- ChimeraX-users - RBVI Mailing Lists

CA atoms connected by tether when trying to show sidechains only in a model
by Samuel Haysom 25 Jan '24

25 Jan '24

Hello, I am trying to show only sidechains in one model, so I can compare rotamers with another model where I am displaying cartoon and sidechains. However, when I display sidechains using the sidechain selector (e.g. "show #1 & sidechain") the CA atoms become linked by tethers. [cid:image001.png@01DA4F98.8C977390] How can I suppress this display? I can see its possible to suppress tethers between cartoon helices and a sidechain in the same model but that doesn't seem to apply here as I'm not showing the cartoon at all in the models where the CA tethers are present. KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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Inquiry on Commercial Licensing for ChimeraX Plugin Development
by Jacky Chen 25 Jan '24

25 Jan '24

Dear Team ChimeraX, My name is Jacky Chen, and I am the sales representative at Oomii. Recently, we initiated a project aimed at developing an innovative ChimeraX plugin, specifically designed to enable interactive augmented reality features. To this end, Oomii has acquired two commercial licenses of ChimeraX in January 2024. As we progress, our intention is to offer the developed bundle for commercial sale to other users. However, upon reviewing the documentation available at: https://www.cgl.ucsf.edu/chimerax/docs/devel/writing_bundles.html, we noticed that it does not specify the licensing particulars for a bundle that utilizes both the ChimeraX API and proprietary code developed by Oomii. We are keen to ensure that our operations align with ChimeraX's licensing policies. Could you please provide guidance on the business rules that apply to the commercial distribution of such plugins? Additionally, if available, could you direct us to any precedent or contact information for companies that have navigated similar pathways? Your assistance in this matter is invaluable to us, and we eagerly await your insights. Thank you very much for your time and support. Warm regards, *Jacky Chen 陳志傑* *Sales Representative* * <https://oomii.com/>* *jackychen(a)oomii.com <jackychen(a)oomii.com>* *2F.-1, No.94, Baozhong Rd. Xindian Dist., New Taipei City, Taiwan 23144* *+886-2-8911-2347* <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> 乾淨無病毒。www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Feature question: "Worms" plots in "Render By Attribute"
by James Lingford 25 Jan '24

25 Jan '24

Dear ChimeraX team, I was wondering if ChimeraX v1.7+ has the function for rendering attributes by "Worms"? For example, rendering B-factors by the thickness of the backbone. I noticed that it's possible in legacy version of Chimera, which I have since installed and generated worm plots with: https://www.cgl.ucsf.edu/chimera/ImageGallery/framedpecworm.html Is this doable in the latest ChimeraX versions, however? Many thanks for any help you can provide, James -- *James Lingford* | Research Officer, Greening Lab Department of Microbiology, Monash Biomedicine Discovery Institute Monash University Google Scholar <https://scholar.google.com/citations?user=4KSRHTUAAAAJ&hl=en> | Website <https://www.jameslingford.com/>

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Re: [Chimera-users] Chimera X menu "View" vs. "Focus"
by Eric Pettersen 23 Jan '24

23 Jan '24

Hi Christian, We named it “View” instead of “Focus” because it issues a “view” command, but your points have merit — “Focus” is more evocative of what the action actually does, and is less confusable with hide/show, so after some discussion we have renamed the menu item to “Focus” and the change will be in the next daily build. The menu item item still issues/logs a “view” command to do its work. We are aware that the direct equivalent of the “Fetch By ID” dialog is missing in ChimeraX and we intend to add it. It’s just a matter of implementation priorities, so it could still be a little while — but it’s useful to know that it’s definitely missed, which will make it more likely to get worked on sooner. Also, there is a list specifically for ChimeraX user issues — chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>, (cc’ed here), which would be better to discuss ChimeraX topics on than chimera-users… --Eric Eric Pettersen UCSF Computer Graphics Lab > On Sep 25, 2023, at 12:47 AM, C. Klein via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera Team > > first of all, thank you very much for your important and good work on the Chimera software. > > Two comments: > > I did some recent work with Chimera X. The menu item "Focus" was changed to "View", which I find less suitable. The term "View" is often applied in other contexts, in particular if a certain residue should be shown vs. not shown. In contrast, "Focus" is not ambiguous, it is not related to showing vs. hiding certain parts of the molecular representation but exactly indicates what is done by the command. > > The direct pdb download from rcsb or whatever repository is a highly useful tool which is more difficult to access than it used to be. Ok I know it is there, I type "open xxxx" and I use the command line quite a lot anyway, but for others who start with the menus it does not appear to be accessible. Perhaps I also missed something, but then others may not find it as well. > > Thank you and best wishes > Christian Klein > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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Does ChimeraX work with tkinter?
by thlin＠oomii.com 22 Jan '24

22 Jan '24

I tried to use `tkinter` instead of `PyQt` but it does not work with ChimeraX 1.6 or 1.7's Python interpreter and the error message is shown below: ``` import _tkinter # If this fails your Python may not be configured for Tk ModuleNotFoundError: No module named '_tkinter' ``` One solution I've found was to `sudo apt install tk-dev` but it was required to`configure` and `make` ChimeraX's Python interpreter after. Does ChimeraX work with tkinter? If yes, then how to?

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Missing comand bar to open proteins
by Marina Contel 22 Jan '24

22 Jan '24

Hello, A few days ago, I was using ChimeraX and the command bar to open proteins disappeared. I have tried everything including uninstalling it and installing it again, and I have no clue how to solve it. I was wondering if you could give me some guidelines to get it back. That will be amazing because I need to start working with it as soon as possible because I have an assignment to hand this week. Thanks in advance! Kind regards, Marina

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[Inquire about the protein protein interaction results using chimeraX]
by ‍정혜연[학생](생명과학대학 유전생명공 학과) 22 Jan '24

22 Jan '24

Hi, I'm HyeYeon from KyungHee University. I am sending you an email because I have some questions while using ChimeraX. When I investigated the interaction between the two proteins using chimeraX, the results of the two runs were different even though they had the same sequence. One is the result from June of last year and the other is from January of this year. Did the PPI results change despite the same sequence as a result of the program update? I would appreciate it if you could check and reply. Thank you.

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Defining a variable that represents the number of models
by kkssy141＠gmail.com 20 Jan '24

20 Jan '24

Hello, Would it be possible to define a variable that represents the number of models? I want to make a chimerax script that aligns #1-#(N-1) to #N. For instance, if I have a script like this where N represents the number of models opened in ChimeraX and save it as test.cxc mm #1-#(N-1) to #N In bash, I can open my PDB files that are aligned to a crystal structure 1be9: chimerax *.pdb 1be9 test.cxc The number of models (N) will be a dynamic variable depending on how many PDB files I have. Thank you. Best, Siyoung ------------------ While writing, I figured the below would work. test.cxc: mm ~#1 to #1 In bash: chimerax 1be9 *.pdb test.cxc But I still want to ask this question to know whether it is possible to retrieve the number of models opened and set this to a variable in ChimeraX. Thanks.

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Colouring clipping plane
by GOVAERTS Cédric 20 Jan '24

20 Jan '24

Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring [Graphical user interface Description automatically generated] -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. [cid:image002.png@01D94092.6E8A2390] Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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Option to convert shape to map?
by Oliver Clarke 19 Jan '24

19 Jan '24

Hi, Would it be possible in a future release to add an option to the "shape" command to output the shape as a map (filled with 1s inside the shape, zeroes outside, maybe with an optional soft edge and an ongrid option)? This would be very convenient for making simple geometrical masks for cryoEM (e.g soft cylindrical masks for classification within a nanodisc). I currently do this using "shape cylinder", use the cylinder to mask the map, and then gaussian filter the resulting masked map to the point where I can choose a threshold that conforms to the shape, but having a way to do the same thing more directly would be very nice to have. Cheers Oli

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Sequential model display controls bound to buttonpanel button?
by Oliver Clarke 19 Jan '24

19 Jan '24

Hi all, I really like the new sequential model display controls in the daily build - thank you so much for implementing these! Would it be possible to add them as a command, e.g. nextmodel and prevmodel? This way I could add them to my box of buttons, and have them in the main GUI window, without needing to switch over to the model panel. Cheers Oli

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Re: Increase cofactor size
by Tristan Croll 19 Jan '24

19 Jan '24

(disclaimer: you should probably follow Elaine’s much more extensive advice) “atomspec” just refers to any selection string - e.g. “#1/A:50”, “:LIG”, “sel” etc. On Fri, 19 Jan 2024 at 18:52, Cameron Larson <cllarson(a)ucdavis.edu> wrote: > Thank you for your help. > A silly question, but what is might 'atomspec' be? a range of atoms? > > Thank you, Tristan > > On Fri, Jan 19, 2024 at 11:51 AM Tristan Croll <tcroll(a)altoslabs.com> > wrote: > >> Try "setattr {atomspec} bonds radius {value in Angstroms}". >> >> Best, >> Tristan >> >> On Fri, Jan 19, 2024 at 4:28 PM Cameron Larson via ChimeraX-users < >> chimerax-users(a)cgl.ucsf.edu> wrote: >> >>> Hello, >>> >>> I am using chimeraX to visualize a ligand. I am familiar with the >>> commands to increase protein thickness ('cartoon style protein thickness') >>> but how can I do this for a ligand or other molecule? >>> >>> Really appreciate the help, >>> >>> -Cameron Larson >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: >>> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>> >> >> Altos Labs UK Limited | England | Company reg 13484917 >> Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, >> United Kingdom, WA14 2DT >> <https://www.google.com/maps/search/1+Ashley+Road,+Altrincham,+Cheshire,+Uni…> >> > -- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

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Increase cofactor size
by Cameron Larson 19 Jan '24

19 Jan '24

Hello, I am using chimeraX to visualize a ligand. I am familiar with the commands to increase protein thickness ('cartoon style protein thickness') but how can I do this for a ligand or other molecule? Really appreciate the help, -Cameron Larson

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Question about Cylinder Representation
by Elaine Meng 19 Jan '24

19 Jan '24

Hi Maxine, Somehow I missed your earlier question about how to make cartoon helix tubes straight instead of curved: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu…> The short answer is that sorry, ChimeraX currently does not have an option to make them straight. This feature request is in our database as ticket #1242: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/1242> There are some possible workarounds mentioned in the comments on that ticket, namely: ---------------- (1) you could try "define axis" with "perHelix true" and some padding value to show straight cylinders for helices, and then hide the ribbon. The main problem with this workaround is that the other parts of the ribbon do not connect well to the straight cylinders in some places. Example: open 2gbp hide atoms define axis perhelix true padding 2.0 hide helix ribbon Also if you only care about one specific helix, you can hide all of the other straight cylinders and only hide the ribbon for the specific residues in that helix. (2) If you want to modify the Python code in your ChimeraX distribution you can change one line and it will always produce straight helix tubes. The line is 154 in file ChimeraX.app/Contents/lib/python3.9/site-packages/chimerax/atomic/sse.py [** NOTE this is an old comment so the python version is higher now, I believe python3.11 instead of 3.9, and the line number is also different, I believe it's line 166 instead of 154 **] ...on Mac (different location on Windows and Linux, ask if you can't find it) change MIN_CURVE_LENGTH = 13 to MIN_CURVE_LENGTH = 1300 ---------------- I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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check waters to a csv file?
by Francisco Murphy Pérez 18 Jan '24

18 Jan '24

In chimerax ... tools -> structure analysis -> check waters Can we get the information from this analysis into a csv file? Can we add also the bfactor? Thanks

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Plotting Difference Map of Electron Density
by Gourav Das 17 Jan '24

17 Jan '24

Greetings everyone! I am trying to plot difference map of electron density using ChimeraX. I have created the cube file using Multiwfn. I want to show red and blue isosurfaces (+0.0012 and -0.0012 a.u., respectively) to represent the regions in which electron density is increased and decreased respectively. Please help me regarding this issue. With regards, Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

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Different ways to crop out a map region
by Thu Nguyen 16 Jan '24

16 Jan '24

Good afternoon, I am looking for several methods to crop out a map region from a larger density map. So far I know the command "volume region" but to use the command I need to know in advance the grid indices of the region I want to crop. Are there any more convenient methods to crop out a map region (maybe using mouse to directly drag a region from the volume map)? Thank you very much. Best regards, Thu

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Hide arrows/axes
by Lluís Eixerés Ros 16 Jan '24

16 Jan '24

Dear ChimeraX developer, I’m Lluís Eixerés, a PhD student at the Biomedicine Institute of Valencia, Spain. I’m using ChimeraX and after opening a mtz file, these arrows/axes (see figure attached) appeared at the centre of the screen. I have tried to hide them (they also appear after snapshotting) but I can’t. Could you explain me how to do it, please? Thank you. Regards, LL

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Help in Extracting pLDDT confidence Scores in CSV Format from ChimeraX AlphaFold
by Amit Singh 14 Jan '24

14 Jan '24

Dear ChimeraX Developer, I hope this message finds you well. I am reaching out as a newcomer to ChimeraX and Alphafold, seeking guidance on extracting the pLDDT score in CSV format from the best model obtained through ChimeraX AlphaFold. Specifically, I am interested in obtaining information such as Binding Protein, Bond Type, Protein Residue, Peptide Residue, Distance (Å), and the "pLDDT Range Score." Despite my attempts with the B-factor, I have encountered challenges in extracting the pLDDT range confidence score. I would greatly appreciate any assistance or guidance you can provide on this matter. Thank you for your time and consideration. Kind regards, Amit

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Re: Question regarding gaussian filtering
by Tom Goddard 13 Jan '24

13 Jan '24

Hi Dennis, You need to be clearer about what you are trying to achieve "So I guess my question is whether there is a good way to mimick/visualize a lower resolution experimental map using a higher resolution experimental map without considering a sophisticated noise model." If you wanted to mimic a low resolution map for purposes of testing an algorithm (e.g. fitting, segmentation, ...) then the signal to noise at various frequencies would be important. If you just want it to look like a low resolution map to the human eye (why?), well I don't know how much having very different signal-to-noise as a function of frequency will visually alter the appearance. The effects of Gaussian smoothing or simply truncating beyond a certain frequency will create a map that has much higher signal-to-noise then a real low resolution map. You won't see the low resolution noise characteristic of an actual low resolution map. I don't know if that would be visually apparent. Tom > On Jan 10, 2024, at 12:40 AM, Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se> wrote: > > Hi Dennis, > > A low-pass filter is what you want then: this doesn't dampen signal and noise, simply discards everything past a certain spatial frequency you choose. Just like the low-pass filter applied on-the-fly when using a map as a reference for a 3D refinement or classification job. > I don't know how this can be done in ChimeraX though. > > Guillaume > > From: Dennis Dannecker via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> > Sent: Wednesday, January 10, 2024 7:15:09 AM > To: Tom Goddard > Cc: chimerax-users(a)cgl.ucsf.edu > Subject: [chimerax-users] Re: Question regarding gaussian filtering > > Hi Tom, > > thank you vey rmuch for the fast and elaborate response. > > I believe I understand it much better now and see why the resolution > per se is not what I am after. > > My intention is to visualize/model the appearance of a lower > resolution map using a higher resolution map. While this should in > principal be possible (the other way around not) but would then > require an appropriate noise model. > > So the gaussian filtering only dampens the amplitudes of the > frequencies in Fourier space. The dampening can be controlled by the > standard deviation of the used gaussian function. The dampening > affects signal and noise equally. > > Does this correspond to a gaussian lowpass filter? Because I was > thinking about removing the high frequencies and setting the cutoff at > different frequencies then corresponding to different "resolutions". > While the resulting map probably has a higher signal-to-noise ratio at > lower frequencies (lower than the cutoff) than an experimental map of > a resolution that this map tries to depict it may still be a good > visual approximation. > > So I guess my question is whether there is a good way to > mimick/visualize a lower resolution experimental map using a higher > resolution experimental map without considering a sophisticated noise > model. > > Thanks again for your help. > > Best > Dennis > > > > Quoting Tom Goddard <goddard(a)sonic.net>: > > > Hi Dennis, > > > > I don't know the answer to your question, but here are some > > thoughts about it. The Gaussian convolution filter just scales the > > Fourier space coefficients by a Gaussian making the higher > > frequencies have lower amplitudes. That is reversible, the high > > frequencies can be scaled back up. So although the real-space > > smoothed map looks lower resolution, it still has the same high > > resolution content. The noise and the signal have both been scaled > > down at high resolutions so the signal-to-noise is just as good at > > those high resolutions. If you did this smoothing on two half-maps > > used to compute the resolution by Fourier shell correlation it would > > still give 2 Angstroms, the smoothing did not change the FSC > > resolution! If you were for example testing a fitting method it > > could easily extract that high resolution information and use it. > > In order to really lower the resolution you would need to add noise > > at high frequencies so the high-frequency signal is lost. > > > > That said you could ask if the noise at high frequencies was not > > scaled down, only the signal, then what would the reduced resolution > > be. We know at the FSC resolution the signal-to-noise ratio is some > > specific value that gives the cutoff correlation. But you would > > need a model of the noise amplitude at other lower frequencies to > > know how attenuating just the signal but not the noise would change > > the resolution. Maybe there is a pretty reliable noise model for > > these cryoEM maps, I'm not sure. > > > > Tom > > > > > >> On Jan 9, 2024, at 2:41 PM, Dennis Dannecker via ChimeraX-users > >> <chimerax-users(a)cgl.ucsf.edu> wrote: > >> > >> > >> Hello, > >> > >> I would like to ask a question regarding the gaussian filtering. > >> > >> I filtered a given map (downloaded from the emdb with the "open" > >> command from chimerax) in chimerax using the following command: > >> > >> vop gaussian #1 sDev X > >> > >> with X taking different values ranging from 0.25 to 20 with different steps. > >> > >> Now I would like to know the resolutions these maps actually > >> correspond to after this gaussian filtering. The originally loaded > >> map is stated to have nominal resolution of 2 Angstroms (GSFSC). > >> sDev defines the standard deviation in Angstrom of the 3D Gaussian > >> function that is used for the filtering. How can one now calculate > >> the resolution these filtered maps correspond to? Is it possible to > >> calculate or state a resolution for these maps that is related to > >> the resolution given for the original map (here 2 Angstroms). > >> > >> Thank you very much. > >> > >> Kind regards > >> > >> Dennis > >> > >> > >> > >> > >> Dennis Dannecker > >> Master Student of Biochemistry > >> Department of Chemistry > >> Faculty of Mathematics and Natural Sciences > >> University of Cologne > >> Albertus-Magnus-Platz > >> 50923 Cologne, Germany > >> _______________________________________________ > >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > >> Archives: > >> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ > > > -- > Dennis Dannecker > Master Student of Biochemistry > Department of Chemistry > Faculty of Mathematics and Natural Sciences > University of Cologne > Albertus-Magnus-Platz > 50923 Cologne, Germany > > _______________________________________________ > 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> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ > > VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. > CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. > > > > > > > > > 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

