single "save" command only saves one file and it does not have option to automatically figure out filename from model name. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> However, ChimeraX does allow writing a single command script (.cxc file) and applying it to multiple input files when the .cxc file is opened with the "open" command and "forEachFile" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> It also allows substituting part of the input file name as the output file name. However, it was intended for the case where all the input files are local files. So as far as I know you would have to first fetch all the files from the PDB so that they are in your local cache (~/Downloads/ChimeraX/PDB/ ) and then in a separate step, use your .cxc file with this forEachFile mechanism. To do so, you would probably also need to segragate these files into their own directory since you don't also want to run the script on all of the other structures you've previously fetched from the PDB using ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 26, 2023, at 9:39 AM, Dmitry Semchonok via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear colleagues, > > Is there a way to > > • download the multiple pdb/mmcif using Chimerax knowing their ID entry? > • save multiple opened pdbs using their corresponding original names in Chimerax? > Thank you in advance. > > Kind regards, > Dmitry

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Electrostatics
by Ryan Gardner 26 Jun '23

26 Jun '23

Hello, I just want to verify that the electrostatic potential is measured in volts (V). Is this correct? Here's an example of my analysis: [image: image.png] Sorry to be a bother! -Ryan

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error opening Swissdock generated output file
by Fussner-Dupas, Eden 26 Jun '23

26 Jun '23

Hello, I am having trouble using ViewDockX with a file generated by Swissdock. When I open the clusters.dock4.pdb file it opens without issues - but when I try to use the ViewDockX tool to view each predicted pose one at a time I get the error “No suitable models found for ViewDockX” Any help warmly appreciated Cheers, Eden

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Save Image Dialog box
by McClean, Phillip 25 Jun '23

25 Jun '23

Hi Everyone, I am using ver 1.6 of Chimerax. I want to save an image for print publication, so I want to save it as 300 dpi. I used the Snapshot icon from the toolbar and it saved a 72 dpi image. In the user guide, there is mention of a Save Image dialog. The guide sounds like I can make use the dialog to select the dpi. But, I cannot find the Save Image menu. Can someone point me to it and add any help/hints on save a 300 dpi image. As always, thanks for your help. Phil McClean

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Aligning two ligands
by Karim Rafie 25 Jun '23

25 Jun '23

Hi all, I was wondering if there's a command that will allow me align two ligands to each other? Couldn't find anything online and when I try the match command I constantly run into an error, even when specifying certain atoms between two ligands. Any help would be greatly appreciated. All the best, Karim ############################################## Karim Rafie; PhD, MRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [cid:e5366e3a-666f-40ea-9f71-eb5b2b395016]

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Changing spin movie default save location?
by Daniel Gilliam 21 Jun '23

21 Jun '23

Hi, How can I change the default filepath that 'Spin movie' saves to? The default for me saves to location without save permissions, so I have been unable to save images or movies. Apologies if I missed an easy answer to this in the documentation. Thanks, Daniel Gilliam

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Invert selection
by Leonardo Talachia Rosa 20 Jun '23

20 Jun '23

Dear ChimeraX community Apologies for the very naive question. In old chimera, there was a "Select - Invert selected models" command which would invert the selection solely in the selected model, whereas in chimeraX I could not find an equivalent command or option in the menu. The select invert menu will invert the selection for all open models. Is there a way to invert selection only in one model? Thank you for your time Kind wishes, Leonardo -- ************************* Leonardo TALACHIA ROSA, PhD Associated professor Department of Biochemistry and Tissue Biology (DBBT) Biology Institute Universidade Estadual de Campinas - UNICAMP Rua Monteiro Lobato, 255 - Campinas - SP - Brasil - CEP 13083-862 **************************

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ChimeraX - Without NVIDIA
by Nguyen, Tuan /US 16 Jun '23

16 Jun '23

Hi, I'm trying to install the ChimeraX 1.6.1 on Ubuntu 22 without NVIDIA driver, I can launch the chimerax, but it gives me an error about the graphic driver, and I'm trying to open a pdb file, I don't see the image at all. Please see attached below. Would you please help? Thanks, Tuan [cid:image001.png@01D9A02C.7D05AF30]

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600 DPI Quality Images
by Dillon P Cao 15 Jun '23

15 Jun '23

Hello, How would I save an image on ChimeraX as 600 dpi? Apologies if this has been answered before. Sincerely, Dillon P. Cao

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Selecting segments overlapping atomic model
by kizziah4＠uab.edu 15 Jun '23

15 Jun '23

Is there some degree to which a segment must overlap an atomic model to be selected with "Over Sel. Atoms"? Can it be changed? I frequently use Segment Map to create custom masks for focused refinement and classification and for signal subtraction. I tend to use reference atomic models to expedite this process, but I am having problems selecting segments overlapping atomic models (compared to older versions of Chimera). I am on Windows 10 with ChimeraX version 1.5 (2022-11-24). I have experienced the same on Ubuntu-20.04 with ChimeraX v1.6.1. For example, I have an unsharpened map estimated at 4.8A resolution from RELION and an atomic model of the same structure downloadeded (via ChimeraX) from the PDB. After deleting some unneeded chains and duplicating others, fitting the model into the map using simulated density (4.8A resolution, 0.77 correlation), segmenting the map at a low threshold that covers all (but a couple of loops) of the atomic model, ungrouping the segments once for granularity, selecting the entire atomic model, and clicking "Over Sel. Atoms", no segments are selected. If I try repeating the process with the backbone only (0.80 correlation), no segments are selected. I have succeeded in some cases by ungrouping all segments ~4 times, but in this particular case it only selects a few segments corresponding to parts of some alpha helices.

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Question about MatchMaker with nucleic acids
by Leonardo BETANCURT ANZOLA 14 Jun '23

14 Jun '23

Hello, I’m currently using ChimeraX to compare different DNA binding proteins and would like to align them using match maker and the DNA helix. The problem is that the structures do not have the same DNA sequence and that is the parameter the MM uses to align. Would it be possible to align DNA using only the phosphate-sugar backbone of the molecule? In that case I’d like to tell chimera which phosphates should one aligned to which. Thank you, Leo B.

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Isolde installation in chimeraX
by Chiara Rapisarda 13 Jun '23

13 Jun '23

Hi, I am trying to install Isolde in chimera, I can successfully download the bundle, but nothing happens afterwards. Can you help me find out what is wrong? Thanks, Chiara

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Missing or invalid "sequence" argument: Sequences argument
by Adetoun Adeniji-Adele 13 Jun '23

13 Jun '23

Hello, I was trying to use the AlphaFold predict function earlier and received the following error. Missing or invalid "sequence" argument: Sequences argument "MNGIDIAVVTDDPAILKSVHERYPDGSKHSIELEHGHNVHIFVRTATLVLSSYIRDNEAIAVLGYSNVHESSMRAILESSPGVAHMNSALGQLIGAQWVVAIRKGAVRIQGTVSGLSRVYWSKRGSRFVASNRSRELARLLGSELDPTQVAFRTIHPMQHPFTSSSCWKDLEGVLPGEYLEVTGRSSPRTERWWTPATSYRSLEDGANETAAALFSVVRNQLSDHSAASCDISGGLDSSSIAAIAANAAKSGETHTVLHGTTSVSRDEFNSDADWAIELSKSLKLDSHSFLSWNDMPKEYDDLDALASYDLDEPSIASISHSRFTHLINVARSKGSQVHLTGFGGDELFIGSPTFCVDLFKTQPLLSARLLLTYRAMYRWTFRSLVRPLTTPMSYQQWMRTKSLSTDRSTLRIPPLSWGFHGVIPPWITRDARHSMYDHVRSASSATFPLAPTPGRHFELENLYQCARLFRTMSDIVSQTSGVLLVAPMLEQAVVEAAISVRTPERLTPHKYKPVLTHATRGLLPAVVAERQTKGGEDTDAAIGFSENISAIRELWDESRLASLGIVDGDYLSNALRRPDSAEFDDCAIAKTLATELWLRSLEK,MPVVGAMAIPSKTRISATERLRLASALSLGKALSHLPPGLLRRSMTAFAAKARPASYREAEAAVVSITQYSKASAGPGSCLQRSISVCILMRLDGRWPTWCVGVPSKPPFRAHAWIEAGGQIVAELGDMNSYSRLMTISTHAERTE" is not a chain specifier, alignment id, UniProt id, or sequence characters I am not sure what the message means and can't seem to find others who have had similar error messages. Any help would be appreciated. Best, Adetoun

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No chains in AtomicStructure
by Dominik Sordyl 13 Jun '23

13 Jun '23

Hi, I have created a python plugin that uses AtomicStructure() class to create a model based on the pdb file and custom trajectory file. The problem is that after creating the structure (adding residues and atoms) it has no chains. Due to this issue, I cannot use some of the ChimeraX features (e.g. rainbow coloring) - at least I think this is the reason. While adding new residues one has to specify the chain_id, but even if I do it those chains are not created automatically. Do I have to create chains separately or there is something that I am missing here. Would be grateful for your help. Best, Dominik

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How to play volume series in chimeraX?
by Rayees Mattoo 12 Jun '23

12 Jun '23

Hi, I want to play a volume series in chimeraX. There is an option "volume series" in chimera but could not find the equivalent option in chimeraX. Also, is it possible to 'movie record' the volume series while it is playing? Any suggestion would be helpful. Best

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Triangle attention for alphaFold2
by Cheng Fei Phung 10 Jun '23

10 Jun '23

Hi, This might not be directly related to use of ChimeraX gui software that this mailing list is targeted for. Might I ask if anyone have any suggestions for the use of triangle attention module in https://twitter.com/salmon_shitake/status/1663176260632346624 ? Regards, Phung Cheng Fei feiphung(a)hotmail.com

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sym command
by postmaster＠cgl.ucsf.edu 09 Jun '23

09 Jun '23

From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> Subject: sym command Date: June 9, 2023 at 11:55:38 AM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Dear All, I am trying to generate symmetric copies of the atomic structure in a filament map and I get the following error sym #1 group c6*h,39.1,19.3,7,-1 coord #2 (atomic structure is #1 and the map is #2) error - Expected a keyword What is incorrect in the command. 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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ChimeraX not able to install for ubuntu22
by himanshi singh 07 Jun '23

07 Jun '23

Greetings! Kindly find the attached screenshot for installing in ubuntu22, it says dependencies unmet. Kindly guide me. Thankyou Regards Himanshi PhD candidate IIT Kanpur India

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ChimeraX .cxs session file
by Moustafa, Ibrahim M. 06 Jun '23

06 Jun '23

Dear ChimeraX, I have a ChimeraX session .cxs file that was created a while ago. I wonder if there is a way to open the file to see the actual commands, parameters used in that session. Is there is tool/way to read .cxs file? Thank you for your help. Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802 Phone: (814) 863 5940 Fax: (814) 865 7927

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clashes & contacts
by Dmitry Semchonok 06 Jun '23

06 Jun '23

Dear colleagues, Probably very simple question, non the less - how to calculate&show the contacts/clashes in the model? We have heptamer and we would like to find out what are the contacts & clashes with 6 surrounding units. I know that chimera can do that. Also, I heard that there is also software called DIMPLOT. Does ChimeraX do the same? Thank you in advance. Sincerely, Dmitry

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Daily builds
by BARRY E DEZONIA 05 Jun '23

05 Jun '23

Hello, I am looking for the daily build for Ubuntu. I go to this page: https://www.rbvi.ucsf.edu/chimerax/download.html No daily build releases are shown for Ubuntu. Are you having trouble with the website?

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Re: how to view Alphafold Run window
by Tom Goddard 05 Jun '23

05 Jun '23

Hi Jim, The AlphaFold predicted model is always saved as best_model.pdb. It would be nice if you could specify a different name when you start the prediction run but that is not available. I made a ChimeraX feature request for that https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9128 You can request new features directly with ChimeraX menu entry Help / Report a Bug.... This can be used for both bugs and new feature suggestions. Tom > On Jun 5, 2023, at 11:51 AM, James Raymond <james.raymond(a)unlv.edu> wrote: > > Thank you. I am slowly learning how to use ChimeraX. > One other question that I haven't solved yet: when I paste a sequence into the box for structure prediction, is there a way to name it right at the beginning? > All my previous jobs are given the same name "best_model".I know I can rename them later, but it would be easier if I could name them at the start. > Jim > > > On Mon, Jun 5, 2023 at 11:30 AM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Jim, >> >> The ChimeraX panels are can be dragged and dropped on the main ChimeraX window to allow stacking them. In your case you dragged the AlphaFold Run panel on top of the Log panel. Then it shows the two tabs (AlphaFold Run, Log) at the bottom and you can click on those to switch between them. You can make the AlphaFold Run window free-floating again by showing its tab then dragging the title-bar of the panel out of the main ChimeraX window. All the ChimeraX panels work this way -- they can be made free-floating windows or "docked" in the main window. >> >> Sometimes it is annoying when you drag a ChimeraX window and it tries to drop it on top of another panel. You can tell ChimeraX to not allow dropping the AlphaFold Run window on another panel using the command >> >> ui dockable false "AlphaFold Run" >> >> Tom >> >> >>> On Jun 2, 2023, at 6:36 PM, James Raymond <james.raymond(a)unlv.edu <mailto:james.raymond@unlv.edu>> wrote: >>> >>> Thanks, Tom, >>> I sent another email to say that I think I solved the problem but you didn't see that one. >>> >> >>> >>> >>> Here's a cool protein structure I made today with ChimeraX. >>> I used Yasara to view it. >>> This is so great! >>> Jim >>> >>> >>> >>> On Fri, Jun 2, 2023 at 4:34 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>> Hi Jim, >>>> >>>> You kind of shoot yourself in the foot if you close the AlphaFold Run. But Google Colab does not immediately kill your AlphaFold job. So you could reconnect to Google Colab in whatever web browser you normally use (search for Google Colab). When it asks if you want to load some previous notebook say Cancel. Then use Google Colab menu Runtime / Manage Sessions and click on your AlphaFold session that you started from ChimeraX. Then you should see your job still running. When it completes it will ask to download the results. The original ChimeraX window you closed would have downloaded the prediction and opened it in ChimeraX. But now you have Colab in a normal web browser so it will simply download to your ~/Downloads folder (not where ChimeraX usually puts it in ~/Downloads/ChimeraX/AlphaFold/prediction_N) so you would have to open the results.zip and load the predicted structure yourself. >>>> >>>> In short don't close the AlphaFold Run window. It isn't quite as bad as opening a terminal, starting a computation, then closing the terminal before it finishes. Since it is running on Google's servers and Google kindly doesn't immediately shut it down, you can rescue it. But it is not intended to work that way. >>>> >>>> Tom >>>> >>>> >>>> > On Jun 2, 2023, at 4:04 PM, James Raymond via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> > >>>> > Dear ChimeraX, >>>> > I keep losing this window, whenever I click on it or move it. >>>> > How do I get it back again? >>>> > thank you >>>> > Jim >>>> > >>>> > >>>> > <image.png> >>>> > _______________________________________________ >>>> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>>> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>>> > Manage subscription: >>>> >> >>

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ChimeraX - windows 10 installation/running issue
by Dmitry A. Semchonok 05 Jun '23

05 Jun '23

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Re: how to view Alphafold Run window
by Tom Goddard 05 Jun '23

05 Jun '23

Hi Jim, The ChimeraX panels are can be dragged and dropped on the main ChimeraX window to allow stacking them. In your case you dragged the AlphaFold Run panel on top of the Log panel. Then it shows the two tabs (AlphaFold Run, Log) at the bottom and you can click on those to switch between them. You can make the AlphaFold Run window free-floating again by showing its tab then dragging the title-bar of the panel out of the main ChimeraX window. All the ChimeraX panels work this way -- they can be made free-floating windows or "docked" in the main window. Sometimes it is annoying when you drag a ChimeraX window and it tries to drop it on top of another panel. You can tell ChimeraX to not allow dropping the AlphaFold Run window on another panel using the command ui dockable false "AlphaFold Run" Tom > On Jun 2, 2023, at 6:36 PM, James Raymond <james.raymond(a)unlv.edu> wrote: > > Thanks, Tom, > I sent another email to say that I think I solved the problem but you didn't see that one. > > > Here's a cool protein structure I made today with ChimeraX. > I used Yasara to view it. > This is so great! > Jim > > > > On Fri, Jun 2, 2023 at 4:34 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Jim, >> >> You kind of shoot yourself in the foot if you close the AlphaFold Run. But Google Colab does not immediately kill your AlphaFold job. So you could reconnect to Google Colab in whatever web browser you normally use (search for Google Colab). When it asks if you want to load some previous notebook say Cancel. Then use Google Colab menu Runtime / Manage Sessions and click on your AlphaFold session that you started from ChimeraX. Then you should see your job still running. When it completes it will ask to download the results. The original ChimeraX window you closed would have downloaded the prediction and opened it in ChimeraX. But now you have Colab in a normal web browser so it will simply download to your ~/Downloads folder (not where ChimeraX usually puts it in ~/Downloads/ChimeraX/AlphaFold/prediction_N) so you would have to open the results.zip and load the predicted structure yourself. >> >> In short don't close the AlphaFold Run window. It isn't quite as bad as opening a terminal, starting a computation, then closing the terminal before it finishes. Since it is running on Google's servers and Google kindly doesn't immediately shut it down, you can rescue it. But it is not intended to work that way. >> >> Tom >> >> >> > On Jun 2, 2023, at 4:04 PM, James Raymond via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Dear ChimeraX, >> > I keep losing this window, whenever I click on it or move it. >> > How do I get it back again? >> > thank you >> > Jim >> > >> > >> > <image.png> >> > _______________________________________________ >> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> > Manage subscription: >>

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AlphaFold2 coloring is not according to the database
by Julia Varga 05 Jun '23

05 Jun '23

Hi, I was preparing a figure and we opened the same AF2 structure both in chimerax and pymol, and colored according to pLDDT. We expected something quite similar, but some of the residues were not colored the same (left chimerax, middle official AF2 coloring, right pymol) [image: image.png][image: image.png][image: image.png] These are the corresponding CA atoms from the file, there are several that are above 70. ATOM 2 CA MET B 1 26.541 -48.983 -34.346 1.00 49.18 C ATOM 10 CA ALA B 2 23.562 -47.870 -36.454 1.00 60.35 C ATOM 15 CA ASP B 3 25.250 -49.497 -39.528 1.00 68.46 C ATOM 23 CA ALA B 4 25.752 -52.804 -37.641 1.00 69.86 C ATOM 28 CA TRP B 5 22.024 -53.025 -36.747 1.00 68.46 C ATOM 42 CA GLU B 6 21.036 -52.590 -40.351 1.00 71.02 C ATOM 51 CA GLU B 7 23.249 -55.575 -41.294 1.00 76.21 C ATOM 60 CA ILE B 8 21.578 -57.739 -38.645 1.00 74.81 C ATOM 68 CA ARG B 9 18.177 -56.653 -39.803 1.00 70.07 C ATOM 79 CA ARG B 10 19.226 -57.507 -43.334 1.00 74.00 C ATOM 90 CA LEU B 11 20.598 -60.932 -42.264 1.00 74.36 C ATOM 98 CA ALA B 12 17.459 -61.553 -40.194 1.00 69.47 C ATOM 103 CA ALA B 13 15.384 -60.625 -43.205 1.00 69.30 C ATOM 108 CA ASP B 14 17.563 -62.981 -45.430 1.00 70.53 C ATOM 116 CA PHE B 15 17.273 -65.769 -42.888 1.00 71.78 C ATOM 127 CA GLN B 16 13.568 -65.190 -42.812 1.00 64.74 C ATOM 136 CA ARG B 17 13.352 -65.300 -46.586 1.00 65.36 C ATOM 147 CA ALA B 18 15.491 -68.455 -46.645 1.00 64.05 C ATOM 152 CA GLN B 19 13.261 -70.000 -44.028 1.00 60.46 C ATOM 161 CA PHE B 20 10.117 -69.389 -46.168 1.00 62.26 C ATOM 172 CA ALA B 21 11.642 -70.083 -49.654 1.00 56.65 C ATOM 177 CA GLU B 22 11.244 -73.693 -49.767 1.00 53.68 C ATOM 186 CA ALA B 23 7.622 -74.493 -50.250 1.00 56.47 C After looking at again the docs, I understood that chimerax has a different coloring [image: image.png] AFDB [image: image.png] Can you maybe change this? Most people are probably used to the database's coloring, and could interpret it wrong (like me... It drove me crazy when showing somebody else, why the plddt-s do not match to what I have shown before, just in a figure by chimerax). I understand that in the documentation the colorbar is according to the coloring that chimerax does, but it would be better if it was according to the standard. Thank you so much! Kind regards, Julia Varga

2 1

smooth object surface
by Jesse Hansen 05 Jun '23

05 Jun '23

dear all, I have an object imported from segmentation in dragonfly that is quite jagged and rough looking. Is there a way to smooth the surface? When I try "surface smooth" that doesn't work because I guess it's looking for atoms/surface render. Is there a way to smooth .stl or .obj files? Thanks Jesse

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makind disulfide bonds in Chimera x
by Vladimir Saudek 03 Jun '23

03 Jun '23

Hello, Is it possible to make a disulfide bond between two Cys in spacial proximity and write it to the PDB file? Thank you Vladimir

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how to view Alphafold Run window
by James Raymond 02 Jun '23

02 Jun '23

Dear ChimeraX, I keep losing this window, whenever I click on it or move it. How do I get it back again? thank you Jim [image: image.png]

2 1

Blast protein results
by postmaster＠cgl.ucsf.edu 02 Jun '23

02 Jun '23

From: Lynne Howell <howell(a)sickkids.ca <mailto:howell@sickkids.ca>> Subject: Blast protein results Date: June 2, 2023 at 2:18:42 PM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> HI I’m a novice ChimeraX user and wondered whether there is a way of saving to an excel file the blastprotein results against the Alphafold database that appear in the session window? Was looking to capture all the information for cross reference to another file. Thanks in advance Lynne This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

2 1

MolecularDynamicsViewer
by Michael Patzschke 01 Jun '23

01 Jun '23

Dear colleagues, I would like to use the MolecularDynamicsViewr more often. My problem is, that I work with small metal organic systems and we never generate pdf files. What I do get a loot are multiple .xyz files. In these files the different images are just put one after the other without any extra new line or anything. Here are the first few lines from the optimisation “trajectory” for water as created by orca: 3 Coordinates from ORCA-job h2o E -76.051642020209 H 1.200000 0.000000 1.000000 H -1.200000 0.000000 1.000000 O 0.000000 0.000000 0.000000 3 Coordinates from ORCA-job h2o E -76.099647985008 H 1.102275 0.000000 0.980787 H -1.102275 0.000000 0.980787 O -0.000000 0.000000 0.038425 3 Coordinates from ORCA-job h2o E -76.150106142663 H 1.008335 0.000000 0.959926 H -1.008335 0.000000 0.959926 O 0.000000 0.000000 0.080147 Would it be possible to enhance the MolecularDynamicsViewr to accept such files? Thank you very much for your time and effort. Kind regards, Michael

2 2

displaying different segmentations together
by Jesse Hansen 01 Jun '23

01 Jun '23

dear all, I have segmented different parts of my tomogram using different software packages. One outputs an MRC file which I Can display as either volume or surface. The other is exported from Dragonfly and I am unable to figure out how to export MRC so I have tried STL and OBJ. STL/OBJ will display in ChimeraX, but then if I try to load in the other segmentation MRC then the STL/OBJ will disappear. I cannot view both simultaneously. If I hide the mrc and "view all" then I can view the object. Conversely, if I hide the object and "view all" I can see the MRC. Any help would be appreciated. Is there any way to convert obj/stl to an mrc? thanks! Jesse

2 1

Virus detected on Chimera X download
by Amy E. Kennedy 30 May '23

30 May '23

To whom it may concern: I downloaded the Windows executable from https://www.rbvi.ucsf.edu/chimerax/download.html this afternoon, and my antivirus software intercepted and neutralized a suspicious item when I opened the file. You may want to do a thorough check of your systems. Best, Amy Amy E. Kennedy (she/her) Doctoral Candidate, Mierke-Pellegrini Lab Biochemistry & Cell Biology, MCB, Guarini School of Graduate Studies PhD Innovation Fellow | E. E. Just Fellow

2 3

Can I use autodock vina
by NAGANO Kyogo 30 May '23

30 May '23

Hello. I started using the ChimeraX from today. And, I want to use the autodock vina with ChimeraX. In the case of Chimera, Tools→Surface/Bindind/Analysis→Autodock vina. But,in the case of ChimeraX, I couldn't find it. So, I want to know how to use Autodock in ChimeraX. Thank you.

2 1

Run Session Command Not Working
by Aashna Soni 30 May '23

30 May '23

Hi, I hope this email finds you well. I am trying to use the ChimeraX Python shell to run commands programmatically. When I try to run this command: run(session, "open <insert filepath>"), I am getting this error: "AttributeError: module 'chimerax.core.session' has no attribute 'models'." I have not written any import statements at the top (this is the first line in the Python shell). I am getting similar errors when I run any run(session, ...) command. Could you please help me resolve this issue? Thanks in advance. Warm regards, Aashna

2 1

ChimeraX server problems
by Tom Goddard 25 May '23

25 May '23

ChimeraX web services (BLAST protein, Modeller, sequence alignment) are currently down. Also ChimeraX bug reporting is down. We updated our servers last week (CentOS 7 to Rocky 8) and are working on restoring these services. Thanks for your patience. Tom

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chimerax-users mailing list 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

1 0

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

23 May '23

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

1 0

ChimeraX 1.5 Issue - Observations
by Ethan Crofut 22 May '23

22 May '23

Hello, I am Ethan Crofut, an undergraduate at UCLA and member of Professor Hong Zhou's lab. I wanted to comment on an issue brought up at the Stanford-SLAC Image Processing Workshop. I am using ChimeraX 1.5, but I have also experienced the issue where scrolling, panning, and zooming stop working in the middle of my session. In my experience, this issue is specific to Apple Macbook trackpads (as someone else commented, I haven't seen the same issue on Linux desktops). Here are my observations on the issue: - The problem can always be resolved by clicking on the ChimeraX window in which the 3D structures are being viewed. - A scroll, pan, and zoom functions are lost if I click on a separate ChimeraX window, such as the Log, an ISOLDE window, etc., but as stated above, I can rescue this by clicking on the main window again. This also occurs for windows that are embedded into the main window, as the Log usually is. - The scroll, pan, and zoom features are more likely to break right after I use a multi-fingered gesture on the trackpad, especially three fingered gestures. I think this may have to do with the Mac's three-fingered swipe shortcut. - Sometimes, some functions are lost but others are retained. I almost always retain the ability to rotate the model using the regular left click, but multi-fingered gestures, such as the zoom and panning options, break more frequently. I am not very technologically savvy, but my guess is that it is very easy for Macs to lose track of the main ChimeraX window being the currently active window, which causes the controls to stop working. For me, this is usually caused by using multi-fingered gestures or toggling between multiple different ChimeraX windows. Best, Ethan

2 1

symmetry axis
by Tianyang Liu (Staff) 22 May '23

22 May '23

Dear ChimeraX team, I have attached my cryo-EM map with C2 symmetry. The symmetry axis is shown with a yellow rod, not along the z-axis. How can I save a new map in ChimeraX with the symmetry axis along z? Many thanks, T

2 1

interfnal error toolshed
by steffen＠sthomas.de 19 May '23

19 May '23

3 4

Support pages are not reachable
by Lars Hangartner 18 May '23

18 May '23

To whom it may concern: There seems to be issues with your web servers, as several pages cannot be reached, e.g. <https://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Sc…> cgl.ucsf.edu<https://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Sc…> [X]<https://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Sc…> Best, Lars –––––––––––––––––––––––––––––––––– Lars Hangartner, PhD Associate Professor The Scripps Research Institute Department of Immunology & Microbiology - IMM2 10550 North Torrey Pines Road La Jolla CA, 92037 U.S.A. Phone: +1 (858) 784 9876 Cell: +1 (858) 952 2282

2 1

UCSF website
by Raneem Akel 18 May '23

18 May '23

Hello, I was trying to download ChimeraX but I’m getting an error saying that the website cannot be reached. Could you please advise. Thanks, Raneem

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Re: [chimerax-users] [Chimera-users] 3D_printing
by Elaine Meng 18 May '23

18 May '23

Dear François-Hugues Porée, In ChimeraX, there is no GUI tool but you can use the "cartoon style" command to increase ribbon (cartoon) width and thickness to specific angstrom values. For details see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> However, ChimeraX also has a "struts" command that will automatically increase ribbon thickness in addition to adding some stick pseudobonds specifically to make a 3D model stronger. So you may want to use "struts" instead : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/struts.html> Another thing to consider for 3D printing is the number of triangles of the object, which you can adjust with "graphics quality": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality> For ChimeraX questions in the future, you may want to use the other address chimerax-users(a)cgl.ucsf.edu (CC'd here) -- since the answers are different for the two programs, we try to not confuse people between them. 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. you may also be interested in the NIH 3D website: <https://3d.nih.gov/> > On May 15, 2023, at 6:58 AM, Francois-Hugues Poree via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > 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

4 3

'Tunnel' hydrophobic colouring
by Kelly May Frain 16 May '23

16 May '23

Hello, Previously you were super quick and helping when answering my ‘tunnel’ question, so I thought I could try another question for chimeraX. I have a protein which via Caver I have found a tunnel which runs through. This tunnel has been exported as a pdb and using your help and python, the tunnel now changes diameter perfectly as it weaves through the structure. I had this idea to colour the tunnel according its surrounding residues and their hydrophobicity. So in chimeraX I can colour my model ‘hydrophobically’ from cyan to gold. Then I wanted to 'zone’ these colours into my tunnel pdb. But when I use color zone #2 near #1 distance 20 for example, the tunnel is coloured in red and blue patches? Even though the model is cyan and gold. Is there a way to achieve my goal please? Best wishes, Kelly

2 1

Duplicate the model
by tim smith 15 May '23

15 May '23

Hello everybody, I would like to create copy of the model in the same session but with a different model number. Please, could you suggest how to do that. Thank you. Best Tim

2 3

rendering of bond making/breaking along a trajectory
by Hassan, Sergio (NIH/NIAID) [E] 15 May '23

15 May '23

Hi, I am not sure whether this is a bug or something not yet implemented or else. I performed QM/MM simulations of a proton translocating along a water chain. This involves the breaking of a bond and the making of a new bond. The visualization of the trajectory does not show this process; instead, the original definition of bond is retained, without being updated at each timeframe. Is there a way to tell ChimeraX to automatically check covalent bonds at each snapshot and update the bond accordingly? A simple distance criterion will do. This is only for rendering purpose. In case further clarifications are needed: D—H.......A (with -- indicating the covalent bond between proton and domor and .... indicating the proximal acceptor) must be transformed to D.......H—A. Instead, it is rendered as D-------H..A (with an artificially elongated DH bond and no new HA bond) thanks s _____________________________________ Sergio A. Hassan https://bioinformatics.niaid.nih.gov/cmm/ BCBB/NIAID/NIH/DHHS 301 761 7221 (office) 301 741 5579 (mobile)

2 3

Trajectory smoothing
by Shubham Devesh Ramgoolam 15 May '23

15 May '23

Hi all, Does chimeraX has a command for trajectory smoothing? Based on previous similar questions, I know a script was written for trajectory smoothing in chimera/chimeraX. However, I cannot not access this script because it is not found on the server anymore. Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

3 6

REMINDER: ChimeraX website downtime
by Elaine Meng 15 May '23

15 May '23

REMINDER: Due to a scheduled power outage at UCSF followed by server upgrades, the ChimeraX website and web services will be unavailable -- the estimated downtime is from Tuesday May 16 8pm PDT through Wednesday May 17 8pm PDT. Please pardon any inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Re: [chimerax-users] Measuring distance between two atoms in a single protein
by Cheng, Jiaxuan (NIH/VRC) [F] 14 May '23

14 May '23

Hi Elaine, I met a problem when measuring the distance between two atoms. I entered “distance #1.16/B:94 at CA #1.35/B:94 at CA” , but the ChimeraX reports “expected a keyword”. Could you let me know how to solve it? Thanks! Jiaxuan [cid:image001.png@01D98530.82126BB0]

2 2

Scrolling wheel feature request
by vincent Chaptal 12 May '23

12 May '23

Dear ChimeraX team, a very useful feature in Pymol is the use of the scrolling wheel on the mouse to clip the view plane and add depthcue. After centering on one element, it is very convenient to focus on some areas and remove things from the view, for both viewing and article figures. I haven't find a similar feature in ChimeraX, would it be possible to implement it? I've tried to play with the depthcue command, but it I find it much harder to get to what I would like. lighting depthcue true depthCueStart 0.3 depthCueEnd 0.5 If the view with the clipping can be saved with the "view matrix" command, it would be extremely useful. Thank you. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

2 1

Re: [chimerax-users] unifold
by Tom Goddard 11 May '23

11 May '23

3 5

coloring a clipped surface cap by property
by Elaine Meng 10 May '23

10 May '23

Hi Noam, Glad you like ChimeraX! (A) The way to color a clipped surface cap by the molecular liphilicity potential (MLP) or Coulombic electrostatic potential (ESP) is covered in this tutorial section: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#c…> (B) The way to color a clipped surface cap by an atomic or residue attribute is to: 1) color the underlying atoms by the atom or residue attribute (with command "color byattribute" or the Render by Attribute tool) 2) use command "color zone" on the surface cap model to make it match the atoms. You may need to use the disclosure triangles in the Models panel to figure out the model number of the surface cap model. Example: color zone #1.1.1 near #1 distance 3 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> Since "N" heads are better than one, we generally recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) unless you are including data or figures that should remain private. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2023, at 7:40 AM, Noam Prywes <noam.prywes(a)gmail.com> wrote: > > Dr. Meng, > > I'm a postdoc at berkeley and I'm trying to make a figure where I slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity. > > Do I need to make a .defattr file that colors by atom instead? > > Thanks for your help and the amazing service that is chimeraX. > > Best wishes, > Noam

3 5

Hiding distance labels during trajectory playback
by Lewandowski, Jozef 10 May '23

10 May '23

Hi, Is there an easy way to hide distance labels during the playback of an MD trajectory? Even if I delete or hide the labels in one frame they get generated when next frame is loaded. I tried to include hiding/deleting the labels command in perframe but they flash on before they are removed. Ultimately, I would like to record a movie where only the pseudobonds are shown but not the labels. Thank you, Józef

3 3

ChimeraX 1.6.1 release
by Eric Pettersen 10 May '23

10 May '23

UCSF ChimeraX version 1.6.1 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html <https://www.rbvi.ucsf.edu/chimerax/download.html> Updates since version 1.5 (Nov 2022) include: - ESMFold protein structure prediction and residue-residue error plot - Add Charge GUI - Dock Prep GUI to repair side chains, add hydrogens, etc. - Render by Attribute GUI for coloring by atomic or residue values - swapna command to mutate nucleic acid residues - invert chiral center - read SwissDock docking results - Blast Protein query sequence can be pasted in or specified by UniProt ID - browse/fetch medical images from The Cancer Imaging Archive - read medical images in NIfTI (.nii) and NRRD (.nnrd) formats For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> For those of you who downloaded plain 1.6 while it was briefly available, please upgrade to 1.6.1. It has several bug fixes that 1.6 should have had but didn't. --Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

Clipped surface coloring
by Noam Prywes 10 May '23

10 May '23

Hi all, I'm trying to make a figure where I slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity. Do I need to make a .defattr file that colors by atom instead? Best wishes, Noam [image: Screenshot 2023-05-10 at 7.42.14 AM.png]

1 0

Question in using ChimeraX ----mesh parameters
by Wang, Shuhui 09 May '23

09 May '23

Hello developers, I have a question in using ChimeraX. May I ask how can I change the density of grids and line size of the mesh for a volume? Best, Shuhui

3 3

Re: [chimerax-users] [Chimera-users] Utilizing Chimera in Web-Based Workflows
by Tom Goddard 09 May '23

09 May '23

Hi Rafi, You could have a Google Colab notebook install ChimeraX and then you could run ChimeraX command in nogui mode or python code through the ChimeraX REST facility, and possibly save images of the graphics to show in the notebook. But I don’t grasp the value of it since ChimeraX is all about interactive visualization where you can rotate and inspect structures. One issue you will face is that ChimeraX cannot be installed without agreeing to a license when dowloading - not sure how you might handle that in a notebook. But I suggest figuring out the valuable use case first. Tom > On Apr 21, 2023, at 5:28 AM, Zach Pearson via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Rafi, > > We are working hard to fully deprecate Chimera, and haven’t made its source code accessible for use or extension outside of the desktop application. I would caution against looking for it; the compilation process is complex and depends on resources that may not even be available anymore. Chimera was also written in Python 2.7, a language the computing community is working hard to put to rest — Colab doesn’t support it anymore! > > We do have plans to release a substantial part of ChimeraX on PyPi this year as a public beta, and I’ll make a note to send you an email when that release happens. Then you should be able to use it in Colab like any other PyPi package. Let me know if I can answer any other questions you may have. > > ------------------- > Zach Pearson > Programmer, ChimeraX Team > UCSF RBVI > zjp(a)cgl.ucsf.edu > > > >> On Apr 20, 2023, at 13:44, Rafi Brent via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >> >> 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 >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