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Chimerax background color gradient
by hu.qi＠mayo.edu 12 Jan '24

12 Jan '24

Hello, Is there a way to set a gradient for the Chimerax background color, or use an image? I know Chimerax can do that but not sure how to do it in Chimerax. Any information is appreciated. QH

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Chimerax background color gradient
by hu.qi＠mayo.edu 12 Jan '24

12 Jan '24

Hello, Is there a way to set a gradient for the Chimerax background color, or use an image? I know Chimerax can do that but not sure how to do it in Chimerax. Any information is appreciated. QH

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Re: [Chimera-users] how to play trajectory frames ?
by Elaine Meng 12 Jan '24

12 Jan '24

Hi Mitch, What program are you using? It looks like you may be reading the ChimeraX help, but ChimeraX is a different program than Chimera. If you are using ChimeraX, you may want to ask questions on the chimerax-users(a)cgl.ucsf.edu list and not chimera-users(a)cgl.ucsf.edu ... We try to keep them separate so that people don't get confused. Also if you are actually using ChimeraX, the "coordsets" option of "open" is only for opening PDB or mmCIF files, not XTC. Just leave it out, and simply open both the PSF and XTC with the "coords" option similar to the third example in the ChimeraX help section linked below, except that your trajectory file is XTC and not DCD: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options> That just opens the trajectory, it does not play it. To play the trajectory in ChimeraX, you would use the slider GUI and/or the "coordset" command, as mentioned in the help section linked above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 11, 2024, at 3:57 PM, Mitch Murphy via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > i tried "open 3ft6.psf coordsets true coords 3ft6.xtc" > but i get "'coordsets' has no suffix" error message. > > and with "open 3ft6.psf coords 3ft6.xtc coordsets true" i get "Expected a keyword". > > how do i play frames of a trajectory. i have the psf and xtc or dcd trajectory files available.

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Angular distribution plot in ChimeraX
by Rayees Mattoo 10 Jan '24

10 Jan '24

Hi, I was trying to make an angular distribution plot using .bild file. I want to show the map inside the plot as in the attachment. Few questions: -My map needs to be flipped to get the correct handedness, I think I need to flip the angular distribution plot as well, how to do that? or do I have to go back and get the .bild file for the flipped map? -How can I change the colors and transparency of the angular distribution plot? -Can I get the particle count for each cylinder in the plot? Wanted to show a scale bar for particle distribution around the sphere of the plot. Best Rayees

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Question regarding gaussian filtering
by Dennis Dannecker 10 Jan '24

10 Jan '24

Hello, I would like to ask a question regarding the gaussian filtering. I filtered a given map (downloaded from the emdb with the "open" command from chimerax) in chimerax using the following command: vop gaussian #1 sDev X with X taking different values ranging from 0.25 to 20 with different steps. Now I would like to know the resolutions these maps actually correspond to after this gaussian filtering. The originally loaded map is stated to have nominal resolution of 2 Angstroms (GSFSC). sDev defines the standard deviation in Angstrom of the 3D Gaussian function that is used for the filtering. How can one now calculate the resolution these filtered maps correspond to? Is it possible to calculate or state a resolution for these maps that is related to the resolution given for the original map (here 2 Angstroms). Thank you very much. Kind regards Dennis Dennis Dannecker Master Student of Biochemistry Department of Chemistry Faculty of Mathematics and Natural Sciences University of Cologne Albertus-Magnus-Platz 50923 Cologne, Germany

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Question about Cylinder Representation
by Bi, Maxine 09 Jan '24

09 Jan '24

Hi there, I've been stuck trying to make my cylinder representation straight instead of curved as the default. I've tried many commands that I can find in the documentation. Could you please guide me if there is a way to just make the cylinders straight? There is a command like that in Pymol as an example (see link: https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefense.com_v3_-5F-… ). Thank you so much, Maxine

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retrieve the sequence of an atom selection
by Engeholm, Maik 09 Jan '24

09 Jan '24

Hi there, I'm looking for a neat way to retrieve the sequence of an atom selection (in this case part of a double-stranded DNA molecule) from within a python script. I've been playing around with: selection = run (session, 'select #1/A:2-4|#1/B:6-9') for a in selection.atoms.unique_residues: print(a) which gives me: 151 atoms, 169 bonds, 7 residues, 1 model selected /A DG 2 /A DG 3 /A DG 4 /B G 6 /B G 7 /B A 8 /B T 9 This is a good start, but ideally I'd like to get back a contiguous sequence string for each chain (like (('A', 'GGG'), ('B', GGAT'))). Also, I do not really understand, why residue names are reported as 'DG' for strand A, but 'G' for strand B, which makes extracting a sequence string from the above output quite difficult. I've also tried: selection = run (session, 'select #1/A:2-4|#1/B:6-9') for a in selection.atoms.by_chain: print(a[1]) print(a[2].unique_residues.unique_sequences[0][1]) which gives me: 151 atoms, 169 bonds, 7 residues, 1 model selected A AGGGAGTAATCCCCTTG B CAAGGGGATTACTCCCT This is obviously also not what I want since it returns the entire sequence of each chain. I guess I could take the residue numbers from the first command and use those to slice the strings returned by the second, but that feels a little awkward, and so I was wondering if there was a better, more direct way to achieve this seemingly simple task. Your help would be much appreciated. Cheers, Maik

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ChimeraX : Cannot recommend to my class until minimization with vital cofactors such as FAD, NADH is built in. Returning to Chimera.
by Anne-Frances Miller 09 Jan '24

09 Jan '24

Dear Sir or Madam, After devoting several days to updating three weeks of my course to use ChimeraX instead of Chimera, I am returning to Chimera. ChimeraX may be a great cutting-edge tool, but it is not ready for a wider audience until it can make ‘common’ tasks easy. Please do not distance research from science. We desperately need science to be exciting and accessible to a wide audience. Chimera does that. ChimeraX does the opposite, sending the clear message that only an elite few are deemed worthy. Please please please, open the door to wider use, for the sake of science, and for the sake of the citizens of our country (who fund your agencies via taxes). Very Helpful - To make images with transparent backgrounds, members of my class as not going to type out ’transparentbackground true’ (even my emailer wants to spell the first string as two words). CRUCIAL - in-program minimization that includes critical cofactors (present in >40% of all enzymes and the actual source of their activities often!!) FAD, FMN, NAD(H), how is this anything more than structural biology if the sources of activity are not included? (‘biology’ implies life. Life REQUIRES chemical reactivity.) CRUCIAL - in-program trajectory analysis that can tabulate (for example) a distance, frame-by-frame and allow export in tabular form. Very Helpful - worms with thicknesses that can represent an attribute. These provide a critical orthogonal way to add a second attribute when color is already in use for a first. Very Helpful - Lighting/effects/side view GUI that allows easy optimization of figure reflectivity, special effects, all in one place and does not require users to remember what Cartesian coordinates they gave their first light. It is so much faster and delivers much better results than ChimeraX. This email records the current worst applicability gaps only, I see others have reported more. I would like to like ChimeraX, but as a person trying to bring science to wide audiences, ChimeraX is the best argument for Pymol I have seen in a while. Do not stop supporting Chimera until ChimeraX can serve real humans, please! Sincerely, and thanks to the team, Anne-Frances Novel Meritorious Research (and teaching) —•—•—•—•—•—•—•—•—•—•—•—•—•— A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

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Depth cueing
by Paul Miller 09 Jan '24

09 Jan '24

Hi How do I depth cue in ChimeraX? In Chimera I used to be able to precisely control this from the side view window but I cannot find any way of controlling depth cueing in ChimeraX. Thank you. Cheers, Paul Paul Miller (he/him), PhD University Lecturer in Pharmacology Department of Pharmacology University of Cambridge Tennis Court Road Cambridge CB2 1PD +44 1223 761267 https://www.phar.cam.ac.uk/research/miller

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Hydrophobic comparison
by M.J. 09 Jan '24

09 Jan '24

Hi Dear ChimeraX developers, I met a problem and cannot find a solution on the website. I have a protein that has two conformations, in those two conformations the hydrophobic character is different, I can show them clearly by the command of mlp in Chimerax, super convenient! My question is that is there a way to show the difference quantitatively? or can be shown in one molecule and color the different on one molecule? (What I means is, for conformation A each residue has a parameter for hydrophobic, so as conformation B, can I get the numbers and do a subtraction correspondingly and know which conformation is more hydrophobic quantitatively, and even I can color one of the conformation by the subtraction). Thanks! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171

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Subscribe
by Hernando J Sosa 05 Jan '24

05 Jan '24

How do I subscribe to this (ChimeraX users) list? When I click the subscribe link in: file:///C:/Program Files/ChimeraX/bin/share/docs/contact.html I get an error message (Page not found). Thanks Hernando ___________________________________ Hernando Sosa, PhD. Dept. of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 emai: hernando.sosa@einsteinmed.<mailto:hernando.sosa@einsteinmed.org>edu ___________________________________ ________________________________ From: chimerax-users-bounces(a)cgl.ucsf.edu <chimerax-users-bounces(a)cgl.ucsf.edu> Sent: Friday, January 5, 2024 12:42 PM To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> Subject: Your message to chimerax-users(a)cgl.ucsf.edu awaits moderator approval CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. Your mail to 'chimerax-users(a)cgl.ucsf.edu' with the subject Python IDE Is being held until the list moderator can review it for approval. The message is being held because: The message is not from a list member Either the message will get posted to the list, or you will receive notification of the moderator's decision.

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Re: Python IDE
by sette＠uniroma2.it 05 Jan '24

05 Jan '24

Yes. Tools --> General -- Shell Best regards, Marco Il 05/01/2024 18:42, Hernando J Sosa via ChimeraX-users ha scritto: > Dear ChimeraX, > > Does chimera-X come with an IDE to edit and run python scripts?, > something like IDLE in Chimera? > > Thanks > Hernando > > ___________________________________ > Hernando Sosa, PhD. > Dept. of Biochemistry > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > emai: hernando.sosa@einsteinmed. <mailto:hernando.sosa@einsteinmed.org>edu > ___________________________________ > > > > _______________________________________________ > ChimeraX-users mailing list --chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email tochimerax-users-leave(a)cgl.ucsf.edu > Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl… -- Dr Marco Sette, PhD. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail:sette@uniroma2.it Tel.: +39-0672594424

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Python IDE
by Hernando J Sosa 05 Jan '24

05 Jan '24

Dear ChimeraX, Does chimera-X come with an IDE to edit and run python scripts?, something like IDLE in Chimera? Thanks Hernando ___________________________________ Hernando Sosa, PhD. Dept. of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 emai: hernando.sosa@einsteinmed.<mailto:hernando.sosa@einsteinmed.org>edu ___________________________________

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Re: [Chimera-users] Changing threshold value of attributes
by Eric Pettersen 05 Jan '24

05 Jan '24

Hi Abril, There are separate mailing list for Chimera and ChimeraX, so you should send ChimeraX questions to chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> . The problem you ran into has been fixed and the fix is in the 1.7 release candidate, so if you use that then things will work. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Nov 28, 2023, at 10:25 AM, Abril Gijsbers via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear community, > > I want to render my model by attribute and change the thresholds (up and bottom limits). I want to change the 0.3 to 0.1 and the 2.6 to 2.7 (see the figure), this way I can compare the colour intensity with other conditions. > <image.png> > > When I do that, I get the following error. My ignorance in command use limits my understanding. Could someone help me out to understand this? I have a colleague that changes the up and bottom limit with no problem. Why? :( > > ui tool show <> "Render By Attribute" > Traceback (most recent call last): > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 759, in _set_value_cb > self._redraw_cb() > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 646, in _redraw_cb > self._bins = left + filled_bins + right > ValueError: operands could not be broadcast together with shapes (0,) (157,) > > ValueError: operands could not be broadcast together with shapes (0,) (157,) > > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 646, in _redraw_cb > self._bins = left + filled_bins + right > > See log for complete Python traceback. > > Traceback (most recent call last): > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 760, in _set_value_cb > self._move_cur_marker(v) > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 570, in _move_cur_marker > self._active_markers._update_plot() > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 1222, in _update_plot > self._update_marker_coordinates() > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 1207, in _update_marker_coordinates > x, y = self._scene_xy(m.xy) > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 1090, in _scene_xy > return self.histogram._scene_xy(abs_xy) > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 512, in _scene_xy > num_bins = len(self._bins) > TypeError: object of type 'function' has no len() > > TypeError: object of type 'function' has no len() > > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 512, in _scene_xy > num_bins = len(self._bins) > > See log for complete Python traceback. > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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volume amount estimation
by Jesse Hansen 05 Jan '24

05 Jan '24

dear ChimeraX users, We have a tomogram volume (.mrc) which we have segmented different components (stl files; surfaces). Is there any tool available to estimate the volume within each of the cellular components (within each surface)? Either some approximation of the cubic Angstrom/nanometers, or as a percentage of the total tomogram volume. thanks in advance! best Jesse Hansen

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looking glass technology for chimerax,
by Krishnan Raman 05 Jan '24

05 Jan '24

Hi guys, Happy new year. I came across this https://www.schrodinger.com/3d-visualization-looking-glass-holographic-disp… . Can we look forward to having this compatible for chimerax since we are having difficulty finding 3D stereo displays for structural biology. Regards Krish Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals 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.

4 3

Tile behavior in Chimera vs ChimeraX - different behavior of independent rotation?
by Oliver Clarke 04 Jan '24

04 Jan '24

Hi all, Happy new year! I have some observations/queries regarding the "tile models" command in Chimera vs ChimeraX. In Chimera, the rotation mode is not linked to a specific mouse mode - so if I change it from "front center" to "independent", this will affect rotation of models regardless of how I do it - whether using the mouse, the trackpad, or using the rock, roll or turn commands on the command line. In ChimeraX, independent rotation is now a separate mousemode - so it only applies to whatever mouse mode (e.g. left mouse) one has it applied to, and does not apply to the trackpad or command line. Is there any prospect of altering this behavior, or mimicking the old behavior? When tiling many models (or maps) for comparison, I like to view them with a rocking motion to give better 3D perception, but now I can't do this (it just rocks the entire "plane" of dispersed models, rather than each independently). Cheers Oli

3 3

Error when trying to run previously working script
by Alexander Hung Lee 04 Jan '24

04 Jan '24

I have a .py script that successfully works on 400 pdb's. I tried using the same script to open a single pdb containing several thousand models. ChimeraX quit and sent me this error message in terminal "Release of profile requested but webenginepage still not deleted" Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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ChimeraX Inquiry
by ‍강유은[학생](대학원 생명공학원) 03 Jan '24

03 Jan '24

Hello I would like to purchase the premium GPU A100 to predict large proteins. How can I get access to the purchasing page? Regards, Yoo Kang

2 1

Problems with installation
by Roger Cole 01 Jan '24

01 Jan '24

Good Evening I wanted to asked about compatibility and installation issues. I am currently using a Chromebook with Linux Debian 11 (Bootstrap) and I am trying to get ChimeraX 1.7 installed onto it. I keep coming into errors when I try to run it by the way specified on the site. For info: " Download is a tarball of the chimerax application directory. Make symbolic link to executable in chimerax/bin/ChimeraX. Do not put on path. It may require additional libraries and/or older versions of libraries to be installed. More Info...built: 2023-12-19 02:49:21 PST committed: 2023-12-19 00:36:03 PST size: 584.1 MiB md5: d44f016e787d45621a077b04852ab66c sha256: 005bd0b6942b5e8c3a32ad39bb6ea1118da173217c2c0c51d3e0c665913e6c3a I used the Generic Linux download and with all i could look up with and try to figure out with ChatGPT, I get this when I try to run it: "NOTE: available bundle cache has not been initialized yet WARNING: Traceback (most recent call last): File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 376, in initialize api._api_caller.initialize(api, session, self) File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1294, in initialize return cls._get_func(api, "initialize")(session, bi) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/__init__.py", line 31, in initialize from .ui.segmentation_mouse_mode import ( File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/ui/segmentation_mouse_mode.py", line 20, in <module> from .segmentations import SegmentationTool File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/ui/segmentations.py", line 55, in <module> from ..ui.orthoplanes import Axis File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/ui/orthoplanes.py", line 51, in <module> from ..graphics import ( File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/graphics/__init__.py", line 1, in <module> from .view import OrthoplaneView File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/graphics/view.py", line 6, in <module> from chimerax.graphics import gllist File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/graphics/gllist.py", line 71, in <module> wrap_opengl_routines(globals()) File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/graphics/gllist.py", line 22, in wrap_opengl_routines from OpenGL import GL File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/OpenGL/GL/__init__.py", line 4, in <module> from OpenGL.GL.VERSION.GL_1_1 import * File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_1.py", line 14, in <module> from OpenGL.raw.GL.VERSION.GL_1_1 import * File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/OpenGL/raw/GL/VERSION/GL_1_1.py", line 7, in <module> from OpenGL.raw.GL import _errors File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/OpenGL/raw/GL/_errors.py", line 4, in <module> _error_checker = _ErrorChecker( _p, _p.GL.glGetError ) ^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'glGetError' ERROR: Bundle 'ChimeraX-Dicom' custom initialization failed NOTE: Traceback (most recent call last): File "<frozen runpy>", line 198, in _run_module_as_main File "<frozen runpy>", line 88, in _run_code File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/core/__main__.py", line 1069, in <module> exit_code = init(sys.argv) ^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/core/__main__.py", line 722, in init sess.ui.build() File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/ui/gui.py", line 191, in build self.main_window = mw = MainWindow(self, self.session) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/ui/gui.py", line 445, in __init__ self.graphics_window = g = GraphicsWindow(self._stack, ui, stereo) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/ui/graphics.py", line 36, in __init__ oc = OpenGLContext(self, ui.primaryScreen(), use_stereo = stereo) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/graphics/opengl.py", line 60, in __init__ _initialize_pyopengl() # Set global GL module. ^^^^^^^^^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/graphics/opengl.py", line 375, in _initialize_pyopengl import OpenGL.GL File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/OpenGL/GL/__init__.py", line 4, in <module> from OpenGL.GL.VERSION.GL_1_1 import * File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/OpenGL/GL/VERSION/GL_1_1.py", line 14, in <module> from OpenGL.raw.GL.VERSION.GL_1_1 import * File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/OpenGL/raw/GL/VERSION/GL_1_1.py", line 7, in <module> from OpenGL.raw.GL import _errors File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/OpenGL/raw/GL/_errors.py", line 4, in <module> _error_checker = _ErrorChecker( _p, _p.GL.glGetError ) ^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'glGetError' BUG: AttributeError: 'NoneType' object has no attribute 'glGetError' File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/OpenGL/raw/GL/_errors.py", line 4, in _error_checker = _ErrorChecker( _p, _p.GL.glGetError ) ^^^^^^^^^^^^^^^^ _See log for complete Python traceback._ NOTE: Exception ignored in: <function OpenGLContext.__del__ at 0x7e24611d5a80> Traceback (most recent call last): File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 85, in __del__ if not self._deleted: ^^^^^^^^^^^^^ AttributeError: 'OpenGLContext' object has no attribute '_deleted'" This is as far as i could get I apologize about the lengthy message, and thank you for any assistance you can give -CJ

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Recover unsaved ChimeraX session?
by André Graça 29 Dec '23

29 Dec '23

Dear all, happy Holidays! I am not very optimistic about this one, but I will just drop the question here and it may simply be that I am unaware of this function: I had a ChimeraX session crashing just when I was about to save it for the first time... is there any way to recover unsaved ChimeraX session, such as temporarily saved files? Thank you, André

2 2

PDB Conversion to Mol2 File Inquiry
by Joel Subach 28 Dec '23

28 Dec '23

Hello Chimerax, I hope you're well:). Towards the above subject, SwissParam has recommended UCSF Chimera to convert my pdb to a Mol2 File for SwissParam subsequent parameterization, however, I could not discover this webpage within your UCSF Chimerax Website? Thanks if you can clarify how I may generate this Mol2 via yout Chimera if able. Best, Joel 🚀

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Error in using alphafold by ChimeraX
by Ping-Hung Chen 陳炳宏 26 Dec '23

26 Dec '23

Hi, I tried to run Alphafold prediction by ChieraX, and it appears below Error. Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. INFO:__main__:Starting prediction on 2023-12-26 UTC time INFO:__main__:Installing ColabFold on Google Colab virtual machine. --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-8-1833a07b73e1> in <cell line: 329>() 327 remove_from_list(seq_list, 'prokaryote') # Obsolete "prokaryote" flag 328 --> 329 run_prediction(seq_list, use_templates = use_templates, energy_minimize = not dont_minimize) 7 frames /usr/local/lib/python3.10/dist-packages/alphafold/data/mmcif_parsing.py in <module> 22 from absl import logging 23 from Bio import PDB ---> 24 from Bio.Data import SCOPData 25 26 # Type aliases: ImportError: cannot import name 'SCOPData' from 'Bio.Data' (/usr/local/lib/python3.10/dist-packages/Bio/Data/__init__.py) --------------------------------------------------------------------------- Would you like to help me with it? Thank you. Sincerely, PH Ping-Hung Chen, Ph.D., Assistant Professor Institute of Biochemistry and Molecular Biology College of Medicine, National Taiwan University Address: R913, No.1, Sec.1, Ren-Ai Rd., Zhongzheng Dist., Taipei 10051, Taiwan (R.O.C.) E-mail: pinghungchen(a)ntu.edu.tw; phcrose(a)gmail.com Phone: +886 2-23123456 Ext. 88864

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Re: How to save a sequence in an mmCIF file?
by Greg Couch 22 Dec '23

22 Dec '23

To answer the general question, ChimeraX doesn't yet have a way to set the full sequence for a mmCIF entity. See https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files for how to fix the mmCIF output from various refinement packages. For example, the Phenix has "mmtbx.prepare_pdb_deposition program to create a mmCIF file with the sequence". In this particular case, where the starting structure is an Alphafold prediction with atoms for every residue in the full sequence, you can get the correct sequence into the mmCIF output with the "bestGuess" option. See https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#mmcif. I'd also recommend, in your case, using the computedSheets option. In older ChimeraX's, you need to run dssp before using computedSheets to get the helix information. In recent ChimeraX's (daily build and 1.7 release candidate), computedSheets will also output the helix information if it wasn't present in the input. Adding a sequence with bestGuess can be deceiving of because missing leading or trailing residues, or gaps of indeterminate length. But in this case, you should be fine. -- Greg On 11/29/23 02:45, Guillaume Gaullier wrote: > *From: *Guillaume Gaullier via ChimeraX-users > <chimerax-users(a)cgl.ucsf.edu> > *Subject: **[chimerax-users] How to save a sequence in an mmCIF file?* > *Date: *November 29, 2023 at 2:45:31 AM PST > *To: *"chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> > *Reply-To: *Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se> > > Hello, > > Starting from an AlphaFold prediction, I refined a model against a map > with ISOLDE. I trimmed the segments not supported by any density. The > resulting mmCIF file that I saved now opens with this warning: > > Unknown polymer entity '1' near line 187 > Missing or incomplete entity_poly_seq table. Inferred polymer > connectivity. > > Displaying the sequence of this chain shows the correct numbering > (with jumps in numbering according to missing segments in the > structure), but the sequence of the missing structure segments is not > displayed. > > When I open the fasta file containing the full-length sequence, the > sequence gets automatically associated to the structure, and the > sequence viewer annotates the segments with missing structure > correctly. I would like to save this full-length sequence in my mmCIF > file so the full-length sequence with annotated missing structure > segments shows up next time I open this file. But when I try to save > at this point, I get the following notice: > > Not saving entity_poly_seq for non-authoritative sequences > > The documentation for "save" and "sequence" didn't help. How can I > make this sequence "authoritative" and save it into my mmCIF file? > > 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_______________________________________________ > ChimeraX-users mailing list --chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email tochimerax-users-leave(a)cgl.ucsf.edu > Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl… >

6 18

autodock Vina
by Michael Sacher 22 Dec '23

22 Dec '23

I am running Chimera X. I downloaded autodock Vina. It should show as a tool>surface binding analysis but it is not there. How do I get the surface binding analysis option to show and to display Vina? Thanks. Michael

2 3

Cannot launch ChimeraX 1.7 GUI on Red Hat Enterprise Linux 9.3
by Wen 21 Dec '23

21 Dec '23

Dear Elaine, I tried to install ChimeraX 1.7 on Red Hat Enterprise Linux 9.3. yum install mesa-libOSMesa-21.3.4-2.el9.x86_64.rpm yum install ucsf-chimerax-1.7-1.el9.x86_64.rpm Everything went well. However, when I tried to launch ChimeraX, I met the following errors: [wenliu@localhost Downloads]# chimerax QStandardPaths: runtime directory '/run/user/800' is not owned by UID 0, but a directory permissions 0700 owned by UID 800 GID 800 QStandardPaths: runtime directory '/run/user/800' is not owned by UID 0, but a directory permissions 0700 owned by UID 800 GID 800 NOTE: available bundle cache has not been initialized yet NOTE: Traceback (most recent call last): File "<frozen runpy>", line 198, in _run_module_as_main File "<frozen runpy>", line 88, in _run_code File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/__main__.py", line 1069, in <module> exit_code = init(sys.argv) ^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/__main__.py", line 664, in init toolshed.init(sess.logger, debug=sess.debug, File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1389, in init _toolshed = Toolshed(*args, **kw) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 396, in __init__ settings.toolshed_last_check = now.isoformat() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/settings.py", line 199, in __setattr__ ConfigFile.__setattr__(self, name, value) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/configfile.py", line 386, in __setattr__ ConfigFile.save(self) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/configfile.py", line 335, in save with SaveTextFile(self._filename) as f: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/safesave.py", line 191, in __init__ SaveFile.__init__(self, filename, open=open_text, critical=critical) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/safesave.py", line 80, in __init__ raise OSError(errno.ENOTDIR, os.strerror(errno.ENOTDIR), save_dir) NotADirectoryError: [Errno 20] Not a directory: '/do/not/run/as/root/.config/ChimeraX' BUG: NotADirectoryError: [Errno 20] Not a directory: '/do/not/run/as/root/.config/ChimeraX' File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/safesave.py", line 80, in __init__ raise OSError(errno.ENOTDIR, os.strerror(errno.ENOTDIR), save_dir) _See log for complete Python traceback._ ChimeraX did not launch. Could you advise me on how to proceed? Thanks in advance. Wen Liu @ UCHC

2 1

ISOLDE 1.7 released
by Tristan Croll 21 Dec '23

21 Dec '23

Hi all, To follow the recent announcement of the ChimeraX 1.7 release, I'm happy to announce the matching release of ISOLDE 1.7. Should now be available for installation from the ToolShed. I've also put up a new build of the QScore plugin compatible with Python, allowing it to be used with recent ChimeraX versions. Happy holidays (and happy modelling)! Best, Tristan -- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

1 0

ChimeraX Log File Question
by Bani Kaur 20 Dec '23

20 Dec '23

Hi, I hope you are doing well! My name is Bani Kaur and I am a ChimeraX user. I wanted to ask you how I would be able to download my log file - I am not able to figure out what line to put into the system. Thank you so much! Best, Bani kaur

2 2

ChimeraX protein-protein binding site modeling question
by Parks, Ryssa 20 Dec '23

20 Dec '23

Hello, I work in a lab that researches biopesticides in the form of insect neuropeptides, which bind to receptor proteins. I am trying to use ChimeraX to model potential binding sites between peptide ligands and their corresponding receptor. Does ChimeraX have this capability? When I was trying to figure this out myself online through the ChimeraX Youtube tutorials and tutorials on the UCSF site, I came across a comment on a video that mentioned I could upload the sequences of my receptor and peptide ligand separated by a comma, and model it as a protein complex, and then I can get information on where the two molecules interact. I'm relatively new to protein research, and so I hadn't yet thought of ligand-protein interactions as a type of protein complex. My specific questions are: * When modeling a peptide ligand and a receptor as a protein complex, will ChimeraX accurately predict the relationship between the two molecules based on binding compatibility? Or is it based on something else, like similarity of sequence alignments...? * If multiple binding sites are possible, is there any way to view the different options for multiple binding sites? Or is there any way to restrict the area on the receptor to which my target peptide ligand is predicted to bind (i.e. the extracellular region only)? * The peptide ligands are only 7-9 amino acids in length and do not take very long to model, but the receptor is about 600 amino acids and takes a much longer time to model. Do I have to model protein complexes by re-modeling everything for each different receptor-ligand combination, or can I combine existing models somehow? I hope these questions aren't too troublesome, and I hope I haven't grossly misunderstood ChimeraX's capabilities. Thank you for your time, Ryssa Parks

3 2

Problem with Snap Installation
by Stephen P. Molnar 20 Dec '23

20 Dec '23

I have had Chimerax.flatpack installed on by Debian Bookworm Platform. As a result of a system crash I was force to reinstall the OS. When I attempted a reinstallation on the New OS I got the following error: error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/22.08 which was not found Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

3 5

ISOLDE messes with view?
by Alexis Rohou 20 Dec '23

20 Dec '23

Hello, I've just noticed that the view command doesn't behave as expected after I have started ISOLDE. Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored. I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE. Cheers, Alexis

3 9

Adjust Torsions section of Build Structure is missing
by duhq 20 Dec '23

20 Dec '23

3 4

Log auto-scrolling
by Alexis Rohou 19 Dec '23

19 Dec '23

Hi, Is there a way to make sure that the Log window stays scrolled all the way to the end of the log? I keep having to scroll back down to see the output of the last command I issued. Perhaps this is because I scrolled back up at some point, I'm not sure. Either way, it'd be nice to have the option to switch on (and off) "auto scroll" for the Log window. Cheers, Alexis

2 2

Support for unknown amino acid and nucleotide
by Vorländer,Matthias Kopano 19 Dec '23

19 Dec '23

Dear ChimeraX team, When depositing models in the PDB, it is often necessary to change the nucleotide or amino acid type to “Unknown” when the resolution is not good enough to identify the register (https://www.wwpdb.org/documentation/procedure) Would it be possible to extend the functionality of the swapna and swapaa commands to support changing residues into UNK for proteins and N/DN for nucleic acids? Many thanks in advance, Matthias

2 2

ChimeraX 1.7 release!
by Elaine Meng 19 Dec '23

19 Dec '23

UCSF ChimeraX version 1.7 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 Updates since version 1.6 (May 2023) include: New graphical interfaces: - Fetch By ID - Map Filter - Adjust Torsions (new section in Build Structure) - Adjust Angles defined by three atoms (also in Build Structure) Open command options to: - specify model number - combine incoming session with existing session - designate map as difference map (show +/-contours automatically) - fetch by IUPAC name (also in Build Structure tool) - fetch EMDB map + fit structures Mouse mode updates: - new mouse mode to center the view on the clicked item - better separation of trackpad multitouch zoom and rotate - Z-translation by additionally pressing Ctrl in a translation mouse mode Other: - invert selection with left/right arrow keys - mcopy command to copy settings from one atomic structure to another - save GLTF options to cull backfaces, omit per-vertex colors, omit normals - volume defaultvalues command to set defaults for subsequently opened maps - info command saveFile option (list selection, attribute values, etc.) - opening docking results automatically starts ViewDockX - button to save Blast Protein results to TSV For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

extract highlighted residue with sequence number
by paul.protein.test＠gmail.com 19 Dec '23

19 Dec '23

Hi All I am highlighting all residues that are involved in a protein-protein interaction. Is there anyway to extract a list including all residues and associated sequence number, or display in log?

2 1

Re: extract highlighted residue with sequence number
by Luca Genz 19 Dec '23

19 Dec '23

Hi, there is a plug-in in the ChimeraX toolshed called PICKLUSTER that can identify the residues in the protein interface, colors them and reports a list of the residues in the interface with their sequence number in the Log. It can also report the contacts and can color the interface residues in the sequence. Hope that helps!