3 3

request for an example command line
by James Raymond 09 May '23

09 May '23

I am having trouble understanding the manual. I wish to show the side chain for a particular amino acid in my protein. What is the command line to do this? thank you James Raymond

3 12

Failing to complete dimer prediction
by Tal Jeffrey 09 May '23

09 May '23

Dear all, I am trying to use ChimeraX to predict the structure of a dimer as part of my Master’s thesis. I was able to produce a model of the monomeric structure without issue have not been able to do the same for the dimer. I am currently subscribed to Colab Pro so had assumed that the 15.0GB GPU RAM would be sufficient. The structure is 1361 amino acids long but AlphaFold2 is still able to produce the first two models successfully. However, I have not been able to produce any iterations past this stage. Any guidance on how to complete the model would be much appreciated! Alternatively, I would also be glad to extract the output of the first two models (e.g. .pdb files, plDDT plots, PAE plots, MSA heatmaps) but because the prediction does not run to completion I don’t know how to access/extract these. I have really enjoyed using the program and hope to include the structure of the dimer in my thesis before I submit in three weeks’ time. Many thanks, Tal

3 4

Map Comparisons vs Model Comparisons: Which represents differences more accurately?
by Kevin Felt 09 May '23

09 May '23

Dear Chimerax Developers, There is a debate in my lab about the best way to compare two PDBs of the same protein bound to different ligands; the goal is to identify subtle differences in the binding pocket between the ligand-bound conditions. One method of comparison is to fit the two density maps together using the FitMap function, and then fit each PDB into their respective maps which have been aligned. Another way is to simply align the two PDBs (such as the align function in Pymol). Using these two methods results in slightly different alignments of the PDBs and thus give slightly different positional differences of the binding pocket and ligands. The resolution of these density maps range from 2.4 - 3.5 angstroms. Which way would be the more accurate way to look at the differences between two similar models? Thank you! Sincerely, -- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University

3 2

pae plot
by John Maximos [Pharma] 09 May '23

09 May '23

Dear Chimerax Team, I have a problem that the pae plot color is not adjusted like the green one. How to solve this problem? I attached here a screenshot from my laptop. Best Regards, John Maximos [cid:image003.png@01D9827F.FEF05100] www.evapharma.com<https://www.evapharma.com/>

2 1

making movie of helical Assembly
by mailman-bounces＠cgl.ucsf.edu 08 May '23

08 May '23

From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> Subject: making movie of helical Assembly Date: May 7, 2023 at 11:53:16 PM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Dear All, I am trying to make a movie where I can show the atomic model of the subunits appearing one after another following the helical pattern forming the filament. How can I do that? Stay safe & Regards Anindito Sen. Ph.D <>

2 1

cannot open chimerax with structureviz (using ChimeraX 1.5 and cytoscape 3.9.1)
by ora.furman-schueler＠mail.huji.ac.il 07 May '23

07 May '23

Dear Support team We are teaching a network course and would like to show an example of analysis of proteins as networks. I have tried to follow the structureviz2 tutorial but I cannot get past the very first step of linking ChimeraX to cytoscape. I did define the Chimera location path /Applications/ChimeraX-1.5.app/Contents/MacOS What am I doing wrong? This is the error message that I get in cytocape. Launching Chimera  Launching Chimera ...  UCSF Chimera could not be launched. Make sure that the correct path to Chimera is set in structureViz -> Settings… thank you for your help! Ora Prof. Ora Schueler-Furman Dept. of Microbiology and Molecular Genetics, IMRIC Jacob Epstein Chair in Bacteriology Hebrew University, Hadassah Medical School POB 12272, Jerusalem 91120 Israel Tel: 972-2-675-7094 FAX: 972-2-675-7308 Furman lab site: www.cs.huji.ac.il/~fora

3 3

Question on Contacts and Distances Tools
by Haleh Shahbazi 05 May '23

05 May '23

Hello, I am using ChimeraX under “version 1.6rc202304182023 (2023-04-18)” and contacting you regarding contacts and distances tools I am working on analyzing biological assembly PDB files including two chains. Simply, I want to identify / calculate distance between residues within each chain and across two chains separately – In the other word, display interchain and intrachain residue distance. To get that done, I’ve already explored “Distances” and “Contacts” tools under “Structure Analysis” but I have difficulty with identifying interchain residue distances and also understanding all those features / options provided. Thanks in advance for your support! Haleh HALEH SHAHBAZI PHD STUDENT @GARTON LAB • she/her • [Personal/Lab LinkedIn] <https://www.linkedin.com/in/haleh-shahbazi> IBME, University of Toronto haleh.shahbazi(a)mail.utoronto.ca<mailto:haleh.shahbazi@mail.utoronto.ca> www.gartonlab.org<http://www.gartonlab.org/> • bme.utoronto.ca<https://bme.utoronto.ca> • [LinkedIn] <https://www.linkedin.com/school/bme-uoft> [Twitter] <https://twitter.com/bme_uoft> [Instagram] <https://www.instagram.com/bme_uoft/> [signature_283494549]<https://bme.utoronto.ca/>

2 1

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 ChimeraX website and web services will be unavailable from Tuesday May 16 through most of Wednesday May 17. Please pardon any inconvenience, --Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

Re: [chimerax-users] Merging and covalently joining two pdb's together in chimeraX
by Elaine Meng 04 May '23

04 May '23

Hi Rayees, For the best chance at getting a good answer, we recommend sending ChimeraX questions to the chimerax-users list (CC'd here) unless you are including private data. If the two models are already positioned appropriately to form the bond, you could first combine them into a single model and then add a bond (e.g. "bond" command or Build Structure tool, Adjust Bonds section). <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> However, if you didn't necessarily put the models in the right place to form the bond, you can use "build join" which will include all of the following: moving one model to the appropriate position to form the bond, combining the models into one, and forming the bond. You cannot use "build join" if the models are already combined or if you don't want the models to move relative to each other. There is also a graphical interface to "build join," which is the Build Structure tool, Join Models section. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#join> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> You can open the Build Structure from the menu under Tools... Structure Editing. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> I don't know much about refinement, but sounds like you should take a look at the ISOLDE plugin for ChimeraX. <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde> <https://isolde.cimr.cam.ac.uk/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 4, 2023, at 11:24 AM, Rayees Mattoo <rmattoo(a)stanford.edu> wrote: > > Hi Elaine, > I am trying to merge two models (say #1 and #2) and join the two models with a covalent bond at amino acid residue number say 240 (#1)and 241 (#2). I first combined the two models (#1 and #2) using combine command. However, when I use build join command it does not seem to work. Is there a better way to covalently join two models in chimeraX? > > Also, is there a way to refine models in chimeraX like Real Space refine in Coot? > > Thanks > > Rayees

1 0

Info on ChimeraX
by Fabrizio Fierro 04 May '23

04 May '23

Hi, I work for a startup called Protai and I am interested in ChimeraX. 1) Are all the functions available in Chimera implemented also in ChimeraX? 2) Specifically, with Chimera it was easy to load, visualize and work with cryoEM maps. Does ChimeraX work in the same way? 3) Would it be possible to get a free trial period for ChimeraX? Thanks, Fabrizio Fierro.

2 2

Installing other python packages in chimeraX
by Shubham Devesh Ramgoolam 03 May '23

03 May '23

Dear ChimeraX team, I have some python scripts for performing computation using chimeraX in the nogui mode. Those scripts rely on packages not available in the python environment of chimeraX and I installed them using: ChimeraX-console.exe -m pip install add_package --user I intend to distribute my scripts to other users and they will also need to install these packages. As such, I have written another python script to automate the installation of these packages (the path to ChimeraX-console.exe (if Windows) or ChimeraX.exe (if Mac) must be supplied in a text file for this to work). The heart of the automation script is as follows: for item in list_packages: subprocess.call([path_chimeraX, '-m', 'pip', 'install', item, '--user']) Is this approach of installing python modules in chimeraX valid, considering that different users may have a different environment for their chimeraX? (I am worried that pip install might not work on some setups.) Regards, Shubham Ramgoolam Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

3 2

Question about viewing chain pdb in ChimeraX
by Thu Nguyen 02 May '23

02 May '23

Hello, I am using ChimeraX to save the .pdb file of chains in a protein. Here are my commands: +) open 7oci +) select #1/E + save /.../E.pdb model #1 selectedOnly true Then I opened that E.pdb model in ChimeraX and saw that chain E only contains helices. However, when I checked the .pdb file of chain E in a text editor, I saw that it contains sheets as well. The number of sheets are even larger (Number of helices: 52, sheets: 76). Do you know the reason why I don't see the sheets of chain E in ChimeraX? Am I missing something? I have attached the screenshots and the pdb of chain E. I took this chain from the pdb ID 7oci. Thank you very much. I am looking forward to hearing from you. Best regards, Thu

2 2

Virtual Crash Course - Understanding PDBx/mmCIF | Tomorrow, May 3rd | REGISTER NOW!
by Brian Hudson 02 May '23

02 May '23

Virtual Crash Course The RCSB Protein Data Bank will provide a course, "Use PDB data to their full extent: Understanding PDBx/mmCIF" on Wednesday, May 3rd 2023 from 1:00-3:00 EDT Understand the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined three-dimensional biostructures in the PDB. Learn about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data. The program: https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-cras… Free registration: https://go.rutgers.edu/u3vpwjet If you have questions, please contact Michelle Sanghera: msanghera(a)iqb.rutgers.edu

1 0

Plugin development: how to install python packages
by BARRY E DEZONIA 01 May '23

01 May '23

Hello, I am developing a chimerax plugin. My code will have some interaction with mdtraj. I need mdtraj to be installed in the python that ships with chimerax. I tried "chimerax -m pip install mdtraj" but I get all kinds of error dialogs popping up in the chimerax instance that gets launched during the installation. I terminate all the error dialogs and then exit chimerax (as the python install seems frozen) and then it indeed says installation has failed and gives unusual error messages (like setuptools was less than version 48.0.0 while chimerax reports it to be 65.x.y and even 66.x.y after upgrading). Can someone tell me the correct syntax to use to install mdtraj in chimerax's python? Thank you.

3 6

How to update the bonding status every frame when viewing a molecular dynamic trajectory?
by 洪冉 30 Apr '23

30 Apr '23

Dear users and developers of ChimeraX, Recently I want to produce some decent movies of a molecular dynamic trajectory, I loaded the pdb file and the trr file into ChimeraX. Everything goes well until some bond broken occurred, the display became very strange since the bond was stretched to an unreasonable length. I have been told a solution by using ~bond, bond #1 to fix the issues. However, it is impossible to do it at every frame when you have to record a movie and your trajectory was with thousands of frames. Thus, I ask for help, is there a solution to update the bonding status of every frame automatically? Yours, Ran

2 2

How to install the "SEQCROW bundle" plug-in for xyz file in ChimeraX1.5?
by 洪冉 28 Apr '23

28 Apr '23

Dear ChimeraX Developers and Users, I want to view some quantum chemical results from ORCA calculation, and information popped up from ChimeraX telling me that I must install a plug-in called "SEQCROW bundle" for this purpose. However, due to some well-known reasons, I can not fetch this plug-in with the built-in method 'Tools-More Tools'. I think I have to do it in a manual way. Could anyone send me a related file to install this plug-in with a guide showing me how to do it in a manual way. Thanks in advance. Yours, Ran Apri 28 2023

2 1

Python scripts while running MD
by Rafael Rocha 26 Apr '23

26 Apr '23

Dear chimera users! During a molecular dynamics simulation, I would like to run a python script that triggers a specific command once the simulation has reached a certain number of steps or a specific amount of time. I was able to programmatically start, pause, continue and stop a simulation using a primary Isolde object. However, it appears that the script is not waiting until the maximum number of MD steps is reached before moving on to the next command. I've tried using the sleep() python command, but unfortunately, this causes chimeraX to get stuck and unresponsive until the script is finished sleeping. Do you have any suggestions for how I can achieve this without causing chimeraX to freeze up? Thank you for your help! -- Rafael E. O. Rocha, Ph. D. Department of Biological Sciences Federal University of Minas Gerais.

2 1

Manual Averaging Enquiry
by Lenka Milojevic 24 Apr '23

24 Apr '23

Hello! I'd appreciate it if you could detail how manual averaging of multiple .mrc maps can be done in ChimeraX. Thank you for your time. Sincerely, Lenka

2 1

Enquires about predicting protein interaction with chimeraX/AlphaFold
by Yiling Lan 21 Apr '23

21 Apr '23

Dear ChimeraX Developers, Hope this email finds you well. I'm currently trying to predict the interaction of 2 proteins after watching the videos on youtube (Running AlphaFold to Predict Protein Complexes from ChimeraX). after installing the CimeraX (UCSF ChimeraX version: 1.6rc202304140213 (2023-04-14) version) but I did not see the check box for "Is prokaryotes? used for predicting complex). May I ask if in newer version the check box for complex prediction is at somewhere else? If it does not bother too much, could you please let me know if there is anyway I can run complex prediction on 1.6rc? Thank you so much. Best Wishes Yiling Lan

2 4

Tunnel visualisation
by Kelly May Frain 20 Apr '23

20 Apr '23

Hello, I am using ChimeraX to visualise a tunnel found in my membrane protein using caver. I can put together the protein pdb and tunnel pdb perfectly. However, crucial to the figure is how the tunnel has a different radius throughout. In PyMol I can see this, but when I set the tunnel to sphere in chimeraX, it’s continuously the same diameter. I can change the colouring to b-factor and here it acknowledges the atom b factor range of 0.8 - 4-8 but I want to visualise the differences. Please can someone help me with a command? BW, Kelly

3 4

Hopefully simple plugin development question
by BARRY E DEZONIA 19 Apr '23

19 Apr '23

Hello, I am looking at writing a plugin for chimerax that takes a pdb and runs some python code that will calc some stuff hand stuff to other programs. I know how to do this. What I want to know is how to find the current model's name / associated pdb filename from my plugin. Imagine my plugin really is just a "Run" button that looks up the current model, generates the associated pdb filename, and passes that name to my python script. Can someone tell me how in a chimerax plugin I can make the call that will give me the pdb filename I want? I've read much of the developer docs and could not find what I was looking for.

4 6

Unable to select individual glycans in ChimeraX
by Coillie, Julie van 19 Apr '23

19 Apr '23

Dear ChimeraX, Is there any way to select one individual glycan on a crystal structure? The crystal structures I'm working with have multiple domains, each with glycans. I want to annotate the glycan per domain (every domain & glycan in a specific color). However, I can't edit individual glycan structures. The glycans are grouped under Non-standard residues, e.g. MAN, NAG, ... However, when selecting e.g. MAN, all the MAN structures light up, which are found on all 3 domains. An alternative would be using the sequence and annotating each individual sugar by using "select". However, these Non-standard residues are not in the sequence (they are when uploading this in Pymol), so I don't know a position to select them on. Is there a way to find the "sequence" for non-standard residues or any other way to annotate an individual glycan. Thank you in advance, Julie Van Coillie ________________________________ Disclaimer: http://www.sanquin.nl/e-maildisclaimer ________________________________

2 2

Command use
by Wojciech Witek 19 Apr '23

19 Apr '23

Dear ChimeraX Team, I am trying to change this mesh properites because it covers the ligand too much (attachment). I wanted to make the lines thinner or transparent or divided in different ways. I could not find anything in the GUI so I searched for commands but apparently I use them wrong. Could you please guide me on how to use commands, let's say like this one : surfaceSmoothing true | false? If I type "true", I see an error in the log file. Where can I find what arguments should be use with a specific function?I had the same struggle with depth cueing, ribbon style edition and many other functions. ChimeraX is a great software but using GUI is so much easier to get familiar with, learn and utilize changes, comparing to command line. See attached file containing ligand, mesh and a log full of errors from pasted commands. Please, keep it confident because it is unpublished yet. Regards, Wojciech Witek -- Logo *Wojciech Witek* *| PhD Student Department of Structural Biology of Eukaryotes* Institute of Bioorganic Chemistry, Polish Academy of Sciences Noskowskiego 12/14 | 61-704, Poznań *email:*wwitek@ibch.poznan.pl *tel.:*61 852 85 03 *int.:*1347 **** ** facebook <https://www.facebook.com/ICHBPAN> twitter <https://twitter.com/ICHBPAN> instagram <instagram.com/ichbpan> WWW <https://portal.ichb.pl/>

2 1

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

1 0

Permission denied to "Spin Movie"
by Pam Cook 17 Apr '23

17 Apr '23

Hi, I just installed ChimeraX on macOS Catalina 10.15.7. During installation, it asked me to allow access to desktop files and I said NO. But now, when I try to create a SpinMovie file, I get the message: Permission denied reading directory "/Users/pam/Desktop" while trying to determine next unused file name movie#.mp4. I guess I should have said YES to the question above. How can I fix this? Thanks, Pam

2 1

Question about using ChimeraX
by 韩磊 17 Apr '23

17 Apr '23

Dear Sir， I hope this mail finds you well. I am a professional researcher from Tianjin Medical University, China. I have encountered some difficulties in learning to use ChimeraX software. First, I would like to know if the software can be used to construct a graph of the process of channeling proteins from closed to open state (e.g., Appendix ). Second, we can currently only download and import a model of the closed state of a protein into the software, but it does not reflect its conformational changes, so I would like to know which option within the software can change the conformation of the protein. Sincerely yours, Lei Han, Ph.D. Tianjin Neurological Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China

2 1

Could you please inform the best advice to solve a structure via colabfold when GPU is an issue? I tried some routes already.
by Josh Gutierrez 14 Apr '23

14 Apr '23

Hello, I recently submitted a job through ChimeriaX and used the "prediction" task for it to be solved via Alphafold2-- the sequence is about 1300 amino acids in length. However, the protein could not be solved by alphafold2 and the colabfold reports the GPU consumption is too high for the structure to be solved. To resolve the problem, I tried breaking the sequence into two to solve this expected bimodal protein individually (into two separate structural parts) and even in combination purchased "compute units" for more memory and storage to do this, but the structure can't be solved without high predicted error. Please let me know what you think may resolve this issue. Currently, I am working with an external professor who may be able to connect me with a collaborator on this issue at UCSF if there is a cluster or core we can use to expedite the process to solve this structure I am addressing. Please let me know your thoughts at your earliest convenience. Please also let me know if you need any more information! Many thanks, Josh Gutierrez

3 4

Measure inertia and measure center on aligned density maps and models
by Kevin Felt 13 Apr '23

13 Apr '23

Dear developers, I am trying to compare the center of mass of multiple cryo-EM maps and models. The receptor is the same in all cases, just the ligand bound in the binding pocket varies. I want to show a directionality to how the ligands are binding in the pocket between the structures, so I have aligned the maps and models together and am attempting to run "measure center" and "measure inertia" to initiate this comparison. However, when I run these commands, the output markers and ellipsoids are not positioned in an aligned fashion as their parent objects, but rather in there initial positions before alignment, which is not useful for comparisons of the subtle movements between structures. Additionally, if I could get the measurements to work on the aligned structures, is there a tool in ChimeraX that would allow me to draw vectors from a reference point to the center of masses? Furthermore, is center of mass the correct parameter for comparison of densities that are variable in shape? (e.g. comparing the relative position of a long and flat density to a short a globular density?) Thank you! Sincerely, -- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University

3 2

Modeling post-translational modifications
by Guillaume Gaullier 13 Apr '23

13 Apr '23

Hello chimerax-users, I am trying to model a PTM, and the most sensible way to me seems to use the swapaa command and specify the sensible monomer from the PDB Chemical Component Dictionary as the target residue. Here is what I tried (residue #1/a:9 is a Lys): open 1kx5 swapaa #1/a:9 KCX And the error I got: Dynameomics rotamer library does not support KCX I tried all the rotamer libraries listed in the swapaa help page ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/swapaa.html#rotLib ), but none of them can provide stereochemical info for KCX. I can open the monomer I want (carbamylated Lys) with: open ccd:KCX But of course in this case it’s floating by itself as a new model, not incorporated in the protein sequence and structure I am interested in. Is this the correct way to model a PTM? If it is, where can I find a rotamer library that will contain the stereochemical info for KCX, and how do I tell ChimeraX to use it? If it is not how modelling a PTM is done, then how else should I do this? Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 5

unifold
by Roger Leng 12 Apr '23

12 Apr '23

Dear Administrators, Is it possible to add "unifold" in your prediction, just like Alphafold? Thank you. Sincerely, Roger Leng

2 3

Problem Installing ChimeraX
by Stephen P. Molnar 12 Apr '23

12 Apr '23

I am running an up-to-date installation of Debian Bullseye on my Linux platform. My attempt to install ucsf-chimerax_1.5ubuntu20.04_amd64.deb generated an interesting error message: sudo apt install ucsf-chimerax_1.5ubuntu20.04_amd64.deb [sudo] password for comp: Reading package lists... Done Building dependency tree... Done Reading state information... Done E: Unable to locate package ucsf-chimerax_1.5ubuntu20.04_amd64.deb I have managed to install Chimera, both Linux and Windows versions, many times without any problems. Guidance would be much appreciated. Thanks in advance, -- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

3 4

ChimeraX Python Shell Errors
by Aashna Soni 10 Apr '23

10 Apr '23

Hi, I hope this email finds you well. I am trying to use the ChimeraX Python shell to run commands programmatically (such as opening different protein structures, extracting the number of hydrogen bonds from a structure, changing the sel number, and saving the log file). When I try to run this command: run(session, "open <insert filepath>"), I am getting this error: "AttributeError: module 'chimerax.core.session' has no attribute 'ui'." I am getting similar errors when I run any run(session, ...) command, such as the first one on this tutorial: https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/introduction.html. These commands were working around a month ago, and I am not sure why they are not working now. Could you please help me resolve this issue? Thanks in advance. Warm regards, Aashna

2 1

Re: [chimerax-users] [Chimera-users] Chimera cannot read multi-molecules .xyz files in
by Elaine Meng 07 Apr '23

07 Apr '23

Hi Francois, I'm told that although ChimeraX itself does not read XYZ files, you can add that capability by installing the SeqCrow plugin. ChimeraX menu: Tools... More Tools wil show the Toolshed website in the ChimeraX browser, in which you can find SeqCrow and install if it you like. Here is the URL where you can see information about SeqCrow, but to install, it is more convenient to use the ChimeraX menu and browser as mentioned above. <https://cxtoolshed.rbvi.ucsf.edu/apps/seqcrow> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 6, 2023, at 9:40 PM, Francois Berenger via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Apparently, chimerax cannot even open a single-molecule .xyz file ?! > > ---------- Forwarded message --------- > From: Francois Berenger <berenger(a)edu.k.u-tokyo.ac.jp> > Date: Fri, Apr 7, 2023 at 1:09 PM > Subject: Chimera cannot read multi-molecules .xyz files in > To: <chimera-users(a)cgl.ucsf.edu> > > > 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. > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

1 0

REQUEST: Vendor Voluntary Product Accessibility Template (VPAT) or Accessibility Conformance Report (ACR) - UCSF Chimerax Software
by Powers, Gina 07 Apr '23

07 Apr '23

Good Morning, I am requesting a copy of the Vendor Voluntary Product Accessibility Template (VPAT) or Accessibility Conformance Report (ACR) for review regarding UCSF Chimerax Software for a user. Gina Powers | Program Analyst Division of Regulatory Science Informatics | CTP-OS | FDA Accelerate the transition to a healthier America Office: (240) 402-3188 Email: Gina.Powers(a)fda.hhs.gov<mailto:Gina.Powers@fda.hhs.gov> CSC Email: CTP-OS-CSC(a)fda.hhs.gov<mailto:CTP-OS-CSC@fda.hhs.gov> Have a CSC question? Feel free to send it to OSCAR<https://oscar.fda.gov/> - the 24/7 CSC chatbot! [cid:image004.png@01D96936.F819C850][cid:image003.png@01D96936.F30B6120] Division of Regulatory Science Informatics

2 1

Multichain comparative modelling
by Prof. Dr. Kay-Eberhard Gottschalk 06 Apr '23

06 Apr '23

Hi There, I am interested in a complex formed by a protein with two domains connected by a long loop in complex with a second Protein, that binds this loop, causing it to form a short helix. I have two pdb stuctures: One with the two domains in the correct relative domain orientation, connected by an unstructured loop, and one with the part of the loop forming a helix in complex with a second Protein. I am sure that comparative modelling can do the trick, but somehow I dont understand the workflow. Do I need do load both templates into chimeraX, oben sequence file conatining both Proteins and load that also, if so in which format? I went over the Manual, but somehow it is not clear to me. Thanks a lot for your help! Best, Kay

4 6

About displaying electron density maps (MTZ format) in chimerax
by Laurent 05 Apr '23

05 Apr '23

Hi, I am currently trying to display an electron density map (from a MTZ file) in ChimeraX, but it seems that the display box size is limited. I would like to display the maps around ligands in an oligomeric protein, where the ligands are quite far from each other. Is there any way to increase the box size of the displayed map so that it covers all ligands ? Thanks ! Laurent Laurent Maveyraud Professor of Biophysics | University of Toulouse | Structural Biophysics Team Doctoral School Biology - Health - Biotechnologies +33 5 61 17 54 35 | +33 6 46 04 21 11 | Laurent.Maveyraud(a)ipbs.fr <mailto:Laurent.maveyraud@ipbs.fr> | L. Maveyraud <https://fr.linkedin.com/in/laurent-maveyraud-8b394a5> | L. Maveyraud <https://orcid.org/0000-0003-4610-8319> UMR5089 | CNRS - UT3 | 205 Route de Narbonne BP 64182 - 31077 Toulouse Cedex 4 ipbs.fr <https://www.ipbs.fr/>| Team Website <https://www.ipbs.fr/structural-biophysics>| pict.ipbs.fr <https://cribligand.ipbs.fr/> @IpbsToulouse <https://twitter.com/IpbsToulouse> ipbs.cnrs <https://www.facebook.com/IPBS.CNRS/>

3 3

Virtual Crash Course - Understanding PDBx/mmCIF | May 3rd | REGISTER NOW!
by Brian Hudson 04 Apr '23

04 Apr '23

Virtual Crash Course The RCSB Protein Data Bank will provide a course, "Use PDB data to their full extent: Understanding PDBx/mmCIF" on Wednesday, May 3rd 2023 from 1:00-3:00 EDT. Understand the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined three-dimensional biostructures in the PDB. Learn about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data. The program: https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-cras… Free registration: https://go.rutgers.edu/u3vpwjet If you have questions, please contact Michelle Sanghera: msanghera(a)iqb.rutgers.edu

1 0

AlphaFold best_model.pdb could not visually overlap the input sequence using matchmaker
by Cheng Fei Phung 30 Mar '23

30 Mar '23

Hi, I am trying do "matchmaker #2 to #1" between colab output ( best_model.pdb which is pasted here at http://ix.io/4rRO ) and https://www.rcsb.org/structure/7CR5 However, as seen in https://i.imgur.com/gHL8to3.png , there is not really much visual overlapping since the structures are not rotated properly to match each other. The log for doing matchmaker command is available here at https://i.imgur.com/78h5CLq.png The colab notebook is also saved as a screenshot here at https://i.imgur.com/LSTdyZe.png Manually doing "turn z 1 270 model #1 center #1" or similar rotations commands also do not help. Please advise. Regards, Phung Cheng Fei

3 12

question about chimerax
by 12119007 30 Mar '23

30 Mar '23

3 6

MICROTUBULE AND SYM COMMAND
by Aleck Dwyer 29 Mar '23

29 Mar '23

Hi, I am trying to model a microtubule Cryo-EM map (my first time).in Chimera I was following the example https://www.cgl.ucsf.edu/chimera/videodoc/MicrotubuleSym/index.html I was able to do the example but when using my data I see issues. The spacing is way off. If anyone has modeled a microtubule in Chimera and/or ChimeraX please let me know.. Thanks, Aleck [image: image.png] <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free.www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

MICROTUBULE AND SYM COMMAND
by Victor Dwyer 29 Mar '23

29 Mar '23

Hi, I am trying to model a microtubule Cryo-EM map (my first time).in Chimera I was following the example https://www.cgl.ucsf.edu/chimera/videodoc/MicrotubuleSym/index.html I was able to do the example but when using my data I see issues. The spacing is way off. If anyone has modeled a microtubule in Chimera and/or ChimeraX please let me know.. Thanks, Aleck [image.png] ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Re: [chimerax-users] Removing unwanted models from the chimerax panel
by Elaine Meng 29 Mar '23

29 Mar '23

Hi Boaz, I don't know what .ctx files are. At first I thought you meant open models in the Models Panel, but I am pretty sure that you already know how to close models. However, my coworker suggests that you actually meant the previously opened files and thumbnails in the File History or Rapid Access panel. If the files no longer exist, you can easily clear them by using the context menu in that tool (File History or Rapid Access), shown with right-click (or on a Mac with trackpad or single button mouse, Ctrl-click): Remove deleted files <https://rbvi.ucsf.edu/chimerax/docs/user/tools/filehistory.html> However, if the files still exist but you don't want to see them in this tool, you would need to delete the specific preferences file that has the file history. The File History help link above says how to figure out what directory on your system contains this file, which is named file_history I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 25, 2023, at 2:25 PM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi, > Excuse the trivial question: I am experimenting with various options and end up filling the panel of sessions with unwanted models. Do I have to delete the .ctx file of the session from outside Chimerax to make it disappear from the panel or is there a way to do this from within the program (i.e. the equivalent of of the Edit option in chimera)? I couldn't find such an option in the 'help' or documentation. Sorry. > Thanks, > > Boaz

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Coloring H bonds black
by McClean, Phillip 28 Mar '23

28 Mar '23

Hi Everyone, I am developing a publication image that shows the hydrogen bonds between two chains. How can I ensure that the dashed lines that show the H+ is displayed in black. From the papers I see in refereed publications, black seems to be the color of dashed lines showing these bonds. Thanks for any help Phil McClean

2 1

Values at atom positions
by Gőcze Máté 27 Mar '23

27 Mar '23

Hello, I have an issue with saving values at atom positions from the command line. I can attach the attributes to the atoms but when i use: save filename attrName a:mapvalue format defattr matchMode 1-to-1 I get: One or more attribute values aren't integer, floating-point, string or None (e.g. 3.8542745); skipping those Saved attribute 'mapvalue' of 0 atoms using match mode: 1-to-1 to filename can you please help me resolve the issue. I have tried reformatting the headers of my map but it didn't help. Thank you for your help.

2 1

Changing line thickness of individual selections
by Raulf, Karoline 27 Mar '23

27 Mar '23

Hi everyone, I have a question about the graphical representation of my model in ChimeraX. Here, I have colored individual proteins and to make them even more visible, I would like to increase the line thickness of the silhouette of these proteins. But when I try this with the combination of the keyword graphic silhouette and sel, I don't get anywhere. Is there any way to change the line thickness of individual selections without changing the line thickness of the silhouette of the entire model? Thanks in advance for the help! Best Karoline

2 1

commandline to change the step and threshold of all the maps
by Rayees Mattoo 23 Mar '23

23 Mar '23

Hi, If there is one, could you please share the command lines for changing the step and threshhold of all or the selected maps in chimeraX. Best

2 1

Integrating Vina into ChimeraX
by Andy Tong 22 Mar '23

22 Mar '23

Hi, So I recently began using ChimeraX on my Windows PC and I'm stuck on how to integrate Vina into ChimeraX. I know that it's no longer automatically included in ChimeraX so I downloaded it separately, but where do I need to insert Vina's files for it to show up in the "tools" section under binding analysis, or how can I add a command to run Vina through Chimera? Thanks

2 1

Right click bond rotation help
by Raneem Akel 16 Mar '23

16 Mar '23

Hello, I am trying to adjust some bonds in my protein model, however, I want to also be able to control which segment of the protein I’m rotating (i.e. C-terminus vs N-terminus). Is there a way to do that? I’m using ChimeraX 1.5 on Mac. Thank you! Raneem

2 1

Importing pdb structures from OPM
by Prathvi Singh 15 Mar '23

15 Mar '23

Hi Elaine, I was wondering where it is possible to use the "open" command to import PDB structures of membrane proteins from OPM. I see in: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#fetch that we can fetch data from various sources but OPM was not listed there. If this were possible, we could directly import membrane protein structures from OPM which have dummy residues that can be used to define membrane boundaries via the *define plane *command. Thank you -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Re: [chimerax-users] [Chimera-users] Selecting planes using command line
by Elaine Meng 13 Mar '23

13 Mar '23

Hi Prathvi, I believe you would have to use ChimeraX to do this, not Chimera. So this answer is for ChimeraX only: You can select the plane models with Ctrl-click in the graphics window, or you can use the selection checkboxes in the Axes/Planes/Centroids tool (ChimeraX) or in the Model Panel, where you may need to use the disclosure triangles to see the submodels and their numbers. Or you can just look in the Model Panel to find out the number to specify that model directly in commands without using selection. You can move them separately from other models in the same was as any other models in ChimeraX. I.e. with "models" keyword of move/turn commands, or with mouse modes that move only the selected and/or clicked models. <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004945.html> Of course, if you do this with the planes defined from the membrane "atoms" from the OPM database, you are no longer using their predicted membrane locations. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 13, 2023, at 5:24 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > 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 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Possible to read a trajectory "lazily" or in the background?
by Ben Webb 13 Mar '23

13 Mar '23

Am I right in thinking that when reading a trajectory (e.g. .dcd file), all requested frames from that trajectory are first read in, after which the "coordset" command can be used to work with the trajectory? I am reading frames from an RMF file (using the RMF plugin, the "rmf readtraj" command) which is quite slow, perhaps a second per frame - because RMF stores local coordinates which must be transformed to make the global coordinates ChimeraX is using. So if the user asks to read 100 frames, ChimeraX becomes unresponsive for ~100s, which is not a great user experience. One possible solution would be to read the 100 frames "lazily", e.g. just create 100 copies of the active coordset, then when the user writes "coordset #1 N" for the first time or scrolls to frame N with "coordset slider", read in frame N from the RMF file and overwrite coordset N. That way there would be a 1s delay only the first time that frame is shown. Is this possible? I see there is an "active coordset changed" trigger - perhaps I could attach to that? Alternatively, is there an API for tools to run long-running processes in the background so that the user can work on other things in the meantime, or cancel it if it takes too long? Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Interface residue plot.
by Amber Smith 10 Mar '23

10 Mar '23

I want to save the 2D image of the residue plot (the gray circles with the interacting residues outlined and numbered by residue number). When I left click I can see the menu but save plot as is not an option. Is there a way for me to save that window as an image? -- ammariesmith(a)gmail.com Amber.Smith(a)ucsf.edu Amber M. Smith, Ph.D Department of Biochemistry and Biophysics Yifan Cheng Lab, Genentech Hall University of California, San Francisco 600 16th Street, San Francisco CA 94158-2517 Lab: 415.514.9708

2 1

Showing atoms of select residues while also showing the remainder of the model
by McClean, Phillip 09 Mar '23

09 Mar '23

Hi Everyone, I would like to show the atoms for just a few of the amino acid residues in a protein model will displaying the remainder of the model using the default format. Here is what I did: 1. Opened the model from my working directory 2. Selected a subset of residues using the select command: sel /A:102,105,106 3. Then used this command: show target a This command gives me the atoms for all of the residues. Is there a way to just show the atoms for the selected residues while also leaving the remainder of the model in the standard format. Thanks for any advice. Phil McClean

2 3

circular balls instead of residue
by Revan Katte 09 Mar '23

09 Mar '23

Hello sir/Madam, I'm labeling (or marking) the residues of my protein structure with Chimerax. So I want to use circular balls instead of residue, but he doesn't have that option. Could you please assist me with this? Thank you! Revan -- Revan Katte, Ph.D. Postdoctoral Research Associate, Prof. Maolin Lu Laboratory, Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, Texas 75708, USA. E-mail: *Revansiddha.Katte(a)uthct.edu <Revansiddha.Katte(a)uthct.edu>* Professional Website: Google Scholar <https://scholar.google.com.tw/citations?user=phuOXjgAAAAJ&hl=en> LinkedIn <https://www.linkedin.com/in/dr-revan-katte-3b53a788/>

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Virtual Crash Course - Understanding PDBx/mmCIF | May 3rd | REGISTER NOW!
by Brian Hudson 09 Mar '23