1 0

how to set pH level from ChimeraX
by Chang Jang 18 Dec '23

18 Dec '23

Dear ChimeraX help, I am using ChimeraX 1.6.1. Would anyone know how to "*set or change and check*" a pH level of a protein or a system from the software? Thanks, Chang Woon

2 1

AUTODOCK VINA - CHIMERAX (Candidate version 1.7rc202312150000)
by Emmanuel Funsho Alakunle 18 Dec '23

18 Dec '23

Good day, Please I am running Chimera-x ( Candidate version 1.7rc202312150000) on windows11, and I cannot locate the autodock vina plugin. Kindly help. Thanks *Emmanuel Funsho Alakunle* *Natural and Environmental Sciences (Biomedical Science)* *American University of Nigeria* *Yola-by-pass, PMB 2250, Yola* *Nigeria.* *P:+234(0)8108074431* *Skype:* *Linkedin: **linkedin.com/in/emmanuel-alakunle-356088154 <https://www.linkedin.com/in/emmanuel-alakunle-356088154>*

2 1

RAMACHDRAN PLOT - CHIMERAX
by Emmanuel Funsho Alakunle 17 Dec '23

17 Dec '23

Good day, Please I am running Chimera-x on windows11, and I cannot generate ramachdran plot. Kindly help. Thanks *Emmanuel Funsho Alakunle* *Natural and Environmental Sciences (Biomedical Science)* *American University of Nigeria* *Yola-by-pass, PMB 2250, Yola* *Nigeria.* *P:+234(0)8108074431* *Skype:* *Linkedin: **linkedin.com/in/emmanuel-alakunle-356088154 <https://www.linkedin.com/in/emmanuel-alakunle-356088154>*

3 3

savefile command
by Bajaj, Ruchika 17 Dec '23

17 Dec '23

Hi I am trying to use the following commands for selected atoms. I am trying this "info atoms sel" and it is working. However, I am not able to use saveFile file commands. Could you please help me with its usage. I'd appreciate your help in this regard. Thanks !! Regards Ruchika info atoms atom-spec<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/atomspec.html> [ attribute attribute-name ] [ saveFile<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#saveFile> file ]

2 1

Density map on ligand
by Louis Fellipe Moreno Oliveira 16 Dec '23

16 Dec '23

Hello, I hope this email finds you well. My name is Louis OIiveira, and I am a Master's student specializing in protein crystallography at the University of São Paulo. I am currently using Chimera X for generating images of the structure I am studying. However, I have encountered some issues that I am struggling to resolve. Specifically, I have successfully validated the structure of the enzyme and am now attempting to present the co-crystallized ligand along with its electronic density map interacting with the enzyme. My challenge lies in isolating the electronic density of the ligand without including the electronic density of the nearby residues. I have attempted to use the "zone" function in the map menu, but I am still seeing some electronic density that I wish to exclude as shown in the picture . I would greatly appreciate your guidance on how to effectively isolate the electronic density of the ligand in Chimera X. If you have any insights or recommendations, I would be grateful for your assistance. Thank you for your time, and I look forward to hearing from you soon. Best regards, Louis Oliveira Master's Student Instituto de Fisica de São Carlos University of São Paulo

2 2

insertion codes in labels
by Alexis Rohou 14 Dec '23

14 Dec '23

Hello, A two part question from me today: Part A. What is the syntax to get the label command to show insertion codes? As far as I can tell, insertion codes are not attributes. I can see that the insertion code is part the residue ID, but I don't know how to specify it as part of the label command. Part 2. Would you consider having residue labels show insertion codes by default? This would be very useful when labeling residues from antibodies with Kabat numbering, for example, and my guess is it wouldn't "hurt" existing usage. My apologies to Elaine in advance if I missed all this in the documentation. Cheers, Alexis

2 2

command line to save multiple models
by Rayees Mattoo 13 Dec '23

13 Dec '23

Hi, I volume flipped 20 different models (#1 to #20) and now I want to save all the 20 flipped maps as .mrc with the same name as before and add flip in their names. How could I modify the save command line to do that? Best

4 6

'Send to Quest' button not available
by Wiesler, Marie-Christin (Manufacturing, Clayton) 12 Dec '23

12 Dec '23

Dear User Guides, I am trying to send a file from ChimeraX to LookSee, in order to visualise it on my Meta Quest Pro headset. The tool 'Send to Quest' is not available in ChimeraX on my desktop, it is supposed to be in Tools/General. Thanks in advance! Mary

2 4

unexpected surface "shimmering" when model argument is given to turn command with soft lighting
by Alexis Rohou 12 Dec '23

12 Dec '23

Hi all, I was playing around with movies where I rotate models around their own centers and noticed an unpleasant (to my eye) rendering glitch. Steps to reproduce (this is with 1.7rc202311150127): close open pdb:7vja; lighting soft; surf; ~show; view movie record; turn y 1 360 model #1; wait 360; movie encode test_spin_model.mp4 movie record; turn y 1 360; wait 360; movie encode test_spin.mp4 So we have two "spin" movies of the same surface, but one of them ("test_spin_model.mp4") has a shimmering artefact. At first I mistook this for a video compression artefact, but it's there in the "live" rendering and it disappears if I drop the "model" argument to the "turn" command. Also, I can't reproduce this if I don't use soft lighting. I will try to send the movies as attachments to a reply to this email (not sure they'll go through). Cheers, Alexis

2 3

rainbow "structures" different from single chain specifier
by vincent Chaptal 12 Dec '23

12 Dec '23

Hi, on a pdb ensemble, when I use: rainbow #1 structures palette blue:cyan it colors the whole chain 1.1 blue and varies the color to cyan all the way to chain 1.20 (which is what I want). However, if I want to color a specific chain differently using: rainbow #1.1-10/O palette red:yellow it colors the rainbow from N-ter to C-ter for all the chains. How can I apply the first type of coloring (structures) to a specific chain? 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 4

augment mousemode center with cofr centerofview; alter animation frames
by leeyang+chimerax＠gmail.com 11 Dec '23

11 Dec '23

Hi, I find the mousemode center function very useful when navigating around a model. One of the features I loved about the original Chimera. Would it be possible to have the option to augment it with a cofr centerofview feature so that the pivotpoint then follows subsequent translation? Also, would it be possible to define a custom number of frames over which the animation occurs? Cheers, Yang

2 3

Re: AlphaFold to run .pkl file and the tax error
by Tom Goddard 11 Dec '23

11 Dec '23

Hi Serhat, AlphaFold does not provide docking scores or energy minimization scores as far as I know. AlphaFold estimates pTM (predicted TM) and ipTM (interface predicted TM) scores related to prediction accuracy. You might want to google molecule TM score to learn about those. And googling Alphafold iptm gives as the top hit a paper describing those scores Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes https://academic.oup.com/bioinformatics/article/39/7/btad424/7219714 ChimeraX does not show you those scores but does have ways of visualizing the pLDDT (predicted local distance difference test) and PAE (predicted aligned error) generated by AlphaFold, described here https://www.rbvi.ucsf.edu/chimerax/data/pae-apr2022/pae.html And you may be interested in ChimeraX videos about visualizing AlphaFold confidence https://youtu.be/oxblwn0_PMM https://youtu.be/TMcjEecFHaI and more ChimeraX AlphaFold videos here https://www.rbvi.ucsf.edu/chimerax/docs/videos/ The .pkl (Python pickle) files contain data such as PAE scores. ChimeraX can read pkl file to show the scores as described in the above links. The alphafold issue #629 you reference about AlphaFold inserting jax data structures into .pkl files was long ago fixed in both AlphaFold and ChimeraX 1.5 as described in the link you sent. The solution is of course to update the version of ChimeraX and AlphaFold you are using. If you are using any ChimeraX version to run AlphaFold it is using a current AlphaFold. But ChimeraX AlphaFold runs don't produce .pkl files so I guess you are running an old AlphaFold in a different. Tom > On Dec 11, 2023, at 4:23 AM, serhat inceer <serhatinceer(a)yahoo.com> wrote: > > Dear Tom Goddard > > > My name is Serhat Inceer Researcher at the University of Vienna department od Molecular Biology, and I am reaching out to seek assistance regarding the interpretation of docking scores and multimer energy minimization scores in AlphaFold. > > Additionally, I have questions about running ".pkl" files to analyze plDDt graphs for the predicted and ranked models that I have already predicted models. > > Specifically, I am interested in understanding the methodology and significance of the docking score and multimer energy minimization score provided by AlphaFold. Could you please provide more information on how these scores are calculated and what they signify in the context of protein structure prediction? > > Furthermore, I have generated ".pkl" files for my predicted models, and I am interested in running them to obtain plDDt graphs. Could you please guide me on the steps to run the ".pkl" files for this purpose? Any documentation or resources that outline the process would be greatly appreciated. > > According my research on GitHub you got also same error and I am wondering about how could you fit it this situation > > https://github.com/google-deepmind/alphafold/issues/629 > > Thank you very much for your time and assistance. I look forward to your response. > > Best regards, > > Serhat Inceer > >

1 0

Smooth-MD script for a trajectory visualisation
by Enrico Martinez 08 Dec '23

08 Dec '23

Dear Chimera-X users. I am trying to record a md trajectory loaded as multi-pdb file: open ./stripped_traj2.pdb coordsets true I have the issue with smooth-md script (enclosed), which produces the following error: open smooth_md_chX.py open /home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.pyTraceback (most recent call last): File "/home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.py", line 23, in <module> avg += weight * coord_sets[j] ValueError: operands could not be broadcast together with shapes (6120,3) (6112,3) (6120,3) Should something be fixed in the script in order that I could observe the MD movie with smooth details ? Thank you in advance Enrico

2 9

Re: Following Up on Drawing Outlines
by Tom Goddard 07 Dec '23

07 Dec '23

Hi André, There is only one selection outline in ChimeraX so you cannot show different color outlines directly in ChimeraX using the selection outline. Here are a couple ideas. You could select all your sites and make one outline around all of them in green and then in Photoshop change the color of parts of the outline to the appropriate colors. Another idea is you can select each patch and make its outline in the correct color and then just save that outline but not the surface. To show just the outline and not the surface you would make the surface 100% transparent and hide atoms transparency 100 hide atoms save outline1.png transparentBackground true. Save each outline as a separate image and then layer them on top of your surface in Photoshop. A problem with both of these methods is that your patches border each other so the outlines will overlap. In fact the selection outline extends outward when you make it thicker (ChimeraX avoids covering the patch with the outline). So two adjacent patches with different outlines are going to draw the outlines intersecting and crossing each other where they adjoin each other. Making the outlines extend inward could be done in Photoshop by fattening the individual layer outlines. This gets into a lot of hand work. Tom > On Dec 7, 2023, at 1:15 PM, Andre Leon <aleon(a)scripps.edu> wrote: > > Hello Tom, > > Thank you for the response! I'm guessing the answer to my next question is no, but I was wondering if there's a way to create these selection outlines around multiple regions to create figures similar to the one below, highlighting all the major antigenic sites on influenza HA. That way I can simultaneously outline the epitopes and also color the figure by sequence conservation as opposed to doing one or the other. If that's not possible, than I will pseudo outline in Illustrator or Photoshop, but it would be ideal to be able to specifically highlight the exact residues using ChimeraX. > > Again, thank you so much for your rapid response! > > > Best Regards, > André Nicolás León > Graduate Student - Ward Lab <https://ward.scripps.edu/> > https://www.linkedin.com/in/andrenicolasleon/ > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, December 7, 2023 12:25 PM > To: Andre Leon <aleon(a)scripps.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Following Up on Drawing Outlines > > Hi André, > > Making a thick colored outline around an epitope on a protein surface is easier in ChimeraX using thick selection outlines. The link you mentioned from 2014 is from our old program Chimera which could only draw thin 1 pixel wide outlines. Here is an example in ChimeraX where I make a thick (10 pixel wide) red outline around some residues. > > open 2x7r > hide ~/C atoms > surface /C > select /C:670-681 > graphics selection color red width 10 > > Tom > > > >> On Dec 7, 2023, at 10:53 AM, Andre Leon via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hello Chimerax, >> >> I was wondering if there has been any progress on making outlines of specific epitopes in ChimeraX since this thread back in 2014? <https://www.cgl.ucsf.edu/chimera/data/outline-may2014/outlines.html> Thank you in advance. >> >> Best Regards, >> André Nicolás León >> Graduate Student - Ward Lab <https://ward.scripps.edu/> >> https://www.linkedin.com/in/andrenicolasleon/ >> _______________________________________________ >> 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> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

2 1

Following Up on Drawing Outlines
by Andre Leon 07 Dec '23

07 Dec '23

Hello Chimerax, I was wondering if there has been any progress on making outlines of specific epitopes in ChimeraX since this thread back in 2014?<https://www.cgl.ucsf.edu/chimera/data/outline-may2014/outlines.html> Thank you in advance. Best Regards, André Nicolás León Graduate Student - Ward Lab<https://ward.scripps.edu/> https://www.linkedin.com/in/andrenicolasleon/

2 1

Add charge to PDB fails
by Daniel Hsu 06 Dec '23

06 Dec '23

Hi All What might cause this action to fail, pH=7.4, H added to protein before adding charge? No errors were thrown. Both DOCK-Prep, and adding H then charge both do not change the PDB file (no charges added to respective atoms). Log reports "Using Amber 20 recommended default charges and atom types for standard residues" Alternative command 'addcharge standardizeResidues 5BU,CSL,MSE,UMS' reports "Using Amber 20 recommended default charges and atom types for standard residues" and no errors but don't add charges to saved PDB file. Charges are added with another structure editor. Thanks for insights! **CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error, be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message.

3 5

Surphace representation of multi-model pdb and moovie recording
by Enrico Martinez 06 Dec '23

06 Dec '23

Dear Chimera-X users ! I am working on molecular visualization of membrane system from the md trajectory loaded in the Chimera-x using the open coordset true command. The issue is with the surface representation of the membrane: transparency :OL,PA,PE,PC 80 target s which are applied only on the current frame (not on the whole trajectory). Also when I try to make a movie of the system the presence of the surface does slow down everything. Which options could be useful e.g. to decrease the quality of the surface representation ? Many thanks in advance Enrico

3 7

ChimeraX & ConSurf
by martin.brehm＠univie.ac.at 05 Dec '23

05 Dec '23

Dear ChimeraX developers, I have a question regarding a potential upgrade of ChimeraX. Would it be possible to include the functionality of ConSurf, a tool to plot the degree of sequence conservation onto a model, into ChimeraX? The code for this is publically available on GitHub: https://github.com/Rostlab/ConSurf See this publication for more information: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987940/ Thanks a lot in advance and have a nice day! Best regards Martin Brehm Martin Brehm - PhD Student Falk Lab - Max Perutz Labs Vienna Room 1.624 - Phone +43 14277 74361 martin.brehm(a)univie.ac.at

4 5

ISOLDE on Mac M1/M2/M3 or on Linux CentOS 7
by Mark Hilge 05 Dec '23

05 Dec '23

Hello, Could you please tell me whether your latest Version of ISOLDE would either run on a Mac with an Apple Silicon chip (M1, M2, or M3) or on a Linux box with CentOS 7 installed? Many thanks in advance! Kind regards, Mark

2 1

Missing tools in ChimeraX
by Lars Backman 05 Dec '23

05 Dec '23

Hi, In Chimera, a tool named “Viewing” was available. It was an excellent tool to adjust appearance of the final png or jpg figure. I have looked for a similar tool in ChimeraX, but it seems to be absent. Or is there a way to create something similar? Best regards, Lars Backman [signature_2226121467] Lars Backman Professor Department of Chemistry, Biochemistry Umeå University SE-90187 Umeå, Sweden Tel: (46) 070 833 9946 e-mail: lars.backman(a)chem.umu.se<applewebdata://6E905793-FDA7-4651-8DC6-A97D8021B9DD/lars.backman@chem.umu.se> http://staff.chem.umu.se/lars.backman/research/ När du skickar e-post till Umeå universitet så innebär detta att Umeå universitet behandlar dina personuppgifter. För att läsa mer om hur detta går till, gå till www.umu.se/gdpr<http://www.umu.se/gdpr> By sending an email to Umeå University, the University will need to process your personal data. For more information, please read www.umu.se/en/gdpr<http://www.umu.se/en/gdpr>

2 2

Exporting scene with .obj and .mtl file
by Berndsen, Zachary 04 Dec '23

04 Dec '23

Hello, I need to export an obj file along with the associated mtl file, however, under the “file > save” option, there is only an option for saving as .obj, not .mtl. I read in the online documentation that there should be the capability to “export a scene” which saves an obj and mtl file, however I do not see this option when using v 1.6.1. Is this still supported? Thanks, Zack

3 3

Python Function that implements the "center" method from the GUI
by tong.you＠icm.uu.se 01 Dec '23

01 Dec '23

Hello, For an automatic pipeline workflow, I want to have a way to center several mrc files using the Python module. However, I can't seem to find the corresponding Python function that I can use in a script to "center" an opened map. Is there a Python function to "center" a map similarily as in the GUI? Kind regards, Tong

2 1

Independent movement of chains in movie
by Caroline Stone (JIC) 30 Nov '23

30 Nov '23

Dear ChimeraX team and list subscribers, I am making a little movie to show a complex of two proteins, but am stuck on individual movements of chain /A and /B. If I use the move command, chain /A and /B both move independently, away from each other: move x -10 atoms /A; move x 10 atoms /B However, if I attempt to do the same movement by going -1 or +1 over a series of 10 frames, I no longer get any movement of /A and /B. move x -1 10 atoms /A; move x 1 10 atoms /B I can achieve movement over a number of frames, but both chains move although I tried to specify only /A. I did this based on "move axis [ distance [ frames ]]". move x -1 10 atoms /A I feel I might be on the right track because when I use turn, I am able to trigger simultaneous independent rotation of /A and /B around their own axes (thank you for this feature by the way, last time I wondered about this it wasn't possible). cofr /A; turn y -1 90 atoms /A; cofr /B; turn y 1 90 atoms /B My ultimate goal is to open the binding interface up a bit like opening a book. I suppose I could achieve a similar effect by setting the centre of rotation for each chain behind, rather than within - if independent movement over a series of frames isn't possible, I might experiment with that. I updated to version 1.6 and searched the list, but I still see this behaviour with the move command. Perhaps I am missing something basic? Thank you for any pointers you might be able to share! Caroline

3 4

"view" in command line vs. menu
by C. Klein 30 Nov '23

30 Nov '23

Dear Eric, Oliver, et al. you may remember my comment on the missing "focus" function. Anyhow, what I noticed now is interesting: The function of the "view" command is different in the menus vs. the command line. in the command line, "view" will zoom out and show everything in the menu, "view" will focus on the selected ligand or whatever (which is what I want a bit more, mostly) Perhaps this could be resolved with modified or rather re-surrected terminology: Focus on selection: "focus" in command line "focus on selection" in menu Zoom to fit all: "zoomall" in command line "zoom to fit all" in menu just some suggestions. But what I think is clear is that the function of commandos should be identical in menu and command line. Again, thank you very much for your important and good work on the Chimera software. Best wishes Christian OpenGL version: 3.3.0 NVIDIA 452.56 OpenGL renderer: Quadro P620/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: LENOVO Model: 30C5004VGE OS: Microsoft Windows 11 Pro (Build 22621) Memory: 17,010,716,672 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 comtypes: 1.1.14 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pywin32: 305 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 WMI: 1.5.1 zipp: 3.15.0 -- Prof. Dr. C. Klein; c.klein(at)uni-heidelberg.de Medicinal Chemistry Institute of Pharmacy and Molecular Biotechnology IPMB Heidelberg University, INF 364 D-69120 Heidelberg Germany Phone: ++49-6221-54-4875 FAX : ++49-6221-54-6430

3 2

How to save a sequence in an mmCIF file?
by Guillaume Gaullier 29 Nov '23

29 Nov '23

Hello, Starting from an AlphaFold prediction, I refined a model against a map with ISOLDE. I trimmed the segments not supported by any density. The resulting mmCIF file that I saved now opens with this warning: Unknown polymer entity '1' near line 187 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Displaying the sequence of this chain shows the correct numbering (with jumps in numbering according to missing segments in the structure), but the sequence of the missing structure segments is not displayed. When I open the fasta file containing the full-length sequence, the sequence gets automatically associated to the structure, and the sequence viewer annotates the segments with missing structure correctly. I would like to save this full-length sequence in my mmCIF file so the full-length sequence with annotated missing structure segments shows up next time I open this file. But when I try to save at this point, I get the following notice: Not saving entity_poly_seq for non-authoritative sequences The documentation for "save" and "sequence" didn't help. How can I make this sequence "authoritative" and save it into my mmCIF file? 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

1 0

transition dipole moments
by gennaro.pescitelli＠unipi.it 28 Nov '23

28 Nov '23

Dear developers, first of all, thnak you for your great software, I just started using it. My question: is there a way to plot transition moments (electric and magnetic), as calculated e.g. by TD-DFT calculations in ORCA or Gaussian? If not directly from a log/out file, is tehre a way to manually add a vector arrow? Thanks Rino Pescitelli

3 7

Inquiry Regarding Feasibility of Implementing Protein Operations in Python
by g0423019 g0423019 28 Nov '23

28 Nov '23

Sorry. The earlier email by ms04000106(a)gmail.com was not sent using a university email address. It has been resent using the university email address. Dear UCSF ChimeraX, I hope this email finds you well. My name is Mayu Shibuya, and I am a student at Iwate University, currently affiliated with the wet biology laboratory. I am reaching out to seek guidance on the feasibility of utilizing the software for a specific task. Specifically, I am interested in performing addh and addcharge operations and automating these processes using a Python script. However, I do not know whether the addh and addcharge operations can be executed in Python. Could you kindly provide guidance on the possibility of achieving this with the software? If it is indeed feasible, I would greatly appreciate any instructions or methods you recommend for implementing these operations in a Python script. Thank you for taking the time to consider my inquiry. I greatly appreciate your assistance and look forward to hearing from you soon. Best regards, Mayu Shibuya Iwate University g0423019(a)iwate-u.ac.jp

3 2

Inquiry Regarding Feasibility of Implementing Protein Operations in Python
by 澁谷まゆ 28 Nov '23

28 Nov '23

Dear UCSF ChimeraX, I hope this email finds you well. My name is Mayu Shibuya, and I am a student at Iwate University, currently affiliated with the wet biology laboratory. I am reaching out to seek guidance on the feasibility of utilizing the software for a specific task. Specifically, I am interested in performing addh and addcharge operations and automating these processes using a Python script. However, I do not know whether the addh and addcharge operations can be executed in Python. Could you kindly provide guidance on the possibility of achieving this with the software? If it is indeed feasible, I would greatly appreciate any instructions or methods you recommend for implementing these operations in a Python script. Thank you for taking the time to consider my inquiry. I greatly appreciate your assistance and look forward to hearing from you soon. Best regards, Mayu Shibuya Iwate University ms04000106(a)gmail.com

1 0

hide dust
by Andrea Smith 28 Nov '23

28 Nov '23

Hi, I have cartoon and map visible for a part of my molecule (one protomer from a tetramer). When I click on hide dust, the dust is hidden but at the same time the map appears for the rest of the tetramer. Is there a way to hide dust around the visible part of the map while keeping a part of the map hidden? Thanks, Andrea

3 4

(no subject)
by Murphy, Kenneth 26 Nov '23

26 Nov '23

Hi, Would there be a way to save convservation scores from a large multiple sequence alignment into a file that could be re-loaded later instead of having to reload the actual alignment file? In looking at WDFY4, the alignment of the 3124 residue protein from 523 different species, the alignment fasta file takes around 10 minutes to load. After calculating the scores, the program shows the alignment and then the showing the convervations of residues in the protein is my goal of analysis. But it takes the same 10 minutes every time I open the session. I haven't found a way to save the scores themselves and load that in directly. Is there a way to do that? thanks it's a great program. ken murphy ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

3 3

Reading .xyz vs. Orca .out file
by Michael Patzschke 24 Nov '23

24 Nov '23

Dear colleagues, Recently the following problem has appeared: When I open an orca output file and chose the ball and stick option for displaying molecules, the radii of the balls are all wrong. This problem does not show up when I open the corresponding .xyz file. I try to attach an example to illustrate the problem. I would appreciate any help in this matter. Kind regards, Michael Patzschke __________________ Dr. Michael Patzschke Institute of Resource Ecology Chemistry of the f-elements Theoretical Chemistry Helmholtz-Zentrum Dresden - Rossendorf e. V. Telefon: +49 (0351) 260 2989 E-Mail: m.patzschke(a)hzdr.de <mailto:p.kaden@hzdr.de> Web: http://www.hzdr.de <http://www.hzdr.de/> Addresse: Bautzner Landstrasse 400 | 01328 Dresden Vorstand: Prof.Dr. Dr. Sebastian M. Schmidt, Dr. Diana Stiller Vereinsregister: VR 1693 beim Amtsgericht Dresden

3 3

Dialog box after dockprep command in 1.7rc202311210000
by r.m.newlon＠gmail.com 23 Nov '23

23 Nov '23

Hello all, I am on an Apple M1 and have just updated to ChimeraX 1.7rc202311210000. I am just starting to learn how to use ChimeraX from the command line (Terminal). My code that ran from Terminal on ChimeraX 1.6 doesn't seem to be working now with 1.7. Specifically, it seems that the dockprep command now ends by automatically popping up a dialog box prompting you to save a Mol2 file. I think this is causing problems when I try to run in nogui mode. I will include the "error message" at the end of this message, in case it is helpful. If this dialog box is the problem, is there a way to suppress it? Thank you! RN ==== Copied from Terminal ==== ... Dock prep finished Unexpected exception, save your work and exit: Traceback (most recent call last): File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/nogui.py", line 232, in execute self._cmd.run(text) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 168, in dock_prep_cmd dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 144, in dock_prep_caller run_steps(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 159, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 107, in prep callback(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 159, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep callback(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 159, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep callback(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 154, in run_steps callback() File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 101, in postscript show_save_file_dialog(session, format=session.data_formats.save_format_from_suffix(".mol2").name) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog _dlg.display(session, **kw) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 31, in display parent = session.ui.main_window ^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'UI' object has no attribute 'main_window'

2 1

ChimeraX-users email frequency
by Siyoung Kim 22 Nov '23

22 Nov '23

Hello, Is there a way to control the frequency of receiving emails from chimerax-users (e.g., once a day, once a week, or once a month)? Thank you. Best, Siyoung

2 1

(no subject)
by Murphy, Kenneth 21 Nov '23

21 Nov '23

Thanks for ChimeraX. I've been loading multiple sequence alignments in fasta format directly into ChimeraX for mapping conservation onto a pdb and it works great. My MSA are directly from clustalo omega and in fasta format not clu formtat. My question is this. My compiled al2co.c as well as the binary I downloaded for al21co.exe doesn't work with input in fasta format. And yet ChimeraX opens and al2co window when I input my alignment. Does ChimeraX use another version of al2co that is configured to open fasta files? thanks for any info. ken murphy ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 2

Sequence via remotecontrol?
by Boris Steipe 21 Nov '23

21 Nov '23

Hi all - I am using the fantastic remotecontrol REST interface in teaching, and I have hit a surprising snag: is it not possible to return the sequence of a selection through the interface? What I need to do is align fragments of sequence I have obtained from external annotations (RADAR in this case), with the SEQRES derived sequence to match the sequence numbers to each other - generally they are not the same. I think I could write FASTA to a file with "save" and process that, and I think I could capture the output of "info" and parse that through a function, but I am wondering if there is not a way to get the sequence directly as a return value? Thanks! Kind regards, Boris

2 1

VR on/off button
by Steffen Thomas 21 Nov '23

21 Nov '23

Hello I'm currently looking into the interesting possibilities of ChimeraX and VR. As I am in a different room to my PC with my glasses, I access the PC desktop via SteamVR with ChimeraX open and start vr on in the command line. This works quite well with a virtual keyboard from SteamVR. Now I'm missing two things so far, which I probably just haven't found yet (I'm a VR newbie even though I've owned a GearView for some time now, but its capabilities are quite limited). Firstly, a virtual keyboard where I can enter commands in the command line with the blue or yellow cylinders (I have now found the command line in vr) and a button in the toolbar (for example in the Molecule Display area) that switches vr on or off, in the same way for example as show and hide ribbon. Are there any possibilities to realize this via python itself? Or plans to integrate something like this? Many thanks to the great ChimeraX community and all those responsible. Steffen --------------------------------------------------------------------------------------------------------------- Steffen Thomas

2 1

measure rotation showAxis does not create a measurable object
by Alexis Rohou 20 Nov '23

20 Nov '23

Hello again, I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes. Two of my axes are #4 and #5. When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)" I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related. Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable? Cheers, Alexis

4 12

Startup cxc scripts
by Siyoung Kim 20 Nov '23

20 Nov '23

Hello, Would there be a way to run some chimerax scripts at the beginning of every ChimeraX session? In particular, I want three things: 1. Change the color of the background. set bgColor white 2. Change the mode of the mouse. ui mousemode right zoom 3. Open the shell. ui tool show Shell The most relevant documentation I found was: "Python files in the directory *~/chimerax_start* (where *~* is the user's home directory) are imported automatically at startup." I put ChimeraX scripts (not python files) in this folder, but no luck. Thank you. Best, Siyoung

2 2

Tutorial
by Mark Rosenberg 20 Nov '23

20 Nov '23

Do you have a tutorial for ChimeraX generating publication quality surface and mesh maps with a docked model, please? Thanks Dr Mark F Rosenberg

3 4

specify id of output of define command
by Alexis Rohou 18 Nov '23

18 Nov '23

Hello, I've been scripting quite a bit with the define command of late, and I wonder if you might consider adding "id" or "modelId" to the set of general options available for this command, so that we could specify the ID of the object that is created. The current workaround is to use rename, which works but is a bit cumbersome. Given that many other commands allow us to specify ID of output objects, I figure it'd be nice for that pattern to apply here. Cheers, Alexis

2 2

Feature request: replace residues in model with residues from other model
by Vorländer,Matthias Kopano 17 Nov '23

17 Nov '23

Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias

7 17

plane-spec
by Alexis Rohou 17 Nov '23

17 Nov '23

Hello, I'm playing around with the define axis command, and noticed that in the documentation the link to "plane-spec" does not lead to anything that defines how to specify a plane (help:user/commands/atomspec.html#othermodels). Or at least, I can't see it. The link to "point-spec" does take me to an informative page (help:user/commands/pointspec.html#point). Is the syntax for specifying a plane defined elsewhere? This is with 1.6.1. Cheers, Alexis

2 2

extracting cryoem density
by Dmitry Semchonok 16 Nov '23

16 Nov '23

Dear colleagues, I have a cryo-EM map with different subunits and models for each unit. Is there a way to extract the cryo-EM density for each unit of this map? The units are pretty numerous😊 Thank you. Kind regards, Dmitry

3 2

Calculating solvent accessible surface area for all residues in a protein?
by Altobelli, Chad 16 Nov '23

16 Nov '23

Hi! Is there a way to calculate the solvent accessible surface area (SASA) for every residue in a protein (5FTL) and output the result to a text file? I am trying to rank order residues by their accessibility. I know I can use the command line to calculate one residue at a time but it's laborious. Is there a way to automate the process or a GUI shortcut? Thanks! Chad

2 2

ChimeraX-1.7.dev202311052311-Ramachandran Plots
by Berkay Ekren 15 Nov '23

15 Nov '23

Hello, FIrst of all, I have been using Chimera for 3-4 years, now, and I would like to thank you for your efforts in the development of Chimera and ChimeraX. Recently, I decided to move to ChimeraX, and stay updated by using the bleeding edge daily version. However, I haven't been able to see the Ramachandran Plots option in either the Model Panel or the Tools section of ChimeraX. Is the Ramachandran Plots function removed from the program? Or is it just that I haven't looked at the correct path. This is a Linux installation in Debian 12 (used Ubuntu 22.04 deb package) It would be great if you could direct me to the right direction. Thank you in advance, I am looking forward to hearing from you at your earliest convenience. --Berkay Y. Ekren PhD candidate in Biostatistics and Bioinformatics

2 1

substitute nonstandard residue
by Dmitry Semchonok 15 Nov '23

15 Nov '23

Dear colleagues, I have a short question - how to substitute nonstandard residue with other ChimeraX. My task is to substitute GTP for GSP. The one may use swapaa, right? Could anyone drop the usage for nonstandard residue? Many thanks. Sincerely, Dmitry

2 1

ChimeraX on Apple M1
by Dennis Dannecker 15 Nov '23

15 Nov '23

Hello, I have a question regarding running ChimeraX on Apple's M1 chip. About two years ago (Nov 2, 2021), there was a post by Tom announcing the development of a version of ChimeraX that would run natively on Apple M1 instead of emulting for the Intel processor. Looking in the download section, I see such a native version is now regularly released. However, I am wondering what is the differen between the "macOS M1 or M2" and "macOS". While the former is only for M1 and M2, the latter on is for M1, M2, and Intel Macs, this one is also quite larger in size. If one is working on a macOS M1 (or M2) machine, is it correct to go for the "macOS M1 or M2"? Would that correspond to natively running ChimeraX and provide the best possible performance, or should one always go for the "macOS" release? I am currently updating my hardware, and since I am working quite a bit with ChimeraX, I would like to also inform my decisions based on the available ChimeraX releases. Thank you very much. Best regards Dennis Dennis Dannecker Master Student of Biochemistry Department of Chemistry Faculty of Mathematics and Natural Sciences University of Cologne Albertus-Magnus-Platz 50923 Cologne, Germany

2 2

Not able to see Glycines in stick form
by Firdous Tarique 14 Nov '23

14 Nov '23

Hi everyone In ChimeraX I am not able to show Gly simultaneously as a stick and cartoon. If I am trying to show Gly as a stick then the cartoon line breaks up at this position. And this is for any of the structures if you see. By showing a cartoon and stick together, the sticks for all amino acids show up except for Gly where it remains in the cartoon (you can try that). My aim is to show the thioester bond between Gly and Cys of two chains which I am able to create in Coot through Molecule Link but not able to see in ChimeraX. The moment I am trying to show Gly in stick form at this position it breaks the cartoon. I realised that this is for all the Glycines in the structure. Showing stick and cartoon together shows all amino acids in the stick except Glycine. (However this is not the case in Pymol and Chimera). Do you know any tricks to fix that in ChimeraX? Best Firdous

2 2

(no subject)
by Enrico Martinez 14 Nov '23

14 Nov '23

Dear Chimera-X users! I am trying to record md trajectory loaded in the chimera as

1 0

Re: [ccpem] Making thioester bond in Chimera/ChimeraX
by Elaine Meng 14 Nov '23

14 Nov '23

Hi Firdous, No trick, it is an option of cartoon (on by default) to prevent showing backbone atoms at the same time. Glycine only has backbone atoms (no sidechain). If you really want to show cartoon and backbone atoms at the same, use cartoon suppress false This is explained in the "cartoon" or "ribbon" command help. Just type command "help cartoon" to see your downloaded copy of the help page, or see the copy on our website here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> The full name of the option is "suppressBackboneDisplay" but you can shorten all options in commands as long as there is no other option that starts with the same letters. Actually Chimera ribbon also hides backbone atoms by default, although you can allow showing both at the same time with the Chimera "ribbackbone" command. The best address to use for ChimeraX questions is the chimerax-users one that I CC'd on this message, unless you are including data that must be kept 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 Nov 13, 2023, at 2:59 PM, Firdous Tarique <kahkashantarique(a)gmail.com> wrote: > > Hi Elaine > > Now I know where the problem is. In ChimeraX I am not able to show Gly simultaneously as a stick and cartoon. If I am trying to show Gly as a stick then the cartoon line breaks up at this position. And this is for any structure if you see. By showing a cartoon and stick together, the sticks for all amino acids show up except for Gly where it remains in the cartoon (you can try that). However this is not the case in Pymol and Chimera. Do you know any tricks to fix that in ChimeraX? > > Best > > Firdous > > On Thu, Nov 9, 2023 at 6:11 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hello Firdous, > Probably the problem is that mol A and mol B are two different models. You can't add a bond in Chimera or ChimeraX until after combining them into one model first. > > ChimeraX combine command: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> > > ChimeraX bond command or Build Structure tool, Adjust Bonds section: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> > > For the best chance of getting an answer to a question about ChimeraX, please use the chimerax-users(a)cgl.ucsf.edu address: > <https://rbvi.ucsf.edu/chimerax/docs/contact.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > From: Collaborative Computational Project in Electron cryo-Microscopy <CCPEM(a)JISCMAIL.AC.UK> on behalf of Firdous Tarique <kahkashantarique(a)GMAIL.COM> > > Date: Thursday, November 9, 2023 at 12:27 PM > > To: CCPEM(a)JISCMAIL.AC.UK <CCPEM(a)JISCMAIL.AC.UK> > > Subject: [ccpem] Making thioester bond in Chimera/ChimeraX > > > > Hi > > > > Does anybody know how to make thioester bonds in Chimera or ChimeraX ? > > > > I am unable to make a bond between Cys321 in mol A with Gly1 in mol B (S-glycyl-L-cysteine) using Chimera or ChimeraX. > > > > I tried Isolde in ChimeraX and Build Structure in Chimera to make a bond between selected atoms but so far have been unsuccessful. I don't know if I am missing something. > > > > Any help would be appreciated. > > > > Thanks > > > > Firdous > > > > To unsubscribe from the CCPEM list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 > > >

2 2

projecting full model from monomer
by Dmitry Semchonok 13 Nov '23

13 Nov '23

Dear colleagues, I have a monomer with biomt information that describes the full model. To see the full model, I use the command sym when opening the monomer in Chimera. Could you please prompt the correspondent command in ChimeraX to project the complete model in ChimeraX based on the information stored in the monomer? Thank you Kind regards, Dmitry