09 Mar '23

Use PDB data to their full extent: Understanding PDBx/mmCIF Wednesday, May 3rd 2023 | 1:00 PM EDT Registration: go.rutgers.edu/u3vpwjet <https://go.rutgers.edu/u3vpwjet> * This RCSB Protein Data Bank (PDB) virtual course will be broadcast on Zoom. Please fill out the registration form to receive the Zoom link. Registration will be available online from March 1, 2023 to May 3, 2023. LEARNING OBJECTIVES Understand the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined three-dimensional biostructures in the PDB. Learn about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data. Main topics: * PDBx/mmCIF format description and examples * PDBx/mmCIF data model * Software tools for generating, editing, and visualizing PDBx/mmCIF files * PDBx/mmCIF dictionary extensions, including ModelCIF for computed structure models (CSM) from AI/ML * Parsing data from PDBx/mmCIF files for your research WHO SHOULD ATTEND Professionals and graduate students interested in learning about strategies to take full advantage of PDB data in the fields of: * Structural biology * Cheminformatics and computational chemistry * Bioinformatics and computational biology PROGRAM | Download Printable Program <https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-cras…> 1:00–1:10 PM Welcome Stephen K. Burley, M.D., D.Phil. Director, RCSB PDB and Founding Director, Institute for Quantitative Biomedicine, Rutgers University 1:10–1:25 PM Introduction and course objectives Gregg Crichlow, Ph.D., RCSB PDB, Rutgers University 1:25–1:45 PM PDBx/mmCIF format - Not your parents’ legacy PDB format Ezra Peisach, Ph.D., RCSB PDB, Rutgers University 1:45–2:05 PM PDBx/mmCIF data files - Lifting the lid off the black box Brian Hudson, Ph.D., RCSB PDB, Rutgers University 2:05–2:50 PM Programmatic data access and analysis using PDBx/mmCIF files Irina Persikova, Ph.D. and Chenghua Shao, Ph.D., RCSB PDB, Rutgers University 2:50–3:00 PM Closing remarks and acknowledgements Stephen K. Burley, M.D., D.Phil. Development and management of the PDBx/mmCIF data dictionary is a collaborative effort involving RCSB PDB, Worldwide Protein Data Bank (wwPDB, wwPDB.org <http://www.wwpdb.org/>) partners, and members of the wwPDB PDBx/mmCIF Working Group (wwpdb.org/task/mmcif <https://www.wwpdb.org/task/mmcif>). CO-ORGANIZERS RCSB PDB Biocurators: Gregg Crichlow, Justin Flatt, Sutapa Ghosh, Brian Hudson, Yuhe Liang, Ezra Peisach, Irina Persikova, Monica Sekharan, Chenghua Shao, Jasmine Young (Rutgers, The State University of New Jersey). QUESTIONS Contact Michelle Sanghera msanghera(a)iqb.rutgers.edu CO-SPONSORS RCSB Protein Data Bank rcsb.org <https://www.rcsb.org/> RCSB PDB is managed by Rutgers, UCSD/SDSC, and UCSF. RCSB PDB is supported by grants from the NSF (DBI-1832184), the US DoE (DE-SC0019749), and the NIH (R01GM133198). RCSB PDB is a founding member of the wwPDB. Institute for Quantitative Biomedicine iqb.rutgers.edu <https://iqb.rutgers.edu/>

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Mutated several residues (amino acids or nucleotides) at the same time
by Vorländer,Matthias Kopano 08 Mar '23

08 Mar '23

Hi there, I wondered if it would be possible to change several residues at the same time using the “swapna” and “swapaa” commands in order to change the model file so that it matches a target sequence. This would be extremely helpful for model building purposes. Many thanks, Matthias

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Re: [chimerax-users] Some beginner's questions
by Elaine Meng 07 Mar '23

07 Mar '23

Hi Boaz, Glad you're getting acquainted with ChimeraX! Now I find it easier to use than Chimera. (1) no, it is not necessary to name the selection. The "save" command for PDB has an option to include selected atoms only, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> (2) do you mean the Side View tool? (ChimeraX does not have a per-model clipping gui currently). There is an icon in the Graphics tab of the toolbar across the top to show the Side View, or you can open it from the menu: Tools... General... Side View (3) if the surfaces are different, yes, that would be the reason for different min/max values found at surface vertices (4) Chimera's ~longbond command just hides the "missing segments" pseudobond group. In ChimeraX, you can look in the Model Panel (may need to use disclosure triangle on the model that contains it) to find the "missing structure" model. In that tool, you can just un-check the display box in the column under the eye icon to hide the whole model, or see what the model number is to use in a hide command, e.g. open 1www hide #1.1 (5) I would need more information: Are you trying to show isopotential surfaces, or to color the molecular surface by the potential value? If the latter, are you coloring the molecular surface of the protein or of the ligand? Do you have your own dx file already or do you just want to calculate Coulombic ESP and color by that? Coloring the protein surface by Coulombic ESP is as simple as clicking the icon in the Molecule Display tab of the toolbar. It is also covered in several tutorials, e.g. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#e…> <https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-channel.html#esp> <https://www.youtube.com/watch?v=FEIJ0lmybXo> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 7, 2023, at 9:12 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi, > > I checked the commands-user guide but couldn't find answers: > • To write out a selection of atoms to a PDB, do I need to name the selection first? > • I couldn't find the clipping tool (after setting a pivot I see only small part of the model). > • The min/max values of a potential from APBS (.dx) seem to be different in Chimerax than they are in Chimera. I'm working on a tetramer and while in Chimera the whole tetramer surface is covered by the potential, in Chimerax it' shown for each monomer. Is that the source of the difference? > • What's the Chimerax equivalent of ~longbonds of Chimera? > • Just wondering, is there a demo for electrostatic potential surface around a ligand? I seem to be making progress on that but a demo would be most helpful. > Thanks, > > Boaz

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Build Structure - peptide
by Jeffrey D. Hartgerink 06 Mar '23

06 Mar '23

Hello, I’m trying to build a series of related peptides with ChimeraX’s Build Structure - peptide tool. The way it currently works is simple and easy to use. However it is cumbersome to input phi/psi angles repeatedly, especially if the peptide sequences is anything more than very short. I am wondering if there is a way for this tool to take in either a text file list containing (Amino Acid, Phi, Psi), to paste in the same data into the input window, or any other related way to more efficiently generate peptide structures for starting points. This would greatly reduce the time needed to compare a variety of related sequences and conformations. Thank you very much for your time and consideration! -Jeff ---------------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University jdh(a)rice.edu / 713-348-4142 https://hartgerink.rice.edu

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Fwd: Request for Help with Chimerax and Protein Visualization
by Eric Pettersen 02 Mar '23

02 Mar '23

> Begin forwarded message: > > From: Ratchanont Viriyakitkosol <ratchanont.vir(a)gmail.com> > Subject: Request for Help with Chimerax and Protein Visualization > Date: March 2, 2023 at 12:26:42 AM PST > To: pett(a)cgl.ucsf.edu > > Dear Eric Pettersen, > > I hope this email finds you well. I am a medical school undergraduate student, and I have been using Chimerax to visualize protein structures that I predicted using AlphaFold. I am reaching out to you as I have encountered some difficulties with visualizing chemical bonding interactions in Chimerax, and I was hoping you could provide some guidance. > > Firstly, I have been using the "contacts" command in Chimerax to visualize chemical bonding interactions that interact with a single amino acid. However, I am not sure if this is the correct command to use. The visualization only shows blue dashlines, which I assume are hydrogen bonds. However, I am not sure if it is showing all direct interactions, including polar and nonpolar, favorable and unfavorable (including clashes). I want to know what is meant by "favorable and unfavorable" interactions in this context. > > Secondly, I have been unable to find a command to show disulfide bonds within a protein in Chimerax. I know that Pymol can show disulfide bonds in the same model, but I find Chimerax easier to use. Could you please let me know how to visualize disulfide bonds in Chimerax? > > As an undergraduate student with limited knowledge of structural analysis, I want to ensure that the bonding I use in my manuscript is shown correctly. I would greatly appreciate any advice or guidance you could provide. > > Thank you for taking the time to read my email, and I look forward to your reply. > > > > Best regards, > > James >

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Inquiry about bond type generated by the "contacts" command with default settings for AlphaFold-generated protein structure
by stomp.pumped0g＠icloud.com 02 Mar '23

02 Mar '23

Dear UCSF ChimeraX team, I hope this email finds you well. I am writing to inquire about the bond type generated by the "contacts" command with all default settings in UCSF ChimeraX for a protein structure that was generated using AlphaFold. I am particularly interested in understanding the nature of the blue line that is generated after running this command. As a reminder, my protein structure was generated using AlphaFold, and I would like to know if the bond type is a hydrogen bond, salt bridge, disulfide bond, or another type of bonding. Any information or insight you could provide on this matter would be greatly appreciated. Thank you for your time and assistance. Best regards, James

2 1

Discrepancies in SASA values between chimera and chimeraX
by Prathvi Singh 01 Mar '23

01 Mar '23

Hi Elaine, I compared the SASA values generated by chimera and chimeraX for a few PDB files and I noticed that whenever the SASA value of a residue is reported to be zero by chimera, the same residue's SASA value is reported to be -1.42 by chimeraX. Few examples are 18.A and 38.A of the PDB ID 1A62. *Method used to calculate SASA of residues in chimera: *Tools > Structure analysis > Render by attribute *Method used to calculate SASA **of residues** in chimeraX: *I ran the following commands: measure sasa protein;info residues attribute area Why is this happening? Kindly help. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Ring fill color
by Luca Pellegrini 01 Mar '23

01 Mar '23

Is it possible to color differently the ring fill for sugar and base in DNA? When I select just the bases or just the riboses and then apply color using the ‘ring fill’ option, they both change to the new color. Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

2 1

Update pdb model in cxs session
by 张一小 28 Feb '23

28 Feb '23

Hi, I'm using ChimeraX to prepare figures. I saved a session containing several pdb files and maps. (The pdb files were saved in the CXS file right?) Now, I manually adjusted one of the models in Coot. Is there a way to update the old model with the new one in the session so that all the settings, such as colors, views, showing residues, hidden ribbons can be kept and applied?" Thanks, Yixiao

2 3

Rotating/moving a chain to a different site
by Lohry, David 27 Feb '23

27 Feb '23

Hello! I am working with a protein dimer with DNA from a crystal structure. The dimer is composed of 2 chains (chain A and chain B) I would like to be able to place one of the chains on a different region of DNA and at a slightly different position. The only tool that I could find was the Movement Mouse Mode in Chimera original. Is there a way to do this a bit more mathematically (keeping the chain in tact)? Move 50 angstroms in the x direction, rotate chain by 30 degrees, etc . Also, I need it to update the actual coordinates in the PDB when saved so it can't be something that just affects the visual output. Thank you!

2 2

Question!
by Matthew Wengler (TSL) 26 Feb '23

26 Feb '23

Hello, I am a PhD student studying the downstream signalling events of a kinase in a fungal plant pathogen. We have differential phosphopeptide data of the kinase itself over a time course during plant infection (i.e., four residues on this kinase are differentially phosphorylated during stages of infection). I had a vision of showing a movie that incorporated the phosphorylated residues x phosphorylation abundance x time on the kinase’s tertiary structure and was wondering if this could be possible with Chimera X: * The tertiary structure would be displayed in grey * The phosphorylated residues would be highlighted in blue * A movie would be played and the highlighted residues would change colour based on phosphopeptide abundance over a time course (ranging from 0-100% abundance = blue -> red) I was wondering if this was currently possible. Alternatively (and maybe this is really the easiest way), because we only have ~6 time points, I could have 6 different stills of the protein with the residues highlighted corresponding to the phosphopeptide abundance values (blue-red 0-100%) and then piece them together in a 6 frame video that will loop…? I think I would prefer the colours to blend slower together dynamically than 6 harsh frames. Would there be a way to do this in Chimera? Thank you, Matt Wengler

2 1

some question about the use of chimera x 1.4
by 游宠昭 24 Feb '23

24 Feb '23

Dear developers, Sorry to bother you. Recently, I notice that chimera x display the DNA/RNA in a different way from that in chimera, and I find that there is a option in chimera called ribbon spline containing two options:B-spline and cardinal which explain why DNA/RNA is displayed in different ways in two softwares. However, I can not find the related actions in chimera x: "ribbon spline" in chimera refers to what in chimera x and how can I adjust this parameter. Sincerely, Chongzhao You

2 1

Help Generating a Volume to use for 2D classification template generation
by Joshua Denson 22 Feb '23

22 Feb '23

Hi, I’m trying to take an alpha fold model of my complex, generate a low resolution map of the model using molmap, and then use it for 2D template generation in CryoSparc. I am able to generate the low resolution map just fine, but the resulting map is in a rectangular volume (48x64x51) and I need it to be a cubic volume for CryoSparc to accept it. Ideally it would have dimensions of 64x64x64. Is there a way to generate a low resolution map in a cell with specific dimensions while maintaining the protein complex dimensions? (eg. I don’t want to simply scale it into a cube) I am using ChimeraX 1.5. Best Josh Joshua M. Denson PhD Candidate (Johnson Group) Dept. of Chemistry and Biochemistry Utah State University

4 4

Matchmaker on a subset of residues
by McClean, Phillip 22 Feb '23

22 Feb '23

Is it possible to use the Chimerax Matchmaker command to obtain the RMSD value between a subset or residues between two different proteins. Phil McClean

2 6

Custom Toolbar Button
by Dominik Sordyl 22 Feb '23

22 Feb '23

Hi, Is there a possibility to add a button to the "File" section on the toolbar? I have installed custom plugin and it can be run from Tools --> General section, but I am wondering if there is a way to add a shortcut button to the toolbar. Best, Dominik

2 2

Making a movie from a group in PDB file
by Aleksandar Donev 21 Feb '23

21 Feb '23

Hi, I am trying to create a simple animation of a demo molecular dynamics program https://github.com/stochasticHydroTools/DemoMD using either chimerax or chimera. The code creates a .pdb file that has multiple time frames in it, which show up in chimerax as a "group". How do I make chimera show the frames one by one and then make a movie out of that or save each frame as an image? I used to be able to do that in chimera but either the interface has changed or I have forgotten. I found lots of instructions about how to make movies by manipulating one data set (say rotating a molecule) but could not find anything about animation in time. Thanks, Aleks -- Aleksandar Donev, Professor of Mathematics Courant Institute of Mathematical Sciences Office: 1016 Warren Weaver Hall, New York University E-mail: donev(a)courant.nyu.edu Phone: (212) 992-7315; Fax: (212) 995-4121 Mailing address: 251 Mercer St, New York, NY 10012 Web: http://cims.nyu.edu/~donev

2 4

Distance maps and all atom distances
by André Graça 17 Feb '23

17 Feb '23

Hi everyone! Does ChimeraX have a tool to calculate distance maps in the same fashion as Chimera does with RRDistMaps? I believe Chimera's RRDistMaps only calculates intermodal distances between C-alpha atoms. Does anyone know a tool or have a script that could calculate all atom distances from two sequence identical models? Cheers, André

2 1

Image saving/exporting options
by Matthew Graneri 16 Feb '23

16 Feb '23

Hi there, I was wondering if there was an option to set the resolution of an image you want to export? In the older Chimera application, there were many more options open to you when you wanted to save an image (I’ve attached a screenshot of the old and new image saving screens for comparison). If not, is there any chance of implementing a resolution specification option sometime in the future? I was also wondering if it was possible to save images from ChimeraX as PDF files? I find that they usually maintain a high resolution without being particularly big, in terms of memory. Apart from that, really enjoying ChimeraX! Regards, Matthew

4 6

Loading MTZ data - volume is restricted to a small sphere within the protein model
by Lewis James martin 15 Feb '23

15 Feb '23

Hi folks, I recently installed Clipper, and on loading some example PDB and MTZ data, I'm seeing just a sphere of density data that does not cover the full protein model. This behaviour is not restricted to a single example. Is it expected? The example files I used are in 6DIL <https://www.rcsb.org/structure/6DIL>. I downloaded "PDB Format" and "Map Coefficients (MTZ Format)" from the drop-down menu. Loading the PDB by drag-and-drop into ChimeraX works as expected (coordinates do show). On loading the MTZ by drag-and-drop, and selecting the PDB model to import data into, I see the below representation. The density does not cover the full set of protein coordinates - it's limited to a sphere within the protein. Curiously, I saw this on coot too - so maybe I'm just getting the options incorrect? I did try shifting the cutoffs in the "Volume Viewer" Tool, and the mesh does change but it's still limited to this sphere. Changing from a mesh surface to "Maximum" shows that the available data is limited to a cube that does not cover the protein. Is there a way to view the full density? Out of interest, I also tried generating the mesh myself, but only got halfway. This at least shows that the data does cover the whole protein: import gemmi import numpy as np import meshplot as mp from skimage.measure import marching_cubes #run 'gemmi mtz2cif 6dil_phases.mtz 6dil_phases.cif' first doc = gemmi.cif.read('/Users/ljmartin/Desktop/6dil_phases.cif') rblocks = gemmi.as_refln_blocks(doc) rblock = rblocks[0] size = rblock.get_size_for_hkl(sample_rate=2.6) full = rblock.get_f_phi_on_grid('pdbx_FWT', 'pdbx_PHWT', size) array = np.array(full, copy=False) complex_map = np.fft.ifftn(array.conj()) scale_factor = complex_map.size / full.unit_cell.volume real_map = np.real(complex_map) * scale_factor v,f,n,_ = marching_cubes(real_map, 0.05) mp.plot(v, f)

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move models relative to each other
by Raik Grunberg 14 Feb '23

14 Feb '23

Dear ChimeraX developers and users, I would like to move to different proteins that I have opened separately into a particular position relative to each other. In the old Chimera, this is possible by going to the Model panel, then selecting one of the two models as "Active" and the other one not and then making the normal rotation and translation moves which will now only happen on the "active" model. However, this "Active" column is missing in the ChimeraX Model panel and I cannot find any alternative way of doing this. Any suggestions? Thanks a lot in advance Raik -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [chimerax-users] Transparency with soft lighting
by Tom Goddard 10 Feb '23

10 Feb '23

Hi Scott, I made a ChimeraX recipe web page to show this transparency and shadows trick. https://rbvi.github.io/chimerax-recipes/shadows/shadows.html That's amazing Esther refound it in that long fitting video. Tom > On Feb 10, 2023, at 12:23 PM, Scott Stagg <sstagg(a)fsu.edu> wrote: > > Thanks, Tom. That’s exactly what I was looking for! Esther Bullit found the video. It’s this one > https://www.youtube.com/watch?v=v3jI43YJQMg > Fitting an atomic model in an electron microscopy map with ChimeraX > youtube.com > Scott > > >> On Feb 10, 2023, at 3:09 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Scott, >> >> I'm not sure what video that is in. But there is some obscure ChimeraX magic involved. If you use the "soft" lighting (shadows cast from all directions) with a transparent surface it looks horrible because transparent surfaces by default don't cast shadows in ChimeraX. The reason for that default is often you are showing a molecule inside a transparent surface and then the molecule is dark (black actually) and hard to see. Because the transparent surface doesn't cast shadows it does not shadow itself so you don't get any of the darkened cavities that help 3D appearance. To make transparent surface cast shadows use ChimeraX command >> >> material transparentCastShadows true >> >> If you have an atomic structure (#2) inside the surface it will look black (shadowed), but you can tell it not to accept shadows >> >> lighting model #2 multishadow false >> >> The model inside can look pretty horrible and flat with soft lighting and you might try full lighting that adds a spot light, and also use silhouette edges. >> >> Here is an example of all these tricks. >> >> open 1080 from emdb >> light soft >> volume level 0.6 >> open 1grl >> preset cylinders >> fitmap #2 in #1 >> transparency #1 80 >> material transparentCastShadows true >> lighting model #2 multishadow false >> graphics silhouettes true >> set bgColor white >> light full >> >> Thanks for asking! >> >> Tom >> >> Opaque map, and transparent map, and transparent map with shadows with soft lighting. >> >> <image1.png><image2.png><image3.png> >> Atomic model is dark inside transparent map casting shadows. Can make atomic model not accept shadows. "Full" lighting instead of soft can make the atomic look less flat. >> >> <image4.png><image5.png><image6.png> >> >> >>> On Feb 10, 2023, at 6:48 AM, Scott Stagg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Hi everybody, >>> >>> I’m writing because I saw in a YouTube video that you used “soft” lighting with transparency for an EM density map. It looked great. I can’t find the video again or the right documentation on how to do it. There was some command with the lighting that you typed in the command line. Do you know what I’m talking about? >>> >>> Thanks, >>> Scott >>> >>> Scott Stagg >>> Professor >>> >>> Institute of Molecular Biophysics >>> Department of Biological Sciences >>> Florida State University >>> Tallahassee, FL 32306-4380 >>> w: 850-645-7872 >>> f: 850-644-7244 >>> sstagg(a)fsu.edu >>> https://www.stagglab.com <https://urldefense.com/v3/__https://www.stagglab.com__;!!PhOWcWs!3QUvw8SGqe…> >>> >>> >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chim…> >> >