2 4

ChimeraX trial license
by Jang,Chang Woon,US-St. Louis 12 Nov '23

12 Nov '23

Dera UCSF ChimeraX Team, My name is Chang Woon Jang working for Nestle Purina. I am interested in ChimeraX for a molecular modeling project. Could I use a trial license for a month before buying the commercial license? Thanks, Chang Woon Jang

2 1

updating ChimeraX for rc/daily build with Isolde
by Dmitry Semchonok 11 Nov '23

11 Nov '23

Dear colleagues, I would like to update ChimeraX to rc version or daily build. Trying to install Isolde / Clipper delivered me the following error (either via the command line within ChimeraX, or via the ChimeraX update button) Clipper toolshed install C:/Users/Dmitry/Downloads/ChimeraX_Clipper-0.22.1-cp311-cp311-win_amd64.whl ERROR: Could not find a version that satisfies the requirement ChimeraX-Core<1.8,>=1.7.dev202306142048 (from chimerax-clipper) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core<1.8,>=1.7.dev202306142048 ISOLDE toolshed install C:/Users/Dmitry/Downloads/ChimeraX_ISOLDE-1.7.dev0-cp311-cp311-win_amd64.whl ERROR: Could not find a version that satisfies the requirement ChimeraX-Core<1.8,>=1.7.dev202306142048 (from chimerax-isolde) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core<1.8,>=1.7.dev202306142048 Is it possible to install Isolde/clipper with rc/daily version? If yes, how to fix the error? Thank you. Kind regards, Dmitry

2 1

Zooming in and out in ChimeraX
by Dale Calleja 10 Nov '23

10 Nov '23

Hello, I am currently learning to use ChimeraX (v1.6.1) and I am having issues with my scroll wheel. I notice when I first open the software using the scroll wheel on my mouse will zoom in and out of the structure but, after some time it simply stops working and the scroll wheel does nothing. Is this a button I am accidentally pressing or have I discovered a bug? It doesn’t seem to have any pattern, I am just clicking around changing the display of my protein. Thanks! Dale. Dale Calleja PhD Student, Komander Lab Ubiquitin Signalling Division WEHI 1G Royal Parade Parkville VIC 3052 Australia Email calleja.d(a)wehi.edu.au<mailto:calleja.d@wehi.edu.au> [WEHI Logo] Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville Victoria 3052 Australia www.wehi.edu.au<https://wehi.edu.au> Twitter<https://twitter.com/WEHI_research> | Facebook<https://www.facebook.com/WEHIresearch/> | Instagram<https://www.instagram.com/wehi_research> | Youtube<https://www.youtube.com/user/WEHImovies> | LinkedIn<https://www.linkedin.com/company/wehi_research> WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. Private and confidential The content of this e-mail and any attachments may be private and confidential, intended only for use of the individual or entity named. If you are not the intended recipient of this message you must not read, forward, print, copy, disclose, use or store in any way the information this e-mail or any attachment contains. If you are not the intended recipient, please notify the sender immediately and delete or destroy all copies of this e-mail and any attachment.

2 2

ui mousemode right when in ISOLDE
by Alexis Rohou 10 Nov '23

10 Nov '23

Hi there, Wondering if anyone else gets this behavior: When ISOLDE is running, setting the right mouse click to translate selected atoms does NOT associate shift-right-click with rotating selected atoms; instead, shift-right click does a zoom. In addition, if I try to force it by issuing the two commands below, the shift right click still isn't a rotate selected atom; instead, it does a translate selected atoms. ui mousemode right "translate selected atoms" ui mousemode shift right "rotate selected atoms" My workaround is to use alt-right for rotating instead. That does work: ui mousemode right "translate selected atoms" ui mousemode alt right "rotate selected atoms" This is with ChimeraX 1.6.1, but I'm pretty sure I noticed this behavior in earlier versions also. Tristan recently posted a screen capture where it's clear he doesn't have this problem, but he's on Windows and I'm on Mac, so I wonder whether that might have something to do with it. Any ideas? Cheers, Alexis

3 5

how to build N-linked glycans
by Alexis Rohou 09 Nov '23

09 Nov '23

Hi there, How would you recommend I go about building an N-linked glycan chain off of an ASN in an existing model using ChimeraX or ISOLDE? Is there documentation on this somewhere? Cheers, Alexis

2 3

Custom calculation of forcefields for ligands in Isolde
by Paul Sauer 09 Nov '23

09 Nov '23

Dear ChimeraX and Isolde experts, I am trying to parameterize a ligand in Isolde 1.6 in order to fit it into my density. The ligand conforms to the requirements that are outlined in the manual (not covalently bound, only consists of certain elements, etc). However, parameterizing the residue using the inbuilt ANTECHAMBER/AMBER utility times out unfortunately, with an error saying that convergence in SCF cannot be reached. Upon investigating the issue I learned that it could be possible to avoid this error with adjusted command line parameters for AMBER in order to let it run longer for correct values. My question is: Is it possible to pass custom flags or command line arguments from Isolde to AMBER in ChimeraX? And if yes, how? The default command ‘Isolde parameterize residue’ does not seem to have any AMBER specific options. For example, how can I add 'adding ndiis_attempts=700’ (or other modifications) to my input sqm file? Thank you in advance, Paul

3 3

How to refine a symmetric model with ISOLDE
by Guillaume Gaullier 09 Nov '23

09 Nov '23

Hello, A question for Tristan, since I know you read this list. :-) I have a cryoEM map that was produced with C7 symmetry enforced. I can fit the alphafold prediction of one protomer, and am pretty confident in this initial rigid fit because the map is good. Now with Tom's help I know how to generate the C7 symmetric assembly and store the symmetry info in a cif file with a single protomer, so I can regenerate the heptamer as needed (and this seems like the correct way to deposit the end result). But this model still needs proper refinement: the rigid fit shows that the conformation predicted by alphafold deviates from the map at several locations. What is a sensible refinement strategy for something like this? Because symmetry was enforced for the map, I am inclined to refine only a single protomer and add the correct symmetry info that will regenerate the heptamer. But don't I need the neighboring protomers during refinement, for the interface residues to behave correctly during MDFF? I would think so. Not sure what to do, some advice would be very helpful. 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

1 0

How to write biological assembly info in PDB or mmCIF?
by Guillaume Gaullier 08 Nov '23

08 Nov '23

Hello, I have a cryoEM map that was generated with C7 symmetry enforced, with its symmetry axis parallel to the z axis in ChimeraX. I fetched a prediction from AlphaFoldDB and docked it in the map. So far, so good. I can generate the other protomers with a command like this: sym #1 C7 axis z center cofr (assuming #1 is the single protomer from AlphaFoldDB, and the cofr is correctly lying on the symmetry axis, which I get sufficiently close if I center the view on the map) Now, because symmetry was enforced for the map, it makes no sense to model, refine and store the entire heptamer. I should be able to do everything with a single protomer, and store relevant info as "biological assembly" so the heptamer can be regenerated from the protomer. At least if I am understanding this correctly. I tried the above command, or this variant: sym #1 C7 axis z center cofr addMmcifAssembly true And subsequently saving in PDB or mmCIF format, but none of this produces what I want, which is a file containing the single protomer + assembly info. I either get a file with the single protomer or a file with the heptamer, in both cases without any biological assembly info. I looked up the options of the save command for PDB and mmCIF format, but found nothing that seemed relevant to this problem. Is there a way to do this? Or am I misunderstanding something? Related question: it might make sense to use the whole heptamer for refinement, so all interfaces between protomers "see" each other (probably important when using ISOLDE). What is the best way to deal with this? Build and refine the whole heptamer and save only a single protomer + assembly info at the very end? Or have the symmetry enforced from the beginning, throughout the whole refinement process, and really ever refine a single protomer? (7 times less work, so probably the preferred option). 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

2 6

Modeller down
by Dominik Dekleva 08 Nov '23

08 Nov '23

Hi My name is Dominik Dekleva, phd student at the University of Ljubljana. I'm attempting to use the Modeller feature in ChimeraX but doesn't seem to be working. Is the webservice down? Best regards, Dominik Dekleva

2 2

Alphafold2_multimer on chimeraX
by Margulies, David (NIH/NIAID) [E] 08 Nov '23

08 Nov '23

Beginning yesterday, I have had repeated failure of alphafold2_multimer running through chimerax to generate models of two protein complexes (Ab H cand L chains, for instance). Individual chains work fine. The error from Colab AI says: The error is due to a bug in the ColabFold library. The kabsch function in the colabfold.py file is using the linalg.svd function to calculate the singular value decomposition of a matrix. However, the linalg.svd function is not guaranteed to converge, and in some cases it can fail to converge. This can cause the kabsch function to fail, and in turn cause the plot_protein_backbone function to fail. The bug has been fixed in the latest version of the ColabFold library, which is available on GitHub. To fix the error, you can upgrade to the latest version of the library. You can do this by running the following command in the Colab notebook: content_copy !pip install colabfold --upgrade Use code with caution<https://g.co/legal/generative-code> Once you have upgraded to the latest version of the library, you can run the code again and the error should be fixed. Can you advise? Thanks for your help. D David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892 Email: dmargulies(a)niaid.nih.gov<mailto:dmargulies@niaid.nih.gov>, dhm(a)nih.gov<mailto:dhm@nih.gov> Ph: 301-496-6429 Fax: 301-480-7352 Web: https://www.niaid.nih.gov/research/david-margulies-md-phd “Public service is a public trust, requiring employees to place loyalty to the Constitution, the laws, and ethical principles above private gain.” – executive order 12674, https://www.federalregister.gov/documents/2016/02/17/2016-03214/standards-o…<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.federalregister.go…> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender’s own and not expressly made on behalf of the NIAID by one of its representatives.

2 1

Zone interaction in rRNA
by tim smith 07 Nov '23

07 Nov '23

How do we select a zone in ribosomal RNA (nucleotide residues of rRNA) to visualize all its interaction interfaces with ribosomal proteins/H2O/ions using ChimeraX? Thank you for your support. Thank you. Best Tim

2 2

Dynamic bonds
by Michael Patzschke 07 Nov '23

07 Nov '23

Dear colleagues, I have a trajectory from an ab initio MD run. The output is in the form of concatenated .xyz information. I can open and visualise this in ChimeraX, but the bond topology is determined from the first step. As the simulation progresses, bonds are stretched and the broken bond in my example just gets drawn, although the distance of the involved atoms gets larger then 7 Å by the end of the simulation. Is there a way to use dynamic bonds in ChimeraX? By this I mean that the bonds are only drawn when the distance of the involved atoms is below a certain threshold. I would appreciate any help in the matter. Kind regards, Michael Patzschke

3 5

Change default colour cycle for EM maps
by James Hooker 06 Nov '23

06 Nov '23

Hello all, I am looking for a way to change the qualitative colour cycle in ChimeraX from the default (grey, yellow, blue, purple, pink, …). I have flicked through the online documentation, but have not yet found a solution. Many people must have desired to do this at some point, right? Any advice is welcome! Best, James

2 1

commandline to hide a map region or set a transparency in chimeraX
by Rayees Mattoo 06 Nov '23

06 Nov '23

Hi, I was wondering if there is a command line in chimeraX to hide a region of the map. To be more specific if I have to hide map around a model #1 chain A, how could I do that? Also, using the same case how do I set a transparency of 50% for the map around the chainA model #1? Actually, I want to make a movie of the vseries where I need to hide/delete/transparent some portion of the map to show the internal details of the map while playing the vseries. Any suggestions are welcome. Best

2 3

problem with color by conservation option
by elzbieta.wator＠doctoral.uj.edu.pl 06 Nov '23

06 Nov '23

Hi, I am trying to color my protein structure by conservation. I prepared alignement file i fasta format and when I upload it to the ChimeraX and use command: color byattribute seq_conservation palette cyanmaroon not the whole structure of my proteins get coloured. Namely despite no mismatch in the PDB file and sequence which is first in aln file there are several residues which stays in the previously selected colour. I've already made sure that the sequence is correct and I have no further ideas how to solve this problems. I will be very grateful for your tips. Best, Ela Wator

3 2

color by conservation problem
by Elżbieta Wątor 05 Nov '23

05 Nov '23

Hi, I am trying to color my protein structure by conservation. I prepared alignement file i fasta format and when I upload it to the ChimeraX and use command: color byattribute seq_conservation palette cyanmaroon not the whole structure of my proteins get coloured. Namely despite no mismatch in the PDB file and sequence which is first in aln file there are several residues which stays in the previously selected colour. I've already made sure that the sequence is correct and I have no further ideas how to solve this problems. I will be very grateful for your tips. Best, Ela Wator [cid:e1499547-d8cf-48a6-89cb-b2ea6e696097]

2 1

Select truncated residues in PDB
by Vorländer,Matthias Kopano 05 Nov '23

05 Nov '23

Dear ChimeraX team, Is it possible to select all residues in a model that have been truncated to backbones rather build as a complete sidechain? Many thanks, Matthias

2 1

installing plugin
by Dmitry Semchonok 04 Nov '23

04 Nov '23

Dear colleagues, Is anything happened with the website https://cxtoolshed.rbvi.ucsf.edu/ It seems to be still down. Kind regards, Dmitry

2 2

mseries oscillate/loop ?
by vincent Chaptal 04 Nov '23

04 Nov '23

Hi again, it is possible to use vseries play #1 loop true, but the same command with mseries doesn't work. Same with oscillate or similar commands. I've also tried mseries #1.1-20-1 or mseries #1.20-1 but these 2 commands don't work. Is there a way to make the movement go back to the origin? 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

ISOLDE and heparin
by Xuewu Zhang 04 Nov '23

04 Nov '23

Dear Tristan, Can ISOLDE handle heparin molecules now? I tried to simulate a heparin chain, it says one residue is not properly parametrized. I am using ISOLDE in Chimerax 1.6. Thanks, Xuewu

2 1

UCSF Chimera 1.17.1
by hj_bowles＠sky.com 04 Nov '23

04 Nov '23

Good Evening, I need to download UCSF Chimera 1.17.1 for a examination, however due to the downtime on your website i am unable to do so. is there any way you can send me a link to download of get around this issue for me? I would be very grateful. Kind regards,Heather.

1 0

fly command
by Sean Connell 04 Nov '23

04 Nov '23

Hello, I have a question about the fly command. I am trying to iterate over a series of saved views (p1-p6) using the fly command. The views are close-up views of residues because I am trying to make a movie similar to that made with resfit. The issue is that the cutting plans don't seem to update as it moves from view to view. Do you have a hint that could let me know what I am doing wrong? Thanks for any tips you have

2 1

Show models from the same file, one by one into a movie
by vincent Chaptal 04 Nov '23

04 Nov '23

Hi, I have a PDB file with 20 models inside(#1.1 to #1.20)that I color as a rainbow. I would like to show them sequentially and make a movie showing one model at a time, back and forth (show #1.1, hide #1.1 and show #1.2, etc...). I've played with the morphing command but it is not what I want, and then with the Coordset command thinking it would be like a trajectory but I can't make it to work. I would appreciate a pointer to get me to the right direction. 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 2

ChimeraX tutorial pages
by Kai Cai 04 Nov '23

04 Nov '23

Hi, Just noticed that the ChimeraX tutorial pages are not accessible. Are they temporarily down or permanently removed? Thanks, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 1

Show models from the same file, one by one into a movie
by vincent Chaptal 03 Nov '23

03 Nov '23

Hi, I have a PDB file with 20 models inside(#1.1 to #1.20)that I color as a rainbow. I would like to show them sequentially and make a movie showing one model at a time, back and forth (show #1.1, hide #1.1 and show #1.2, etc...). I've played with the morphing command but it is not what I want, and then with the Coordset command thinking it would be like a trajectory but I can't make it to work. I would appreciate a pointer to get me to the right direction. 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/

1 0

Middle mouse click to center and move to atom
by Adrián González López 27 Oct '23

27 Oct '23

Hi, I do not know if this is possible already (I could not find it), but is there a way in ChimeraX to set the middle click mouse button (or any other button) to center and orient the atom you click? Similar to what happens on PyMOL by default. This helps so much when navigating around a structure. I know you can do it in some other way, but it takes more time and it is not so user-friendly. If there is no way to do this, could it be implemented? Many thanks! Best, Adrián 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

4 4

Cap clipped atoms or bonds
by Daniel Larsson 27 Oct '23

27 Oct '23

Is it possible to have atoms or bonds capped when they are truncated by a near clipping plane, similar to how surfaces can be capped. Currently, you can see the interior polygons when you clip the middle of a molecule. See the attached image for an example. I tried to search the mailing list and the documentations, but could not find anything. Regards, Daniel [cid:image001.png@01DA08BB.1559BC80] 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

2 1

ChimeraX for WSL: release request
by Dmitry Semchonok 27 Oct '23

27 Oct '23

Dear Elaine and Eric, Since the number of Windows WSL systems is increasing do you consider releasing the compatible version of ChimeraX? Thank you Kind regards, Dmitry

4 8

Chimera(X) website and web services down Oct 30-31
by Elaine Meng 26 Oct '23

26 Oct '23

Dear users, Due to system upgrades, the Chimera and ChimeraX websites, associated web services hosted by the UCSF RBVI (Modeller, Blast Protein, etc.), and the ChimeraX Toolshed will be unavailable -- the estimated downtime is from Monday, Oct 30 8:00 am PDT through Tuesday, Oct 31 11:59 pm PDT. Please pardon the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Re: Selection with coordinates
by Tom Goddard 26 Oct '23

26 Oct '23

Hi Siyoung, The movie recording needs a "wait" command to actually render frames. If you have 300 frames in your coordinate set it would be perframe "open select_atoms.py" movie record coordset #1 wait 300 movie encode test.mp4 Also I would suggest that your python code not use "atom.hide". That is an obscure attribute for hiding backbone atoms with ribbon display. Instead use atom.display = True atom.display = False It might be possible to record the movie entirely in Python, but I've never tried it. I would not suggest trying that approach unless you want to waste a lot of time since the movie recording code was not designed to work in a Python script. Tom > On Oct 24, 2023, at 6:01 PM, Siyoung Kim <kkssy141(a)gmail.com> wrote: > > Thank you very much for the helpful information. I think I am very close to what I want to do. > > I would like to make a video of a molecular dynamics trajectory and want to show only the atoms whose x coordinates are smaller than 0. Here is what I tried. > > a) I made a python script that can be applied to each frame and named it "select_atoms.py" > --------------------------------- > from chimerax.atomic import all_atoms > atoms = all_atoms(session) > for atom in atoms: > if atom.scene_coord[0] < 0: > atom.hide = 0 > else: > atom.hide = 1 > ---------------------------------- > > b) I opened up a trajectory in ChimeraX. > > c) In ChimeraX, I executed > --------------------------------------------- > perframe "open select_atoms.py" > movie record > coordset #1 > movie encode test.mp4 > ---------------------------------------------- > > Interestingly, if I just move a frame by myself using a slider, perframe is applied well. i.e., only the atoms whose x coordinates < 0 are shown in EACH frame > However, if I record a video like the above or click a play button, perframe is not successfully applied. Only the atoms whose x coordinates < 0 in the last frame are shown in all frames. Updating a selection in each frame does not work with this approach. > I have attached the video. Would you please help me with this? Thank you. > > I would be also curious if it could be done inside a python script. In the above, I made a script that should be applied to each frame and then called this script using perframe in ChimeraX. Would there be something like RED in the below? Thank you very much! > > RECORDING A MOVIE > for s in all_atomic_structures(session): > for cs_id in s.coordset_ids: > s.active_coordset_id = cs_id > atoms = s.atoms > atoms.selecteds = atoms.scene_coords[:,0] < 0 > atoms[atoms.selecteds].hide = 0 > atoms[~atoms.selecteds].hide = 1 > SAVE THIS IMAGE > ENCODING A MOVIE > > > On Mon, Oct 23, 2023 at 11:52 AM Siyoung Kim <kkssy141(a)gmail.com <mailto:kkssy141@gmail.com>> wrote: >> Hi Eric, >> >> Thank you very much for the very helpful information! I learned a lot. >> >> Best, >> Siyoung >> >> On Fri, Oct 20, 2023 at 8:58 PM Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >>>> On Oct 17, 2023, at 1:53 PM, Siyoung Kim via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> Hi Tom, >>>> >>>> Thank you for your help. I can confirm that making a text file, select.py, that contains the below and running "run select.py" in the ChimeraX command line works. >>>> >>>> from chimerax.atomic import all_atoms >>>> for a in all_atoms(session): >>>> if a.scene_coord[0] < 0: >>>> a.selected = True >>>> >>>> I am quite interested in learning more about the chimerax.atomix library. Would there be any helpful resources about this? >>> >>> There is automatically generated documentation, but I don't recommend it because it is poorly formatted and littered with rarely used constants and functions from base classes (e.g. Structure inherits from Model and Drawing and therefore documentation for first_intercept_children() [from Drawing] is included). Instead, I'd browse through the code for atomic class definitions themselves. The Cython class definitions for Atom, Element, and Bond are here: https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/atomic_cpp… . The definitions for the other classes are here: https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/molobj… . The latter only has the base class definitions for Structure and PseudobondGroup (StructureData and PseudobondGroupData respectively). The final definitions are in structure.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/struct…> and pbgroup.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/pbgrou…> . >>> >>> Another approach is to find a bundle that does something similar to what you want to do and look at its code to see how it does it. All the ChimeraX source code is in the repository linked to above (and the Python code is included in every ChimeraX installation). >>> >>>> Would it be also possible to loop over a molecular dynamics trajectory and select wanted atoms in this way? >>> >>> Yes. A structure that is a trajectory will have multiple "coordinate sets" (sets of coordinates for the atoms). Therefore you can loop through the trajectory like so: >>> >>> from chimerax.atomic import all_atomic_structures: >>> for s in all_atomic_structures(session): >>> for cs_id in s.coordset_ids: >>> s.active_coordset_id = cs_id >>> for a in s.atoms: >>> a.selected = a.scene_coord[0] < 0 >>> >>> It may also be useful to know that the value returned by s.atoms is an "Atoms" instance (see molarray.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/molarr…>) which in many ways can be treated as a vector for efficiency, which could definitely matter when processing a trajectory. So the above code could instead be: >>> >>> from chimerax.atomic import all_atomic_structures: >>> for s in all_atomic_structures(session): >>> for cs_id in s.coordset_ids: >>> s.active_coordset_id = cs_id >>> atoms = s.atoms >>> atoms.selecteds = atoms.scene_coords[:,0] < 0 >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> >>>> >>>> Thank you. >>>> Best, >>>> Siyoung >>>> >>>> On Tue, Oct 17, 2023 at 4:06 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>>> Oops. If you put this code in a file it needs to have a ".py" suffix, so call it select.py. The ".cxc" suffix is for ChimeraX commands. >>>>> >>>>> Tom >>>>> >>>>> > On Oct 17, 2023, at 12:58 PM, Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > >>>>> > Hi Siyoung, >>>>> > >>>>> > Here is Python code to select all atoms with x < 0. >>>>> > >>>>> > from chimerax.atomic import all_atoms >>>>> > for a in all_atoms(session): >>>>> > if a.scene_coord[0] < 0: >>>>> > a.selected = True >>>>> > >>>>> > You can type this in the ChimeraX Python shell (menu Tools / General / Shell), or probably easier, put it in a text file "select.cxc" and open that in ChimeraX to run it. >>>>> > >>>>> > Tom >>>>> > >>>>> >> On Oct 17, 2023, at 9:04 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> >> >>>>> >> Hello Siyoung, >>>>> >> Sorry no, I can't think of a way to do it with a ChimeraX command. Maybe you could do it by using the initial orientation of the structure (just opening and not rotating) and veerrryyy carefully using the mouse to select a rectangle (Ctrl-click drag) but that is probably too difficult. Also you would need to know where X=0 is from just looking at the structure. >>>>> >> >>>>> >> Certainly you could do it with Python, but somebody else would have to advise on that. >>>>> >> >>>>> >> Best, >>>>> >> Elaine >>>>> >> ----- >>>>> >> Elaine C. Meng, Ph.D. >>>>> >> UCSF Chimera(X) team >>>>> >> Department of Pharmaceutical Chemistry >>>>> >> University of California, San Francisco >>>>> >> >>>>> >>> On Oct 17, 2023, at 5:33 AM, Siyoung Kim via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> >>> >>>>> >>> Hello, >>>>> >>> >>>>> >>> Would there be a selection keyword that selects atoms based on their coordinates? For instance, is there a way that I can select atoms whose x coordinates are below 0 (e.g., x < 0)? >>>>> >>> >>>>> >>> Thank you. >>>>> >>> Best, >>>>> >>> Siyoung >>>>> >> >>>>> >> >>>>> >> _______________________________________________ >>>>> >> 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> >>>>> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>>> >> >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > 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> >>>>> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>>> > >>>>> >>>> _______________________________________________ >>>> 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> >>>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>> > <test.mp4>

2 4

crop the map
by Dmitry Semchonok 25 Oct '23

25 Oct '23

Dear colleagues, Could you advise on how to crop the map to the new 3D box size and save those changes? Thank you. Sincerely, Dmitry

3 7

Fwd: [ccpem] Help with pairing RMSD in Chimera like COOT
by JAMES MICHAEL KRIEGER 25 Oct '23

25 Oct '23

Dear Rajnandani and all, I am adding in the chimerax users list (I don't know the plain chimera one) as I think this is a better question for people there. Just to clarify, by adjust the RMSD for the map, I guess you mean scrolling the cutoff value? Best wishes James ----- Mensaje reenviado de Alfredo Jose Florez Ariza <0000b1a72b269dbc-dmarc-request(a)jiscmail.ac.uk> ----- Fecha: Tue, 24 Oct 2023 11:49:00 -0700 De: Alfredo Jose Florez Ariza <0000b1a72b269dbc-dmarc-request(a)jiscmail.ac.uk> Responder-A: Alfredo Jose Florez Ariza <alfredo.florez(a)berkeley.edu> Asunto: Re: [ccpem] Help with pairing RMSD in Chimera like COOT Para: CCPEM(a)jiscmail.ac.uk You mean you wanna show just the density corresponding to certain region of the model? If so, you can use volume zone command. It will be something like: volume zone #X near #Y/Z: aaa-bbb range 3 X and Y are the ID numbers of your map and model. Z is the chain of your model and aaa and bbb are the residues you are interested in showing the map around. The range 3 can be modified accordingly to ‘how much of your map’ you wanna show around the model region, I guess. Alfredo On Tue, Oct 24, 2023 at 10:24 AM Rajnandani Kashyap < rajnandani.kashyap(a)health.slu.edu> wrote: > Hello Everyone > > I am at a stage of preparing figures for one of my manuscripts. And I was > wondering if we could adjust the RMSD for the map file (density) in chimera > as we do it in COOT. Basically, I want to show the electron density for a > flexible N-term residues for which I do observe the density at a lower RMSD > level in chimera. > > Any help would be greatly appreciated. > > Thanks, > Rajnandani Kashyap > Postdoc Fellow > > > ------------------------------ > > To unsubscribe from the CCPEM list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 > ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 This message was issued to members of www.jiscmail.ac.uk/CCPEM, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ----- Terminar mensaje reenviado -----

2 2

ISOLDE error: Please remove “TER” card after the single residue
by Dmitry Semchonok 25 Oct '23

25 Oct '23

Dear colleagues, I have an issue with the validation website after working with my model in ISOLDE. More detailed: When starting the simulation in ISOLDE, I am running into the error: At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parametrized. Launching the unparameterized residue widget to help sort this out. So certain ligand info is missing (MYR). Then appears the window that allows me to add the information about this ligand and proceed with the refinement. After finishing refinement in ChimeraX/ISOLDE, I loaded the model and the map on https://validate-rcsb-1.wwpdb.org/. But this website showed me the error: File upload failed. Please review the errors below and try again. Coordinates issues. ERROR: Please remove “TER” card after the single residue “MYR A 1” in line 136 and upload the file again. Some more observations: Although MYR is the first residue in the ChimeraX sequence, it is not visible. At the same time, COOT can see it. Please let me know how I can proceed with the https://validate-rcsb-1.wwpdb.org/ after refinement with ISOLDE. Please let me know if you require a model/map file for the investigation. Thank you Kind regards, Dmitry

2 4

Distinct clipping planes per model
by Dorien Pastoors 24 Oct '23

24 Oct '23

Hi, Thanks for maintaining such a nice software package! I'm still learning, and I'm currently stuck on clipping. I'm trying to clip models differently in ChimeraX. My aim is to have a global clipping plane to visualize two drugs binding to two domains (in the image in yellow/blue). Now I would like to offset the clipping plane slightly for surrounding protein (in beige). I would like to do this to increase the depth in my image and to emphasize that these domains are embedded in a bigger protein. As it is in fact a huge protein (its an alphafold predicted structure) making the entire protein transparent will still obscure the view on the compounds in their domains. As you can see, by using clip model I've been able to turn off clipping for the drugs in their binding pockets. However, with clip model I can only switch on or off the entire clipping plane , not offset it for a particular model. I've tried: clip model #2.3 front -10 clip model #2.3 offset -10 With clip model I can't specify an offset as it gives an error, I can only turn clipping off completely with "clip model #2.3 false", while "clip front -10" affects the total clipping plane, and I cannot specify a particular model for this clipping plane. (the beige protein model is #2.3) Hope this is clear enough and you have a solution! Thanks in advance! Kind regards, Dorien Pastoors

2 1

Image rendering artifacts with silhouettes and pixelSize value
by Vorländer,Matthias Kopano 24 Oct '23

24 Oct '23

Dear ChimeraX team, I am having issues when using silhouettes and saving an image while specifying the pixel size, as I get the artefacts shown in the attached image. If I don’t use silhouettes or don’t specify the pixel size things look fine. I updated to the latest daily version and uninstalled Isolde and ArtiaX, but the problem persist. I work on a MacBook Pro under Mac OS Ventura 13.5.2. Any ideas for fixes? Many thanks, Matthias [A white structure with colorful strands Description automatically generated with medium confidence]

2 2

Difference maps in chimerax?
by Francisco Murphy Pérez 23 Oct '23

23 Oct '23

When I open a map* in chimerax, how do I specify it is a difference density map? * maps are generated with `phenix.mtz2map finalpdb.pdb finalmtz.mtz` ... both files from the pdb-redo. Thanks

4 10

Morphing problem
by Raphael Bader 23 Oct '23

23 Oct '23

Dear all, I would like to ask for some information/help for a problem I am facing at the moment: I am currently working on a pentameric protein (C5 symmetric) that undergoes a big conformational change (translational & rotational movement) and would like to utilize the morph function in ChimeraX to come up with a good animation for it. For one single protomer the animation works fine – however, for the full pentamer the subunits follow both directions, clockwise and counterclockwise, during their rotational movement which obviously leads to a lot of clashes and therefore does not look very convincing. Since I tried almost all options listed as parameters for the morph (linear & corkscrew method, cartesian true and false, rates, coreFraction, etc.) and it did not affect the direction of rotation at all, I was wondering whether there are additional values I could modify or any other trick that might equalize the movement? Thank you very much in advance! Best regards, Raphael P.S.: I would be happy to provide data if it might help solving the problem.

3 2

Selection with coordinates
by Siyoung Kim 23 Oct '23

23 Oct '23

Hello, Would there be a selection keyword that selects atoms based on their coordinates? For instance, is there a way that I can select atoms whose x coordinates are below 0 (e.g., x < 0)? Thank you. Best, Siyoung

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Re: [Chimera-users] How to obtain transformation matrix between protein structures
by Elaine Meng 22 Oct '23

22 Oct '23

Hi Qiancheng Xia, Please use the chimerax-users(a)cgl.ucsf.edu address (CC'd here) for ChimeraX questions so that people don't get mixed up between Chimera and ChimeraX. Chimera does not have the reportMatrix option. As for ChimeraX, you didn't show the exact command that you tried so I can only guess what went wrong. My guess is that you need to include "reportMatrix true" not just "reportMatrix" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 20, 2023, at 4:39 AM, 夏前程 via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > I want to use chimera to obtain the transformation matrix between two protein structures. I know that matchmaker can superimpose them together, but I still want to obtain the transformation matrix. I've noticed that matchmaker in chimerax (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html) offer a keyword "reportMatrix" to do that. But when I use that keyword in chimerax, "Expected a keyword" will be returned without match or a matrix. > With Regards, > > Qiancheng Xia > > National Institute of Biological Sciences > > Beijing, China > > 2023/10/20 >

2 2

Export Isolde residue paramters (xml) for phenix
by Sean Connell 21 Oct '23

21 Oct '23

Hello, Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement? Sean

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Re: Movie Record/Encode with GPU?
by Tom Goddard 20 Oct '23

20 Oct '23

No. The only way to show multiple frames of a trajectory in ChimeraX is to open them as separate models. Tom > On Oct 18, 2023, at 9:37 AM, Alexander Hung Lee <Alexander.Lee(a)uga.edu> wrote: > > Oh, and I forgot to ask… Is there an option in command line to show all the hbonds in a trajectory concurrently, even if the bond shows up at a different point in time but not current frame? >

2 1

Surface calculation in ChimeraX
by Dennis Dannecker 20 Oct '23

20 Oct '23

Hello Chimera/ChimeraX team I recently asked already a question regarding the saving/exporting of vertices generated during the surface calculation in ChimeraX and the associated parameters with this surface generation. On a related note, I wanted to ask whether it is possible to also extract the surface (SESA and/or SASA) on a per atom basis. MSMS calculates not only the vertices for each atom (usually several vertices per atom) but it also calculates the SESA and SASA on a per atom basis. Now, I was wondering whether something is possible in ChimeraX too. As I was parsing through the docs, I was wondering whether ChimeraX calculates the surface no longer using MSMS. The vertices density supported by ChimeraX is considerably higher than what I can get with my standalone MSMS program (at least factor 6). So, if ChimeraX does not longer employ MSMS, what else does it use? With "MEASURE CONVEXITY" I get the surface vertex positions, normals, convexity values, and triangles. Unfortunately, the association with the corresponding residue is lost (however, can be regained with a little bit of work I guess, simply using euclidean distance). Question: Is there something similar for the SESA or SASA of the different atoms in the model/chain. In theory, this information should be available, at least the SESA. I am just wondering whether there is a way to write this out as a raw txt file in ChimeraX The closest I found in the save command is the .obj or .vtk format. However, both are semi-satisfying in that that they both do not provide the data looked for and are in somewhat special formats, at least the vtk. The .obj file is much much bigger than what MSMS or "measure convexity" generates, and not really handy for then working with the data in other programs, mainly python. As always, I very much appreciate any help and wish to thank the team for their contributions to the field. Best regards Dennis

3 5

ChimeraX Help
by Bani Kaur 20 Oct '23

20 Oct '23

Hi, I hope you are well! My name is Bani Kaur and I am a ChimeraX user. I wanted to ask you about how I can specify labels on ChimeraX, specifically with finding the names of the residues on a protein. Additionally, how does info residues work and info resattr. I would appreciate any help and guidance! Thanks! Best, Bani Kaur

2 2

ChimeraX fading?
by Elaine Meng 19 Oct '23

19 Oct '23

> On Oct 19, 2023, at 4:21 AM, Carl Johan Hagstromer <carl.johan.hagstromer(a)ki.se> wrote: > > Would love fading options, like in PyMOL > Hi Carl, We aren't Pymol users so we don't know exactly what you are referring to, but it may well be possible in ChimeraX if you could give more detail. We can put this discussion on chimerax-users(a)cgl.ucsf.edu (CC'd here) so that more folks can weigh in. ChimeraX can do: depth cueing (fading front->back), gradual fading in/out of structures and/or 2D labels by increasing or decreasing transparency over a number of image frames, and/or color modification (e.g. increasing whiteness of all current colors). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