1 0

Transparency with soft lighting
by Scott Stagg 10 Feb '23

10 Feb '23

Hi everybody, I’m writing because I saw in a YouTube video that you used “soft” lighting with transparency for an EM density map. It looked great. I can’t find the video again or the right documentation on how to do it. There was some command with the lighting that you typed in the command line. Do you know what I’m talking about? Thanks, Scott Scott Stagg Professor Institute of Molecular Biophysics Department of Biological Sciences Florida State University Tallahassee, FL 32306-4380 w: 850-645-7872 f: 850-644-7244 sstagg(a)fsu.edu https://www.stagglab.com

3 2

About plotting independent component analysis vectors
by Tianming Qu 09 Feb '23

09 Feb '23

Dear all, Is there any way I can display the eigenvectors I got from the independent component analysis on ChimeraX, which is calculated from the protein MD trajectory. Best, Tianming

3 7

Show palette range scale
by Gomez Barillas, Andrea 08 Feb '23

08 Feb '23

Dear ChimeraX developers, I've mapped sequence conservation into my protein structure by defining a specific attribute and I colored it using a specific palette. I was wondering how I can show in my model the scale of colors for the range I've stablished in my map. Maybe there is a command I can use to show the range I used for mapping and what the colors represent. Thank you for your help, Andrea

2 1

Re: [chimerax-users] Help getting rmsd value per residue of 2 similar structures.
by Elaine Meng 08 Feb '23

08 Feb '23

Hi Binh, This is almost the same question as asked yesterday on chimerax-users(a)cgl.ucsf.edu, so I have the same answer: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html> That answer assumes you are using Matchmaker to superimpose these structures first, which has an option to display the pairwise sequence alignment with RMSD values per column, which can then be written out, used for coloring, etc, as detailed in that answer. Note that this RMSD is only using CA atoms so for two structures, it is simply the distance between the 2 CA atoms. You can use the Sequence Viewer settings to make it use the 4 backbone atoms per residue instead (N,CA,C,O): <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html> Secondarily, remember that Chimera and ChimeraX are two different programs and if you are viewing help/answers for Chimera they may not pertain to ChimeraX. Finally, for the best chance of getting a good answer to ChimeraX questions in the future, please use chimerax-users(a)cgl.ucsf.edu unless you are including private data. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 8, 2023, at 12:39 PM, Binh Nguyen <AnBinh.Nguyen(a)UTSouthwestern.edu> wrote: > > Dear Elaine, > > Is there a way to generate the rmsd per residue of 2 similar structures using chimeraX? I have searched through but I can only manage to get the overall RMSD. > > I have found this too but I have no idea how to get such information. > https://www.rbvi.ucsf.edu/pipermail/chimera-users/2019-February/015415.html > > Please help, thank you. > > B

2 1

Questions about MultiAlign Viewer
by Beate Aftret 06 Feb '23

06 Feb '23

Hi, I have some issues accessing the Multiaglin Viewer in ChimeraX. I’ve tried to look at this response: https://www.rbvi.ucsf.edu/pipermail/chimera-users/2019-February/015415.html . However, I’m unable to access it. I’m trying to access the multialign viewer so I can get individual RMSD values on structures compared using Matchmaker. Thank you in advance. Let me know if I need to give more detail. Kind regards, Beate Aftret

2 1

No Access to Personal Files
by Anna Popa 02 Feb '23

02 Feb '23

Good afternoon, I am a college student using your ChimeraX software to complete an assignment in my biochemistry course. I have downloaded your app to my HP Chromebook using the most recent Ubutun version. Despite being on my personal computer, ChimeraX cannot open the files needed from my computer. When I tried to find out why this is happening, I concluded that it might be a software issue because I wasn't even able to set up the ChimeraX app completely. I would greatly appreciate some guidance and assistance. Thank you, Anna Popa

2 1

Fwd: Your message to ChimeraX-users awaits moderator approval
by Eric Pettersen 02 Feb '23

02 Feb '23

> Begin forwarded message: > > From: Krishnan Raman > Subject: RE: Your message to ChimeraX-users awaits moderator approval > Date: February 2, 2023 at 9:47:12 AM PST > To: "chimerax-users-owner(a)cgl.ucsf.edu" <chimerax-users-owner(a)cgl.ucsf.edu> > > Hi guys > > is there a way to get structures + other numerical data into chimerax? > I get the structures using a sdf file. I want to get in someother data associated each structure. > > How to start multiple instances of chimerax from a html-commands file? > Thanks > Krish > CONFIDENTIALITY NOTICE > > This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >

3 5

Obtain electrostatic potential from PQR/DX via script
by Lohry, David 02 Feb '23

02 Feb '23

Hi everyone, I'm performing an analysis where I want to select different regions on a molecule and obtain a list of all of the electrostatic potentials from that region. My input is a PQR file with a DX file. These were generated from a PDB and APBS. The electrostatic potential can be viewed when the option "Report value at mouse position" is selected in the Surface Color tool (Tools...Volume Data...Surface Color...Options button) In the status bar at the bottom, it will show the value along with the coordinates. Is there a way to obtain this information via a ChimeraX command that I could script? Thank you!

3 3

Multi-chain single macromolecule .pdb file read as two molecules
by Lenye Dlamini 31 Jan '23

31 Jan '23

Hello, I have a homo-oligomeric model that I've refined using phenix and the ISOLDE tool in ChimeraX that's read during deposition as 2 separate molecules, a larger 14mer and a smaller tetramer. It's read as one molecule in Coot, Chimera and Pymol but read as two distinct molecules in ChimeraX exactly like the deposition. I found this curious and thought that perhaps you might have some idea of what's wrong with the file. There is nothing that appears obviously incorrect to me in the text of the .pdb file, all TER cards follow the chains and all amino acids and their identifiers are in sequence and correct. I'd appreciate any ideas you may have and I'm happy to send the file to you if you prefer. Thank you, Kind regards, Lenye Dlamini Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

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Fwd: EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection
by Eric Pettersen 30 Jan '23

30 Jan '23

> Begin forwarded message: > > From: Tom Goddard <goddard(a)sonic.net> > Subject: Re: [chimerax-users] EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection > Date: January 30, 2023 at 11:54:02 AM PST > To: Paul Korir > Cc: Martin Schorb > > Hi Paul, > > ChimeraX does not specify what distance units the open models use. For atomic structures and cryoEM map it is usually Angstroms. For light microscopy images it is often microns. For medical image scans (MRI, CAT) it is I think meters. The file formats for the data define the physical distance units, not ChimeraX. So if EMDB SFF provides a segmentation for say an MRC or CCP4 density map file the scaling of that density map in the ChimeraX graphics is taken from the file header which has a field "cell dimensions in Angstroms". If a segmentation of that density map is made that is say a bounding surface it might use x,y,z coordinates in Angstroms or it might use grid index units when it writes out a file, that would depend on the segmentation file format and the software that is writing the segmentation. In ChimeraX it always tries to scale the data into physical units so that different data sets, like an atomic structure and 3D image data have the correct relative scale. So ChimeraX never displays images using grid index units. > > So from what you say about EMDB SFF the first transform goes from grid index units to physical units and ChimeraX should apply that transformation to the segmentation data so that it has the same scaling as the map data that the segmentation was derived from. I see there is a function in the ChimeraX EMDB SFF file reader called "guess_scale_and_shift" that is trying to figure out what transform to apply, but it is just a hack and looks for any non-identity transform. > > https://github.com/RBVI/ChimeraX/blob/da72f2cd9b23c0c35a66122b7edc453d593ea… <https://github.com/RBVI/ChimeraX/blob/da72f2cd9b23c0c35a66122b7edc453d593ea…> > > And another comment in the code suggests it is doing that hack because it was needed for EMDB SFF test data EMDB 1547. > > If I understand you correctly ChimeraX should instead always apply the first transform from transforms_list. I can make that change. The main thing will be to test it on pairs of EMDB SFF segmentations and corresponding maps to make sure it produces the correct alignment. > > Tom > > >> On Jan 30, 2023, at 2:20 AM, Paul Korir via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hi Tom/ChimeraX admin, >> >> Just to clarify: what are the units of physical space in ChimeraX: Å or nm? >> >> Kind regards, >> >> Paul K. Korir, PhD >> 3D Visualisation Lead >> CS3DB >> EMBL-EBI >> >> On 30/01/2023 08:51, Paul Korir wrote: >>> Hi Tom, >>> >>> To the best of my understanding, ChimeraX displays images and associated segmentations in physical space not image space. However, segmentations are performed in image space. EMDB-SFF uses the first transform in the transforms_list field (with id=0) as the image-to-physical transform. (https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html… <https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html…>) >>> >>> I've tested with two files having the same segmentation but different values for transform 0 and they render the same. >>> >>> Could you please implement this feature in ChimeraX? >>> >>> Kind regards, >>> >>> -- >>> Paul K. Korir, PhD >>> 3D Visualisation Lead >>> CS3DB >>> EMBL-EBI >>> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >

1 0

EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection
by Paul Korir 30 Jan '23

30 Jan '23

Hi Tom, To the best of my understanding, ChimeraX displays images and associated segmentations in physical space not image space. However, segmentations are performed in image space. EMDB-SFF uses the first transform in the transforms_list field (with id=0) as the image-to-physical transform. (https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html… <https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html…>) I've tested with two files having the same segmentation but different values for transform 0 and they render the same. Could you please implement this feature in ChimeraX? Kind regards, -- Paul K. Korir, PhD 3D Visualisation Lead CS3DB EMBL-EBI

1 1

How to license AlphaFold with ChimeraX
by Asma Rehman 28 Jan '23

28 Jan '23

Hi, I'm currently a chimeraX user and would like to also use AlphaFold along with it. I was wondering if you could help us with directions. I appreciate your support. Thanks, Asma

2 1

Isolde in with VR Headset ?
by Thibault TUBIANA 27 Jan '23

27 Jan '23

Dear all, I tried to use my Occulus Quest with ChimeraX Isolde Pluggin, while it works amazingly, the "tugging" function doesn't work. I thought that maybe it is the mouse mode that is node configured, so I tried "vr button trigger select" or 'vr button trigger "isolde tug atom"' but nope... It is not a request of course, just a question to know if someone already tried it ^^ Best regards, Thibault Tubiana. -- Thibault Tubiana, PhD Postdoctoral Fellow @ [ https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism… | IMAPP ] Institute for integrative biology of the cell ( [ https://www.i2bc.paris-saclay.fr/ | I2BC ] ) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: [ http://www.tubiana.me/ | http://www.tubiana.me/ ]

3 4

Select ring atoms of ligand using python in chimerax
by Dr. Vijay Masand 26 Jan '23

26 Jan '23

Dear all I am looking for an efficient method to select ring atoms of ligands using python in chimeraX. Also, is there any python code/method to get the sum of charges on ligand atoms only? Thanks in advance. From Vijay With Warm Regards *Dr. Vijay H. Masand* Department of Chemistry, Vidya Bharati College, Amravati, 444 602 Maharashtra, India. Phone number- +91-9403312628 https://sites.google.com/site/vijaymasand/

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Re: [chimerax-users] recent query
by Rangarajan, Amith 26 Jan '23

26 Jan '23

Dear Eric, thanks for taking time to answer my query. It was very detailed and i am beginning to understand how bundles work on chimerax. i am working on a methods paper that uses sidechain center of masses as a representation of mutation position and generates clusters to intrepret the impact of the mutations. i tried scripting this, but i realised that pandas library is not present in chimerax (?) and i did not proceed further. is there a way to include scikit learn , pandas libraries in chimerax script? thanks once again for all your support ! best amith

2 3

Macbook Pro, fans, and ChimeraX
by Lewis James martin 26 Jan '23

26 Jan '23

Hi all, Ever since I got my Macbook Pro (16-inch, 2019, 2.3GHz 8‑core Intel Core i9) I noticed the fans can go full bore for seemingly small tasks. ChimeraX is one of those - swinging a protein view around is enough to set them off, and Activity Monitor reports around 200% usage for the "UCSF ChimeraX" process. I can see that GPU usage on the inbuilt AMD Radeon Pro 5500M can get up to about 50%, too. The bottom can get quite hot - it's Summer here now, but this happens in Winter too. A couple of questions: - Is this expected (for ChimeraX, not generally)? Do other people experience this? - Does ChimeraX use the GPU for rendering? If so, what's driving the CPU spike when I move the protein on screen? Is it just from calculating the coordinate rotations? Thanks, Lewis

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Re: [chimerax-users] [Chimera-users] Rotation along symmetry axys
by Tom Goddard 25 Jan '23

25 Jan '23

Hi Leonardo, As Elaine said, rotating the view in ChimeraX does not change what is saved in the map (*.mrc) file. The data needs to be rearranged in the 3D array. That can be done with the ChimeraX "volume resample" command (in Chimera it is called vop resample) but that interpolates the data on a new grid, and it would be better to just rotate the 3D data array so you don't get interpolation errors. I made a ChimeraX command to do that "volume rotate_90" available on the ChimeraX Recipes web site. https://rbvi.github.io/chimerax-recipes/rotate_90/rotate_90.html We no longer develop Chimera so I provide this for ChimeraX. Tom > On Jan 25, 2023, at 6:14 AM, Leonardo Talachia Rosa via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > 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 > ************************** > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

1 0

color palette in transprency ?
by vincent Chaptal 25 Jan '23

25 Jan '23

Hi, I'm rendering a series of models using this command line (which works very well): rainbow #1 structures palette cyan:blue I would like to do the same but in a series of transparent models, with a range from 0 to 80 (or similar). Is there a command for this, I couldn't find it? Thanks a lot. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

2 4

vector
by Dr.S.Somasundaram 25 Jan '23

25 Jan '23

2 2

Pseudobonds change style
by Samo Lešnik 25 Jan '23

25 Jan '23

Dear ChimeraX developers, I am wondering if it is possible to change the style of pseudobonds, specifically "Distances", from "dotted disks" to "whole undotted lines"? It is very easy to do this in Chimera, with just changing the style in the graphical interface of Distances. Thank you very much, dr. Samo Lešnik

2 2

Re: [chimerax-users] downloading pdb files from another webserver
by Rangarajan, Amith 24 Jan '23

24 Jan '23

hi, i mostly resort to using the resource from dunbrack's lab to download structures renumbered as per uniprot numbering. i currently do it using a simple .py script: [cid:14eb2e7f-deaa-4341-92eb-3f9c56db264b] i want to make this as a chimerax script that i can call from command line with open {scriptname.py} { pdbid} wondering if some one has tried to do similar things and some tips regarding which modules to use might be helpful. thanks a lot , best amith

3 3

Memory problems with Orbital Viewer
by Michael Patzschke 24 Jan '23

24 Jan '23

Dear colleagues, I am using ChimeraX mostly for small molecular complexes, typically up to 100 atoms. I am running the code on a MacBook Pro with 16 GB of memory under macOS 11.8.8. When I try to render molecular orbitals from an orca calculation I get even for very small molecules the warning message: Estimated peak memory usage (0.0GB) is above or close to the available memory (0.0GB). Exceeding available memory might affect the stability of your computer. You may attempt to continue, but it is recommended that you lower your resolution, decrease padding, or use fewer threads. Press "Ok" to continue or "Abort" to cancel Is there any way to fix this problem? Kind regards, Michael Patzschke

2 4

electrostatic surface of docking model
by Citterico, Matteo 23 Jan '23

23 Jan '23

Hello everyone, I am trying to visualize the electrostatic potential surface of a docking model generated with ClusPro2.0 (job: https://cluspro.bu.edu/models.php?job=898454) When I click on the electrostatic button on ChimeraX 1.3 to visualize the charge, it gives the error: "Using Amber 20 recommended default charges and atom types for standard residues. Hydrogen copy of model.000.00.pdb #/A PHE 244 H1 bonded to atom that should not have hydrogens (copy of model.000.00.pdb #/A PHE 244 C)." How can I solve this problem? Thank you for the help and always a big up to the Chimera staff! Matteo

2 6

Coot view in ChimeraX
by Cryo EM 23 Jan '23

23 Jan '23

Hi everyone, Does anyone know of a command for getting a coot view of map in ChimeraX? I remember seeing it in chimera, so I guess there should be something of such sort in ChimeraX too? Regards and thanks

2 1

Error in opening Chimera
by Ashfaque Rahman 22 Jan '23

22 Jan '23

Why is this error showing? What is the solution? [image: image.png]

2 1

Non contiguous residues selection from command line
by LEONARDO SORCI 22 Jan '23

22 Jan '23

Hello there! I wondered if there is a way to quickly select noncontiguous residues from the command line (useful, for example, when selecting a set of residues defining an active site, a template for docking, etc.). In standard chimera, I would use the command SELECT with numbers, commas, and hyphens (e.g., SELECT: 172,192,193,208:214). Thanks, Leonardo Polytechnic University of Marche, Ancona, Italy

2 2

How to select best pose from docking model?
by Luigi Marongiu, PhD 22 Jan '23

22 Jan '23

Dear all, I am new to docking analysis. I have obtained a list of poses from VINA analysis, but what of them shall I choose? Is the first the best choice? The problem is that, according to the pose, the ligand binds the protein in a different position. Different ligands might or might not bind on the same position, thus choosing the right pose is essential to determine whether there is a position that allows binding of multiple molecules. What is the procedure to determine whether such a multiple binding site exists? What is the protocol to choose the right pose? Thank you

2 1

Re: [chimerax-users] overwrite session aliases from the startup options
by Helge Paternoga 20 Jan '23

20 Jan '23

Hi Elaine, Thanks for the tip with "alias delete all", I had not considered that one. My solution so far was to open the startup screen and copy all new aliases, then paste them in the command line and hit enter which overwrites everything with the newest ones. So a toggle option to "re-run startup script upon session loading" or something similar could alleviate the issue. Best, Helge Am 18.01.23 um 21:00 schrieb chimerax-users-request(a)cgl.ucsf.edu: > Dear Helge, > I don't have an elegant solution, but faced with this problem I would > > (1) open old session > > (2) use "alias delete" to get rid of the old versions of the aliases (or "alias delete all" if you are OK with getting rid of all of them) > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alias.html> > > (3) re-save session > > I understand that it is a pain to do this if you have a large repertoire of saved sessions, however. > I hope this helps, > Elaine

2 4

ChimeraX image saving automation
by Attana, Fedaa 19 Jan '23

19 Jan '23

Hi all, I have started to use Chimera recently and found it very cool. I liked the way I can edit all of my structure with one command when no model is selected. However, to save images, I have to manually show each structure (model) and run the same saving command with a new name. I wonder if there is an easier way to do this or if somebody did automate this process so one can save images of individual models with a script? Thanks in advance, Fedaa

3 2

scalemol extension not working
by André Graça 19 Jan '23

19 Jan '23

Hi everyone, I hope to at least get a reply from Tom, but this may need a bit of troubleshooting (?). I looked into a very old post of yours, Tom, about rescaling an atomic model (see it at the end of my email). I put everything in place but I get an error and I wonder if anything has changed with the PDB format since 2005, or some incompatibility with new chimera versions... If there is actually a way of doing the same with ChimeraX, that would be incredible =) Cheers! André Error and forwarded message comes now: __________________________________________________ AttributeError Exception in Tk callback Function: <bound method MidasUI.processCommand of <Midas.midas_ui.MidasUI instance at 0x00000000079092C8>> (type: <type 'instancemethod'>) Module: <module 'Midas.midas_ui' from 'C:\Program Files\Chimera 1.16\share\Midas\midas_ui.pyc'> (line: 618) Args: (<Tkinter.Event instance at 0x00000000198D8AC8>,) Event type: KeyPress (type num: 2) Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\share\Midas\midas_ui.py", line 628, in processCommand midas_text.makeCommand(cmdText) File "C:\Program Files\Chimera 1.16\share\Midas\midas_text.py", line 69, in makeCommand f(c, args) File "C:\Program Files\Chimera 1.16\share\scalemol\ChimeraExtension.py", line 23, in scale_molecule x, y, z = a.coord().xyz.data() AttributeError: '_chimera.Point' object has no attribute 'xyz' ================================================ Event contents: char: delta: 0 height: ?? keycode: 13 keysym: Return keysym_num: 65293 num: ?? serial: 14638 state: 8 time: 154527203 type: 2 widget: .121252488L.126915336L.428746824L.428747592L.428747720L width: ?? x: 228 x_root: 288 y: -22 y_root: 941 ______________________________________________________________________ ------- Start of forwarded message ------- Date: Wed, 27 Apr 2005 11:05:55 -0700 (PDT) From: Thomas Goddard <goddard at cgl.ucsf.edu<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> Hi Jinghua, By "virus cage pdb file" I guess you mean you placed atoms at icosahedral positions, and want to show them connected up to show some icosahedral pattern. I think the easiest approach is to open your old session, run a command to change the diameter of the cage, then save a new session. Below is some Python code that provides a "scalemol" Chimera command. Make a directory chimera/share/scalemol in your Chimera distribution and put the code below in file chimera/share/scalemol/ChimeraExtension.py. Then start Chimera, open the cage PDB model, use menu entry Favorites/Command line, and type a command: scalemol 0 1.5 to make model number 0 bigger by a factor of 1.5. If you have more than one model open you can see the model numbers using Favorites / Model Panel, the model number is shown in the left hand column. Tom - ---- scalemol/ChimeraExtension.py code follows: # ----------------------------------------------------------------------------- # def scale_molecule(cmdname, args): from Midas.midas_text import error fields = args.split() try: model_num = int(fields[0]) factor = float(fields[1]) except: error('Syntax error: scalemol <model-number> <factor>') return import chimera mlist = chimera.openModels.list(id = model_num) if len(mlist) == 0: error('scalemol: No model number %d' % model_num) return for model in mlist: for a in model.atoms: x, y, z = a.coord().xyz.data() c = chimera.Coord() c.x, c.y, c.z = (factor*x, factor*y, factor*z) a.setCoord(c) # ----------------------------------------------------------------------------- # import Midas.midas_text Midas.midas_text.addCommand('scalemol', scale_molecule) ------- End of forwarded message -------

2 1

missing or invalid sequences
by Liang, Junyi 19 Jan '23

19 Jan '23

I would like to predicate interaction between two proteins, and tried chimerax version 1.5 after noticing a youtube video https://www.youtube.com/watch?v=6lXeCPuTePs. [https://www.bing.com/th?id=OVP.95Ygyv4AXQTgCS0WB9iXtgHgFo&pid=Api]<https://www.youtube.com/watch?v=6lXeCPuTePs> Running AlphaFold to Predict Protein Complexes from ChimeraX<https://www.youtube.com/watch?v=6lXeCPuTePs> How to predict the structure of a photoreaction center complex of 3 proteins from ChimeraX using AlphaFold-Multimer. Requires a ChimeraX daily build newer than December 2, 2021 or version 1.4. It is not in ChimeraX version 1.3. Web page describing steps https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html www.youtube.com I input the two protein sequences in same way as shown in the video and hit predict. But your software says "missing or invalid sequences". How come? Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

2 5

Is RR Distance Maps implemented in ChimeraX?
by Michael Bruist 19 Jan '23

19 Jan '23

I use RR Distance Maps in Chimera for my teaching. I want to switch to ChimeraX, but I have not bee able to find this tool. Is it available in ChimeraX? Mike Bruist Michael F. Bruist Professor of Biochemistry Department of Chemistry and Biochemistry St. Joseph’s University 215-596-8530 mbruist(a)sju.edu

2 1

Reasign secondary structure for back-bone trace
by Enrico Martinez 19 Jan '23

19 Jan '23

Dear Chimera-X users! I am working on the visualization of a trajectory containing only back-bone atoms of the protein obtained from the PCA. When I load this multi-pdb ensemble to Chimera-X I can see only back-bone traces without any secondary structure information. I've tried to use dssp command to re-assign the secondary structure but it did not change the visualization state. Would it be possible to do it in some automatic fashion via some built-in command? Many thanks in advance Cheers Enrico

2 4

incomplete output from matchmaker embedded in python script
by Borchert, Milan 19 Jan '23

19 Jan '23

Hello ChimeraX community, I have been trying to use the Chimerax tool to sequentially check one query pdb against multiple (later up to 10000) pdb files. For this I have been working with the python scripting functionality. With the following code I was able to get the resulting data (number of matched atoms and resulting RMSD) saved as a html log file: import os from chimerax.core.commands import run as rc # change to folder with data files os.chdir("/home/ubuntu/Desktop/Chimerax_search/N_crassa_pdb") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # give path to query file to be searched against pdb library query = "/home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb" # open the query file as #1 in ChimeraX rc(session, "open /home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb") # loop through the files for fn in file_names: # open first target pdb as #2 rc(session, "open " + fn) # match both structures rc(session, "match #1 to #2") # save log with ID matching input filename, close #2 and clear log rc(session, "log save " + fn.split(".")[0] + ".log") rc(session, "close #2") rc(session, "log clear") Instead of trying to gather the relevant data from thousands of rather large html output files I instead would prefer to only get then resulting values from matchmaker. I learned that the command actually has all the values I wanted as return values, so I tried to write a modified script, that saves these values in a variable and collects the values for every target pdb file in a dict: import os from chimerax.core.commands import run as rc # change to folder with data files os.chdir("/home/ubuntu/Desktop/Chimerax_search/N_crassa_pdb") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # give path to query file to be searched against pdb library query = "/home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb" # open the query file as #1 in ChimeraX rc(session, "open /home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb") # create empty dict to collect matchmaker output output = {} # loop through the files, opening, processing, and closing each in turn for fn in file_names: id = fn.split("/")[-1].split(".")[0] rc(session, "open " + fn) match = rc(session, "match #1 to #2") output.update({id : match}) rc(session, "log save " + fn.split(".")[0] + ".log") rc(session, "close #2") rc(session, "log clear") # display dict print(output) For now I just used 4 target pdbs with my query and only tried printing the result to quickly check if it fits. However the result is a bit baffling to me. I do get the RMSD values, but not the other data: {'NCU01382': [{'full match atoms': <chimerax.atomic.molarray.Atoms object at 0x7f1944492130>, 'full ref atoms': <chimerax.atomic.molarray.Atoms object at 0x7f194448f610>, 'final match atoms': <chimerax.atomic.molarray.Atoms object at 0x7f1946694430>, 'final ref atoms': <chimerax.atomic.molarray.Atoms object at 0x7f1946694550>, 'full RMSD': 63.065617285514556, 'final RMSD': 1.365365439813019, 'transformation matrix': <chimerax.geometry.place.Place object at 0x7f194669c130>, 'aligned ref seq': <chimerax.atomic.molobject.Sequence object at 0x7f19f7b8f8b0>, 'aligned match seq': <chimerax.atomic.molobject.StructureSeq object at 0x7f19f7b8f610>} here is one of the resulting hits, for my first target pdb (NCU01382). As you can see, the RMSD scores are correctly given, but for other values the internal object names and no resulting value are displayed. Any help with figuring this out would be greatly appreciated. Best Wishes Milan Borchert

2 2

select displayed atoms via command line / transfer saved views
by Helge Paternoga 18 Jan '23

18 Jan '23

Dear ChimeraX users, I have to unrelated questions: 1) Is there a way to select displayed atoms via the command line? 2) Is it possible to transfer saved views from one session to another one? Many regards and thank you for reading, Helge

3 3

Clipper's strange behaviour
by André Graça 16 Jan '23

16 Jan '23

Hi everyone! Is there any known issue with Clipper plugin for ChimeraX? After installing clipper and restarting ChimeraX, the software is not responding after I execute the Open command. I expect that it takes some time to open an .mtz file as the map needs to be calculated, however I have waited more than 45 minutes and ChimeraX keeps unresponsive... I am using Chimera 1.5 and I installed the (hopefully compatible) version of Clipper 0.19.0 Did anyone faced the same problem? Let me know if you have a fix or trick ;) Thanks for any feedback in advance, André ____________________ [cid:image001.png@01D9272E.120B2740]

2 2

Movie clipping planes in chimera x
by Greg Martin 13 Jan '23

13 Jan '23

Hi, I’m trying to make a movie where I highlight different parts of a large complex. For one scene, I’m trying to interpolate between a zoomed out view of the whole complex (view p1), and then a zoomed in view of an interface (view p2), which shows a series of interactions. What I want is a smooth transition of both the view and clipping plane from p1 to p2. However, when I give the command: view p1 p2 100 it interpolates the two positions/zooms fine, in 100 frames, but then after the movement adjusts the clipping plane all at once. Is there a way to have the plane adjusted smoothly during transition between p1 and p2? I’ve also tried fly, but this disregards clipping planes altogether. Views are saved with view name p1 view name p2 Thanks in advance, Greg -- Gregory Martin, PhD. Staff Scientist Lab of Andrew Ward Department of Integrative Structural & Computational Biology The Scripps Research Institute La Jolla, CA 92037

3 3

Inquiry: Map sequence conservation onto a protein structure
by Gomez Barillas, Andrea 13 Jan '23

13 Jan '23

Dear ChimeraX developers, I am trying to map sequence conservation onto a protein structure. I am using ChimeraX version (version 1.4 (2022-06-03). For this purpose, I was trying to use a tutorial from 2014 for Chimera for Mapping Sequence Conservation onto Structures (Showing Sequence Conservation in Chimera (ucsf.edu)<https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html>). It seems that some the tools mentioned in this tutorial are no longer available, or maybe work differently. Specifically, the tutorial's "Case 4" (calculating values outside of Chimera but showing them in Chimera) has you set an attribute, and then render/color the structure based on the attribute. The Tools > Structure Analysis > Define attribute mentioned in the tutorial is no longer available. I was as able to assign values directly to structure residues in a text file and read it in using the command defattr instead. The next step would be to use the tool Render by Attribute for coloring but I cannot find this option anymore. Is there a different command I can use for this step, or a new functionality built into ChimeraX I could use for my purpose of mapping sequence conservation onto the structure? One relevant point is that I already have my sequence identify values calculated from another program, and I want to import those values. Thank you in advance for your help, Andrea Showing Sequence Conservation in Chimera<https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html> Example 2B Chimera session: ConSurf-1hd2-chimera19.py [show this last!] (result of submitting 1hd2 to the ConSurf server and choosing to show results in Chimera; alignment has 150 sequences including that of the query, 1hd2) . Given a protein structure, the ConSurf server estimates the evolutionary conservation of amino acid positions based on the phylogenetic relations between homologous ... www.cgl.ucsf.edu

2 1

Inquiry: Map sequence conservation onto a protein structure
by Gomez Barillas, Andrea 13 Jan '23

13 Jan '23

Dear ChimeraX developers, I am trying to map sequence conservation onto a protein structure. I am using ChimeraX version (version 1.4 (2022-06-03). For this purpose, I was trying to use a tutorial from 2014 for Chimera for Mapping Sequence Conservation onto Structures (Showing Sequence Conservation in Chimera (ucsf.edu)<https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html>). It seems that some the tools mentioned in this tutorial are no longer available, or maybe work differently. Specifically, the tutorial's "Case 4" (calculating values outside of Chimera but showing them in Chimera) has you set an attribute, and then render/color the structure based on the attribute. The Tools > Structure Analysis > Define attribute mentioned in the tutorial is no longer available. I was as able to assign values directly to structure residues in a text file and read it in using the command defattr instead. The next step would be to use the tool Render by Attribute for coloring but I cannot find this option anymore. Is there a different command I can use for this step, or a new functionality built into ChimeraX I could use for my purpose of mapping sequence conservation onto the structure? One relevant point is that I already have my sequence identify values calculated from another program, and I want to import those values. Thank you in advance for your help, Andrea

1 0

ChimeraX Log window remains blank
by Scott White 13 Jan '23

13 Jan '23

Hi, Sorry if this is a dumb question, but recently when starting ChimeraX the Log window is not on Display. Opening the Log window (Tools> log) opens it as a separate window, and whether docked or free-floating the Log window remains blank no matter what I do. Even just "open 1nov" on the command line will download and open the PDB entry 1NOV, but no text appears in the Log window. I've tried a fresh install of ChimeraX 1.5 to no avail. I've tried opening an older version of ChimeraX, which despite having worked countless times before, now shows the same behaviour regarding the Log window as my abberant ChimeraX 1.5. I've tried rebooting the computer - no fix. I've tried "log clear" and "log show". It's a Windows 10, university owned PC. I don't have the issue on other computers. Is it a software clash? Thanks in advance for any help or advice. Scott _______________________________________ Dr Scott A. White SFHEA School of Biosciences, Room T716 University of Birmingham, B15 2TT E: s.a.white(a)bham.ac.uk<mailto:s.a.white@bham.ac.uk> T: +44-(0)121-414-7534 Office Hours Generally Tues 10am - 11am, Wed 3 pm - 4 pm Please contact me for an appointment. ______________________________________

2 2

Changing MD trajectory default frame rate
by Visvaldas K. 12 Jan '23

12 Jan '23

Dear all, Is there a way to change frame rate when I hit that red "record" button when playing MD trajectory? I could do "movie record", but then it becomes interactive (I hit triangle "play", and then "movie encode /Users/visvaldas/Desktop/movie.mp4 framerate 5"), so inadvertently can record some undesired frames. Of course I probably can reduce framerate using external programs, but how to that non-interactively in ChimeraX? Best regards, Vis

3 3

How to integrate ChimeraX with phenix
by Suresh K 12 Jan '23

12 Jan '23

Hi, We integrate pymol and coot with phenix but unable to integrate ChimeraX. In internet we found that you using ChimeraX with phenix. Could you help us with way to integrate ChimeraX with phenix? Thanks and regards, Suresh K

2 1

Select complelementary of range
by Pranav Shah 12 Jan '23

12 Jan '23

Hi Team, How do I go about selecting everything that does NOT lie between a given range of residues? For instance I want to select everything that is NOT r.410420. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 1

Smooth MD trajectory during moovie making
by Enrico Martinez 12 Jan '23

12 Jan '23

Dear Chimera-X users! I am trying to make a movie using MD trajectory (in multi-model pdb file) by means of the Molecular Dynamics Viewer (v 1.2). is it possible to introduce smooth effects on the snapshots transition in the same way like it could be done via V*D ? Many thanks in advance Cheers Enrico

3 10

Trouble displaying missing structure dashed lines in cartoon mode
by Jonathan Jih 11 Jan '23

11 Jan '23

Hello ChimeraX team, I'm having quite a bit of trouble displaying missing structure dashed lines when my models are shown in cartoon mode. This is despite the "missing structure" sub-model box being ticked in the model panel. I recall finding a workaround for this nearly a year ago on ChimeraX 1.3, but I cannot for the life of me remember how I did so (now using ChimeraX 1.5). Interestingly, old sessions that I saved in 1.3 and 1.4 with whatever workaround I applied back then display the missing structure dashed lines properly in 1.5. However, opening the exact same pdb files from those older sessions in 1.5 yields no dashed lines in cartoon mode. Full atom mode appears fine. I also found this thread ( https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html) which seems to indicate the issue has been fixed, so not sure if I'm just doing something wrong? My OS is Windows 11 if that matters. Thanks in advance for the help! Jonathan -- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles

2 6

Saving .mrc volume as coordinates
by Joshua Jenkins 10 Jan '23

10 Jan '23

Hi, I've segmented a tomogram using EMAN2 neural network workflow. I then use the segger function to extract regions of interest within the segmented volume, and save these to .mrc. I wondered if there is a way in chimera, or chimeraX, to convert/extract/save the .mrc volume as a simple 3D coordinates file (txt or tbl)? Best wishes, Josh

3 2

Morph movie saving from a script file
by Pranav Shah 09 Jan '23

09 Jan '23

Hi Team, Would there be a way to record a morph between two structures using the command line? Currently, I am clicking the play and record buttons from the GUI in quick succession to achieve this. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

3 2

Re: [chimerax-users] [Chimera-users] Stereo glasses
by Jonathan Sheehan 06 Jan '23

06 Jan '23

I'm always on the lookout for new options for 3D stereo display hardware (Chimera or Chimerax). I just saw this Asus system with glasses-free stereo, using eye-tracking cameras and a lenticular screen. It looks to me like a premium OLED laptop targeted to gamers and CAD designers. I'm unfamiliar with Asus Spatial Vision and Acer SpatialLabs, but one reviewer said that it works with multiple people viewing it- I'm slightly sceptical. :-) https://arstechnica.com/gadgets/2023/01/asus-new-16-inch-workstation-laptop… Tom, you suggested that VR headsets were the best option a few years ago. What are your thoughts about this release? (Replies from non-Tom individuals are also welcomed.) Thanks! -Jonathan On Thu, Jun 13, 2019 at 10:32 PM Jonathan Sheehan <jonathan.sheehan(a)gmail.com> wrote: > > Thanks for the information, Tom- I was hoping somebody had better > news. It sounds like we're in a dead zone between the epochs of stereo > glasses and VR headsets. > > I suppose I'll have to start looking into VR systems. > > Thanks, > -Jonathan > > > On Mon, Jun 10, 2019 at 1:19 PM Tom Goddard <goddard(a)sonic.net> wrote: > > > > Hi Jonathan, > > > > Nvidia was the main distributor of 3D active LCD stereo glasses, and they dropped support for their Nvidia 3D Vision glasses and emitters in April 2019 as described here > > > > https://www.ghacks.net/2019/03/11/nvidia-3d-vision-end-of-support/ > > > > https://nvidia.custhelp.com/app/answers/detail/a_id/4781 > > > > Nvidia graphics driver released after April 2019 won't work with these glasses. You can continue to use Nvidia 3D Vision with old graphics drivers, maybe that is the best option. > > > > The LCD active stereo glasses technology appears to be nearly dead. If you try to use it be prepared for problems getting it to work and to pay a lot of money. We have been using active stereo LCD with a stereo projector for many decades. We use it infrequently now, instead using virtual reality headsets with our ChimeraX software. Virtual reality headsets give better immersion but don't yet easily handle having a half-dozen people viewing the same scene in the same room (would require 6 separate computers driving the 6 headsets). > > > > Here are details on the old LCD glasses projector system we are have which is working: > > > > 10 pairs of RealD CE4 and CE4s stereo glasses ($280 each) > > > > http://www.colorlinkjapan.com/brand/product/ce4s.html > > > > A Stereo Graphics EXXR extra long range emitter ($780) > > > > http://www.colorlinkjapan.com/brand/product/exxr-emitter.html > > > > A Christie Mirage S+4K projector circa 2006, (1440 x 1050 resolution), no longer in production > > > > https://www.projectorcentral.com/Christie-Mirage_S+4K.htm > > > > An Nvidia Quadro P6000 graphics card ($3700) > > > > https://www.amazon.com/PNY-Quadro-P6000-Graphic-Card-x/dp/B01M0S2FKR > > > > with a stereo emitter bracket > > > > http://www8.hp.com/h20195/v2/GetPDF.aspx/c04658472.pdf > > > > This system breaks about once a year after graphics driver updates, the fix usually being to set the projector to be either the primary display or secondary display (depends on graphics driver version). Also the glasses fail at maybe the rate of 1 out of 10 pairs per year. > > > > Tom > > > > > > On Jun 7, 2019, at 8:30 AM, Jonathan Sheehan <jonathan.sheehan(a)gmail.com> wrote: > > > > Hi all, > > > > What stereo setup are people recommending these days? It seems that > > NVIDIA has discontinued the 3D Vision 2 goggles+emitter. Is there > > something else that is available and works well? > > > > Thanks for any advice! > > -Jonathan > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

3 3

Coloring according to the secondary structure
by Enrico Martinez 06 Jan '23

06 Jan '23

Dear ChimeraX users! I need to color cartoon representation of a protein according to its secondary structure (e.g. to color helix in red, b-stands in blue and coils in violet etc). I have already seen a built-in plugin in UCSF Chimera (but not in Chimera-X) that could do this job! Could you suggest commands that would be useful in Chimera-X? Many thanks in advance Cheers Enrico

2 2

Unable to find the distance between centroid & any other atom in chimeraX
by Prathvi Singh 05 Jan '23

05 Jan '23

Hi Elaine, I declared the centroid of a tyrosine residue's ring by first selecting its ring members & then using the command: *define centroid sel radius 0.5* Next, when I try to find the distance between the centroid, I get an error whose screenshot I have attached with the email. The command that I am using to find the distance are: *dist sel* dist #1.1 #1.2 (here the distance is being calculated between two centroids) Please help - Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

Unfocus in chimeraX using command line
by Prathvi Singh 05 Jan '23

05 Jan '23

Hi Elaine, Is there any equivalent of the "~focus" command in chimeraX? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

Re: [chimerax-users] Remote control / Threading in ChimeraX
by Albert Smith-Penzel 05 Jan '23

05 Jan '23

Hi Tom, Thanks for the explanation. I’ll have to think and investigate a bit to see if my thread use is causing some problems elsewhere. Most of our code has been pretty stable, but there are still a few occasional glitches that I haven’t completely understood. Anyway, session.ui.thread_safe is perfect for resolving the issues we have with adding the surface to the empty session and running commands remotely. The curl solution also works; I had something like this implemented previously for some other purposes, but my own preference is to send commands/data directly rather than writing out a file to be read on the other end. Thanks again! Cheers, Albert ––––––––––––––––––––––––––––––––––– Albert Smith-Penzel, Ph.D. DFG Project Leader Institute for Medical Physics and Biophysics Leipzig University 04107 Leipzig, Germany E-mail: albert.smith-penzel(a)uni-leipzig.de <mailto:albert.smith-penzel@medizin.uni-leipzig.de> > On 4. Jan 2023, at 21:41, Tom Goddard <goddard(a)sonic.net> wrote: > > WARNUNG: Diese E-Mail kam von außerhalb der Organisation. Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge, es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist. > > WARNUNG: Diese E-Mail kam von außerhalb der Organisation. Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge, es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist. > > Hi Albert, > > ChimeraX is not designed to run arbitrary Python code multithreaded. There are many reasons. First the Qt window toolkit is not thread safe -- all Qt GUI calls have to be done in the main thread. Violating that often results in a crash. But even without the GUI, imagine the main thread is looping over the list of open models while a second thread decides to add a model to that list -- this could break the looping thread many ways. Python has a global interpreter lock which means it only can run one thread at a time. Still if you pause one thread and then change the state of the ChimeraX session in another thread, the first thread could throw errors in countless ways when it resumes at an arbitrary point in the code with the data structures changed. In general very little software is thread safe because it is very difficult to implement. Usually that is only done by making threads not modify any data structures used by other threads. > > Here are two solutions. 1) Have your listener thread run the Python code it receives in the main thread rather than the listener thread. There is a ChimeraX function that takes a function and queues it to be run in the main thread. > > session.ui.thread_safe(func, args...) > > Here is the code if you want to see how it works > > https://github.com/RBVI/ChimeraX/blob/2e33222fabb48edec76df6e82a10efedb54a8… > > A second solution is to use the ChimeraX remotecontrol communication for everything. That mechanism just runs ChimeraX commands, but you can run Python code using it by just sending the command "open script27.py" where you put the Python you want to run in a file script27.py. > > Tom > > >> On Jan 4, 2023, at 4:40 AM, Albert Smith-Penzel via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hello, >> >> I am working on a Python project that uses ChimeraX (currently running 1.5 to interactively view dynamics data by mapping it onto a molecule. All the figures/movies in this paper, https://www.nature.com/articles/s41467-021-27417-y <https://www.nature.com/articles/s41467-021-27417-y>, were made possible by Chimera! Also thanks to Tom Goddard for explaining to me how some of those figures could be made awhile ago (https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo… <https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo…> ). >> >> So we’re controlling ChimeraX remotely; we launch a session and then can send commands from Python over to Chimera and edit images from within our python code (while still allowing us to interact via the ChimeraX interface). The basic way this works is as follows >> >> launch chimeraX from our code, including a short python script >> python script imports our libraries, launches “cmxr” (chimeraX remote) >> cmxr uses multiprocessing.connection.Listener to listen for commands/data coming from Client in our python code >> !!!The Listener runs in a thread (threading.Thread) so that we continue to be able to interact normally with ChimeraX (launching the Listener without using a thread freezes ChimeraX while waiting for commands, rendering it unusable) >> Then, we just tell it to run some function(s) that we’ve imported into ChimeraX, and provide some data, atom ids, etc. over the Client/Listener connection >> >> There are a few things that I can’t figure how to make work via this process. We’ve had a few long-standing workarounds, but I’ve always been a little disturbed that we can’t get this all to work from python alone. At the moment, when we launch ChimeraX, we also enable remote control via curl, and some commands are then sent that way (remotecontrol rest start port XXXX) >> >> In particular, if I want to send commands that would normally be executed at ChimeraX’s command line, in principle I should be able to use chimerax.core.commands.run. If I execute “run” from a simple python script, everything works, but if I run it from within a thread (as required by our Listener setup), then ChimeraX freezes. So, we send these commands via curl on the remotecontrol instead. >> >> Second, is there a right way to open models/surfaces from the ChimeraX python shell? At the moment, we also open pdbs via curl commands. For pdbs, maybe I just don’t know the right python command. However, I am re-implementing spherical harmonics referenced above. Once I have prepared the surface (“s”), if I add it to session.models, it crashes chimeraX if it is being added within the listener thread, and if there are no models already open. If another model is already open, then it works just fine, and if I load the same modules/execute the same commands from within the python shell provided in ChimeraX, it also works (regardless of other models being open). It seems like maybe ChimeraX isn’t able to fully initialize the session from within a thread. >> >> I’ve grouped these problems together because I guess mainly they have to do with being unable to do some actions from within threads, and if there’s an explanation/workaround for dealing with that. >> >> Thanks for your help! >> >> Cheers, >> Albert >> >> >> >> ––––––––––––––––––––––––––––––––––– >> Albert Smith-Penzel, Ph.D. >> DFG Project Leader >> Institute for Medical Physics and Biophysics >> Leipzig University >> 04107 Leipzig, Germany >> E-mail: albert.smith-penzel(a)uni-leipzig.de <mailto:albert.smith-penzel@medizin.uni-leipzig.de> >> >> >> >> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >

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Remote control / Threading in ChimeraX
by Albert Smith-Penzel 04 Jan '23

04 Jan '23

Hello, I am working on a Python project that uses ChimeraX (currently running 1.5 to interactively view dynamics data by mapping it onto a molecule. All the figures/movies in this paper, https://www.nature.com/articles/s41467-021-27417-y <https://www.nature.com/articles/s41467-021-27417-y>, were made possible by Chimera! Also thanks to Tom Goddard for explaining to me how some of those figures could be made awhile ago (https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo… <https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo…> ). So we’re controlling ChimeraX remotely; we launch a session and then can send commands from Python over to Chimera and edit images from within our python code (while still allowing us to interact via the ChimeraX interface). The basic way this works is as follows launch chimeraX from our code, including a short python script python script imports our libraries, launches “cmxr” (chimeraX remote) cmxr uses multiprocessing.connection.Listener to listen for commands/data coming from Client in our python code !!!The Listener runs in a thread (threading.Thread) so that we continue to be able to interact normally with ChimeraX (launching the Listener without using a thread freezes ChimeraX while waiting for commands, rendering it unusable) Then, we just tell it to run some function(s) that we’ve imported into ChimeraX, and provide some data, atom ids, etc. over the Client/Listener connection There are a few things that I can’t figure how to make work via this process. We’ve had a few long-standing workarounds, but I’ve always been a little disturbed that we can’t get this all to work from python alone. At the moment, when we launch ChimeraX, we also enable remote control via curl, and some commands are then sent that way (remotecontrol rest start port XXXX) In particular, if I want to send commands that would normally be executed at ChimeraX’s command line, in principle I should be able to use chimerax.core.commands.run. If I execute “run” from a simple python script, everything works, but if I run it from within a thread (as required by our Listener setup), then ChimeraX freezes. So, we send these commands via curl on the remotecontrol instead. Second, is there a right way to open models/surfaces from the ChimeraX python shell? At the moment, we also open pdbs via curl commands. For pdbs, maybe I just don’t know the right python command. However, I am re-implementing spherical harmonics referenced above. Once I have prepared the surface (“s”), if I add it to session.models, it crashes chimeraX if it is being added within the listener thread, and if there are no models already open. If another model is already open, then it works just fine, and if I load the same modules/execute the same commands from within the python shell provided in ChimeraX, it also works (regardless of other models being open). It seems like maybe ChimeraX isn’t able to fully initialize the session from within a thread. I’ve grouped these problems together because I guess mainly they have to do with being unable to do some actions from within threads, and if there’s an explanation/workaround for dealing with that. Thanks for your help! Cheers, Albert ––––––––––––––––––––––––––––––––––– Albert Smith-Penzel, Ph.D. DFG Project Leader Institute for Medical Physics and Biophysics Leipzig University 04107 Leipzig, Germany E-mail: albert.smith-penzel(a)uni-leipzig.de <mailto:albert.smith-penzel@medizin.uni-leipzig.de>

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How to get the average pTM scores from an Alphafold multimer prediction
by Chen, Henry 04 Jan '23

04 Jan '23

Dear Chimarax devs/users, I'm using ChimeraX Alphafold tool to do a multimer structure prediction. I was wondering how can I determine the average pTM score for each structure prediction? I get PAE.png and plddt.png file, but not a text file or anything that tells me the average pTM. (I was hoping the ranking file would give the average score but it does not) The models come with the pdb file as well as the scores.json files, but again I don't see anything that tells me the average pTM for the structure. Clearly the pTM per residue scores are saved in my pdb file, is there a command to average them all up? Thanks! Henry

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Capping termini ends
by Pranav Shah 04 Jan '23

04 Jan '23

Hi Team, Happy New Year! I look forward to all new developments you guys have in store for ChimeraX in 2023. Speaking of, is it possible to somehow display the ends of a protein termini with a spheres or something? I have certain view of my model in which the termini get partially obscured so it would be nice to prominently have them displayed in some manner... Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Extracting the color name/hex code of a colored ribbon
by Theodora Bruun 23 Dec '22

23 Dec '22

Hello, I am just curious if there is a command for listing the current color name or hex code of an atom/ribbon that is colored in ChimeraX. For example, I open a previously colored structure and like the color of chain A and now I would like to use that same color and maybe apply to other chains in the structure. Is there a way other than just eye-balling it? Best, Theo

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using atomic coordinates to measure volume
by Harrison, Daniel P 23 Dec '22

23 Dec '22

Hello: I would like to calculate the maximum volume made by selection of atoms in a given structure. Can you provide guidance on how to go about this process? It seems like there should be a simple procedure in ChimeraX but I have failed to locate it. My specific problem: I would like to calculate the volume of the void created by ice under various conditions so that my physical chemistry students can quantify and visually understand partial molal volume non-ideality. I would greatly appreciate any assistance you can provide. Dan

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PDB upload TER card error
by HONG ZHAN 21 Dec '22

21 Dec '22

Dear all, I saved my protein coordinates in ChimeraX as pdb (it has multiple chains), however, when I was doing upload on the PDB, it shows this error, I am using ChimeraX 1.5rc202211091945 on Linux ubuntu 22.04 LTS. Coordinates issues: ERROR: There is no TER card at the end of polymer chain 'X'. All polymer chains should have a TER card at the end of each chain. Please add TER card and restart again. Many thanks! Hong

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phosphorylation
by Fabian Glaser 21 Dec '22

21 Dec '22

Dear experts, I would like to mutate a ser and a thr to phospo-serine and phospho-threonine, what is the easiest way to do it? Thanks a lot, fabian -------------------------- Fabian Glaser, PhD Structural and Computational Biology Unit The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel

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ChimeraX linux binary problems
by Добромир Калчевски 19 Dec '22

19 Dec '22

Hello, I have installed Chimera linux from binary and everything was OK from the get-go. ChimeraX however, fails to start for library dependencies. As I understand the source depends on around 50 packages. I don't know (and I can find no indication on internet) how many libraries am I missing, but I'm also kind of limited in terms of disk space / linux size and my distro does not have a very nice package manager - Clear Linux (it installs entire bundles of similar packages, instead of single packages and once removed the disk size does not go down). Is it possible to make a ChimeraX linux binary which is as easy to run as the Chimera linux binary - universal for all distributions and including all necessary dependencies ? Best Regards, Dobromir

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ChimeraX linux binaries too inconvenient
by Добромир Калчевски 19 Dec '22

19 Dec '22

Hello, Can you provide ChimeraX linux binary as useful as the Chimera linux binary ? - without all of the dependencies being outside of the package. Also, can the package simply install in the /home/username/.local/CHIMERAX... directory, just as Chimera or in a similar path ? (makes uninstallation easy, saves disk space). Many distros do not have package managers as convenient as those of Red Hat or Debian. For example I use Clear Linux (for the performance) and the dependencies are not even in the package manager. There is also no explicit list of dependencies and according to your web site there are about 50 of them, anyway. Basically whatever I do there is always a missing library I cannot easily find / compile / have no time for it, etc., so ChimeraX for me is out of reach. I tried Chimera from the linux binary and it ran just fine, but it lacks something in the GUI, which ChimeraX does not. The visualization settings fields can be scrolled up and down, so if I load let's say 12 molecular orbitals - I can easily hide / show the ones I need, instead of having them all on the screen and using the "Data set list" to manually show / hide each one. Best Regards, Dobromir

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Re: [chimerax-users] color
by Elaine Meng 19 Dec '22

19 Dec '22

Hi Guan, To ensure you get an aswer, we recommend sending ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here). You can click the square "color well" for each model listed in the Model Panel to open your system color browser, which will show the code. See also this page for the names of the initial model colors... <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html> ...and then this page which shows the codes for the names <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#builtin> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 18, 2022, at 5:46 PM, Guan, Lan <Lan.Guan(a)ttuhsc.edu> wrote: > > Dear Elaine: > I like the color usage in chimeraX. I wonder if we could know the color code for the color auto-painted when we open it. > Thanks, > Lan

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Aligning atoms
by Noriega, Heather 18 Dec '22

18 Dec '22

Hello, I have a question about the alignment. Is there a way to get the glycans to align, one has a PEG docked to it and I was hoping to place the PEG and delete the glycan #2. I am unsure if it is possible. It gives me an error because the number of atoms are not equal. I attached the session. Thanks in advance. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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ChimeraX Alphafold Multiple jobs
by Rayees Mattoo 16 Dec '22

16 Dec '22

Hi, I was wondering if I could run multiple Alphafold jobs via ChimeraX using my Colab Pro. Also, very often Alphafold job submitted gets disconnected after some time (15 min or so) without completing the job, any solution to that? Best Rayees

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help please - electrostatic potential units and fit in map correlation
by Leslie Bridges 15 Dec '22

15 Dec '22

Dear All What are the units for electrostatic potential in ChimeraX? Is it possible to say whether the fit in map correlation represents a "good" fit for the atoms (e.g. if my correlations are above 0.75, can I conclude all the fits are good?) All the best, thanks Dr Leslie R Bridges Hon Snr Lecturer in Neuropathology St George's University of London

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no conformation comparison category in ChimeraX1.5 and ChimeraX-daily
by Jiang Xu 14 Dec '22

14 Dec '22

Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions? Thank you, Best, Jiang Xu

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