3 2

Isolde usage in Chimera
by Dmitry Semchonok 19 Oct '23

19 Oct '23

Dear colleagues, How to drag the structure, preserving the secondary structure (alpha-helix and beta-sheet) geometry in Isolde? Can I set up certain restraints to keep the correct geometry of the structure while dragging it? Many thanks! Kind regards, Dmitry

2 1

Uncaught bounce notification
by postmaster＠cgl.ucsf.edu 19 Oct '23

19 Oct '23

From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> Subject: command for moving atomic models in ChimeraX Date: October 18, 2023 at 5:51:07 PM PDT Dear All, I have a set of 8 proteins forming a mega complex that we are working on. The density map of the mega complex has a resolution of 2.7Ang. The atomic structures of the proteins were determined. Out of the 8, proteins 3 have C5 symmetry. I am trying to generate potential models using the atomic structures where these pentameric proteins can be expanded out (kindly see the schematic diagram S1 to S2). Is there a command (move command ??) to do so? Thanks 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/>

1 0

Movie Record/Encode with GPU?
by Alexander Hung Lee 18 Oct '23

18 Oct '23

Hi everyone, I have another question about scripting. I decided to use the morph command over a trajectory with 200 frames (imported as separate pdb's) to make a really smooth movie. Currently, my .cxc has matchmaker #2-200 to #1; morph #1-200 frames 8 same true play false; close #1-200 (< 5 mins) hbonds #201:UNL restrict :UNL :< 5 reveal true interModel false cacheDa true coordsets true (< 5 mins) movie record supersample 4; perframe "~label; label hbondatoms" ; coordset #201 1,1593; wait 1593; ~perframe; movie encode output movie.mp4 bitrate 6000 framerate 25 (> 1 hr) The output is buttery smooth, and the hbond calculation only takes 3-4 mins even with 1600 frames. However, I have a problem with the speed of recording/emcpdomg... it's more than an hour. I found it strange since if I played the trajectory from morph using coordset/slider, it barely takes any time and is very smooth. I was wondering if there was a way to make this recording/encoding faster or to switch from cpu to gpu if that was possible (and if it would help any)? On another note, I'm experimenting with smooth_md.py script but with trajectory files instead of pdb's. I'll see which one looks better/is faster Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

2 2

Open small molecule cif
by Jaremko, Matt Joseph 18 Oct '23

18 Oct '23

Hello, How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: [cid:image001.png@01DA0026.3D6BC080] Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko(a)merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

3 8

memory questions
by Tintos-hernandez, Alonso A 18 Oct '23

18 Oct '23

Hi i was trying to do some modeling using the alfafold colab but it says that i need to buy more memory to run more modeling, hos should i do that ? Jesus Tintos Childrens Hospital of Philadelphia Senior scientist II

3 2

model becomes invisible behind the map when color with hexadecimal color codes
by Kai Cai 17 Oct '23

17 Oct '23

Hi, I've got this weird bug that hope you can help me with. When I try to color a selected protein model with nonmajor hexadecimal color codes (e.g. #f17d21cc), the selected model will become invisible behind the map it was fit with. The map is set as transparent surface. Once it becomes invisible, it won't come back no matter how I change the color. This appears to be a recent issue. Not sure if it's a bug caused by recent macOS update. I am running the most recent ChimeraX daily update on a macOS 14.0. Here is an example if you would like to test it: open 25428 fromDatabase emdb open 7sth transparency 50 select #2 color sel #f17d21cc Thanks, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 2

Opening series of pdb's in incorrect sequential order
by Alexander Hung Lee 13 Oct '23

13 Oct '23

I have a series of pdb's in a folder numbered 1 - 500 (so 1.pdb ... 500.pdb). I'm opening them in ChimeraX using *.pdb. I'm expecting 1.pdb to have ID1 and 2.pdb to to be ID2, but it appears ChimeraX is only looking at the first digit and not the whole number. Is there a way around this? For now, my work around is to use 001, 002 ... 500 instead [cid:d19d2d17-71bb-430f-8a09-65921a0ca962] Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

2 1

Gaussian surface visualization of a subset of residues
by Stefano Pellegrini 13 Oct '23

13 Oct '23

To whom it may concern, I am a PhD student at the Biomedical Genomics Lab at the Institute of Biomedicine of Barcelona. I am using ChimeraX to produce figures for the publication of an in-house recently developed tool for cancer driver gene discovery. I am new to using ChimeraX, so I am sorry if my question might seem very naive to you. Anyway, I can't find this information anywhere else. My problem is simple: I want to show the surface (or volume) occupied by the atoms of a selected number of residues within a chain. I can easily achieve this by using the Gaussian surface (GS) by adding the parameter "resolution" to the "surface" command as "surface :10-20 resolution 6" The problem is that the surface visualized in this way has "gaps" where it overlaps with other atoms that are not from the selected residues. As expected, these gaps get larger when using a greater resolution. Now, I would like to show the complete surface around these residues, without gaps. Could you please provide any suggestions? Thank you in advance, and best regards, Stefano Pellegrini -- *Stefano Pellegrini, **PhD student* Barcelona Biomedical Genomics Lab Institute for Research in Biomedicine (IRB) Carrer de Baldiri Reixac 10, 08028, Barcelona, Spain http://bbglab.irbbarcelona.org

2 1

About saving alphafold2 predictions
by Luz Cristina Vallejo Garcia 12 Oct '23

12 Oct '23

Hi there! I have a problem using ChimeraX. I tried to use the aphafold2 tool to predict a large protein structure. The process to predict the structure of my protein was successfully completed, but the downloading of my results failed. I observed that the folder for the prediction was created but is empty. So my questions are: Why did the program fail to download my results? Is there a possibility to obtain my results without to re-run the process? Thanks in advance Cris Vallejo IBt, UNAM, México <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus.www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

saving alignment in ESP format using chimerax
by Ferreira Ramos, Ana Sofia 11 Oct '23

11 Oct '23

Hi, I would like to save a sequence alignment in ESP format but in my chimerax the option "Save EPS" is not present in the menu of the sequence viewer. The menu is only show if I right click inside the sequence viewer and I do not have all options there: [cid:55913c6a-a21d-45c9-b616-c60bdb4a6b4a] Please, could you let me know how can I save the alignment in the ESP format? Is there a way to do it through the command line? Thank you very much for your attention. Kind regards, Ana

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Re: [Chimera-users] ChimeraX Redistribution Policy Question
by Tom Goddard 10 Oct '23

10 Oct '23

Hi Pat, The ChimeraX license does not allow redistribution. But we have sometimes given permission for that, for example the Structural Biology Grid Consortium (SBGrid). The main issue is our project is funded almost entirely by grants and we have to document how widely the program is used to continue to get funding. Could you explain more details about your distribution? In what way does it use ChimeraX? Can ChimeraX visualization use desktop graphics rendering accelerated by the graphics card within in a Docker image? In general we recommend using ChimeraX on laptop/desktop computers, not containerized, not remotely displayed, because the interactive 3D rendering is often slow or broken in virtualized setups. Let's continue this discussion on the ChimeraX mailing list, not the Chimera mailing list. Tom > On Oct 8, 2023, at 5:53 PM, Patrick Rynkiewicz (RIT Student) via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello! > > I am a co-developer on a molecular dynamics software package that relies on UCSF ChimeraX, and am looking to package this software in a docker container. It's unclear to me from the licensing process what the policy is for ChimeraX redistribution, such as including the .deb package in a docker build. Can you please clarify if I would be able to cite and redistribute ChimeraX 1.6, Ubuntu 22.04 to non-commercial users in my software package, or does each individual user need to accept the non-commercial license agreement separately? > > Thanks! > > Pat Rynkiewicz > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

2 2

ChimeraX- protein protein interaction parameter
by Elaine Meng 06 Oct '23

06 Oct '23

Hi Ali, My colleague shared your question with me and I will try to answer it here. For the future, please send your ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here so you don't need to do anything this time) so that other users can benefit, unless you are including data that needs to be kept private. Sorry, ChimeraX does not calculate binding affinities (binding free energy) or predict their changes when you mutate the protein. You can only get a an approximate, first-order impression of whether they appear to improve or disrupt favorable interactions by measuring things like the surface area in the interface or the number of hydrogen bonds or clashes (bad packing) between the binding partners. See command "measure buriedarea" and the tools "Hbonds" "Contacts" and "Clashes" : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> The picture that you get from these tools might still be incorrect if any of the 3D structures are predicted inaccurately (wrong sidechain conformations, wrong binding interface, wrong fold, etc.). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > From: Ali Aljasser <aljassera(a)cua.edu> > Subject: ChimeraX- protein protein interaction parameter > Date: October 5, 2023 at 5:12:46 PM PDT > > I am part of Dr. Choy's group at the Catholic University of America. I work on studying the protein-protein interaction for two kinetochore proteins. Based on alpha fold prediction, we utilized Chimerax to predict the strength of the interaction of these two proteins. We also added some mutations that are known to influence the interaction. However, I still struggling with how to find parameters such as delta G that would help me to predict the strength of the interaction and whether the mutations affect the interaction. > > Please let me know if you can assist me in this regard. Thank you for your time and I am looking forward to hearing from you soon. > Regards, > Ali

1 0

Saving Looking Glass shots and movies
by tolung.bio＠gmail.com 05 Oct '23

05 Oct '23

Hi, Once I open a structure, create a scene and adjust the depth in the Looking Glass display, is there way to save that in a format that can then be imported into the Looking Glass Studio to be displayed in the stand-alone mode of the display? It is possible to do the same thing with animation, such as a 360 rotation or rocking? Thanks, Gökhan

2 1

Surface representation - Dots
by Dennis Dannecker 04 Oct '23

04 Oct '23

Hello, I would like to ask a question regarding the surface representation of protein molecules in ChimeraX. I remember from Chimera that one could very customize the surface representation in terms of probe size, vertices density, and dot size used in the dot surface representation. While ChimeraX also allows to show dot surface representation, does it also allow for setting these attributes? But the more important question of mine is, can one export/extract the coordinates (spherical or cartesian) of the dots generated during dot surface representation. I would be interested in a file that holds the coordinates of these dots/particles around the molecule. In principal that should be possible, but as always, how amenable is that data? Thank you very much. Cheers Dennis

2 2

Showing CAVER channels and tunnels
by Tom Goddard 04 Oct '23

04 Oct '23

I wrote a brief tutorial on how to show channels and tunnels computed by CAVER using ChimeraX. https://rbvi.github.io/chimerax-recipes/caver/caver.html Tom

1 0

worm plots?
by Gabriel Lander 03 Oct '23

03 Oct '23

Is it by any chance possible to do b-factor worm plots in ChimeraX yet? I recall this was going to take a lot of effort since the code for ribbon depiction would have to be overhauled, but hoping maybe there's been some progress. If not I'll keep exporting from Chimera. thanks, -gabe

2 1

Speeding up commands from cxc
by Alexander Hung Lee 02 Oct '23

02 Oct '23

Hello everyone, I'm working to automate making movies from 10,000 frame trajectories. Currently, my cxc contains the following commands windowsize 1920 1080 set bgColor white view zalign ligand inFrontOf #1 sel protein surface; surface color salmon; transparency protein 60 target s sel :UNL color sel dark slate gray; color sel byhetero sel :SIA color sel dim gray; color sel byhetero sel :UNL hbonds :UNL reveal true surface zone #1 nearAtoms ligand distance 15 select zone ligand 15; select add ligand select ~sel ~cartoon sel delete sel ~sel view ligand movie record supersample 4 perframe "~label; label hbondatoms" ; coordset #1 1,10000,50; wait 200; ~perframe movie encode output hbond.mp4 bitrate 6000 framerate 4 The above takes ~ 30 mins, and it's something I would like to do for whole libraries I'm screening. I think the longest process is "hbonds :UNL reveal true" while second longest is movie record and perframe. Is there a way to speed this up? Is there a way to take advantage of multi-threading if it isn't already enabled? If multi-threading is already being used, what can I change to be more efficient? I deleted the parts that I didn't need "delete sel" since they're not involved in the binding site, and I thought it would help speed up surface calculations while recording. Regards, Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Bright light while using fly command
by Haselbach,David 02 Oct '23

02 Oct '23

Hi, I am trying to make a fly movie in which I move from one rotation state of the molecule to the next. Unfortunately, the lighting during the flight is not nice. The light goes very bright while moving and in the end jumps back to normal. However, if I do the turn life with mouse the light is fine. I am using soft lighting. Find attached an example movie. What could I do? Can anyone help? Best, David

3 2

ChimeraX Alphafold Question
by Vincent Candela 02 Oct '23

02 Oct '23

Hello, I am an undergraduate researcher at McGill University using the Alphafold feature of ChimeraX to study the role of tau on microtubule dimers, and I was wondering if you could point me to detailed documentation on the energy-minimization feature of Alphafold. I’ve been looking at the ChimeraX documentation and couldn’t find an in-depth documentation on what it does. Thank you so much, Vincent Candela

3 2

Color info
by Margulies, David (NIH/NIAID) [E] 29 Sep '23

29 Sep '23

If I color, say, “bychain” how do I get the info on what the displayed color is. Is there an info color command? David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892 Email: dmargulies(a)niaid.nih.gov<mailto:dmargulies@niaid.nih.gov>, dhm(a)nih.gov<mailto:dhm@nih.gov> Ph: 301-496-6429 Fax: 301-480-7352 Web: https://www.niaid.nih.gov/research/david-margulies-md-phd “Public service is a public trust, requiring employees to place loyalty to the Constitution, the laws, and ethical principles above private gain.” – executive order 12674, https://www.federalregister.gov/documents/2016/02/17/2016-03214/standards-o…<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.federalregister.go…> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender’s own and not expressly made on behalf of the NIAID by one of its representatives.

2 2

wildcard used within SAVE command
by 洪冉 29 Sep '23

29 Sep '23

Hi all, I have been trying to produce some high-resolution pictures recently using ChimeraX. And "save C:/xxxx/xxxx/test.png" was used to produce the pic, then I had to change the context "test" into each structure name manually. e.g. save C:/xxxx/xxxx/benzene.png or save C:/xxxx/xxxx/methanol.png Actually, the structure loaded into chimeras was with the right name. Hence, I want to ask for help if is there a wildcard that could be used in the "save" command for saving the picture with the name of the structure. e.g. save C:/xxxx/xxxx/${nameofstruc}.png Of course, it does not work. I just want to give this as an example to suggest my opinions. Thanks in advance. Yours, Ran

2 2

How to activate the Extract button in Segment Map function?
by Bo Chen 25 Sep '23

25 Sep '23

Dear ChimeraX, I tried to use Segment Map to remove some portions of the cryoEM map, and extract the selected portion, but the extract button remains shaded. The only tab in the "other tools" row that appears to be activated is "Fit". I have the most recent version of ChimeraX installaed(Sept 19). Could you give me some hints how to activate the extract in "Other tools" under the "Shortcut options" in "Segment Map"? Thanks! Bo

3 2

Changing mesh size to save as STL file
by Arthur Melo 25 Sep '23

25 Sep '23

Dear colleagues, Is there a way to refine or decimate a mesh of a map to save as an STL file? All the best, Arthur

2 2

symmetrizing the model
by Dmitry Semchonok 22 Sep '23

22 Sep '23

Dear colleagues, A very quick question - what is the command to apply the symmetry to the 3D model? (please provide a usage example if possible). Will the soft generate the symmetrized model after this command application? I found the one for Chimera but not for ChimeraX. Many thanks. Sincerely, Dmitry

3 4

Equivalents to sop split & mask?
by Oliver Clarke 21 Sep '23

21 Sep '23

Hi, Is there a direct equivalent to the command “sop split” in ChimeraX? In the documentation for the “surface” command, I can see that there is an option to split by color, but not to split into individually selectable blobs. We use this a lot in Chimera, as a quick way to make a starting point for a mask to use in refinement, so it would be great to have in ChimeraX too. Also, is there an equivalent to the “mask” command from Chimera? I can’t seem to find it but perhaps it has a different name? Cheers Oli

3 3

Labels of selected residues even with their model name
by svle＠tiscali.it 21 Sep '23

21 Sep '23

Hi, I have used matchmaker with four loaded models to compare the side chains orientation of some selected residues. It is possible to label the selected residues even with the information of the model name they belong to? Thanks. Saverio

3 3

Open and play volume series in ChimeraX
by Wout Oosterheert 20 Sep '23

20 Sep '23

Dear ChimeraX team, I’m currently trying to open a volume and play a volume series in ChimeraX. According to the website (https://www.cgl.ucsf.edu/chimerax/docs/user/trajectories.html) opening a volume series should work like this: “Volume data can be opened as a series with open, employing filename wildcard symbols or globbing as needed to specify multiple files in a single command”. This seems simple enough, I indeed can open the volumes as a group. However, when I then try to play the series using: vseries play #1 direction oscillate loop true, I get the error: no volume series specified. Could you explain to me how I can get my group of volumes recognized as a volume series? The vseries page (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/vseries.html) is very elaborate, but I cannot find alternative options of opening my volumes as a series. I know how to do things in regular Chimera, but would prefer to stick with ChimeraX because I make all my other figures with it. Thank you very much in advance!! Best, Wout Wout Oosterheert, PhD Humboldt Postdoctoral Fellow Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany Phone +49-(0)231-133-2357 Email: wout.oosterheert(a)mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de>

2 2

seq_rmsd and align command
by dng26＠mrc-mbu.cam.ac.uk 19 Sep '23

19 Sep '23

Hello, I have two PDB models I am comparing, but I am having some issues generating the seq_rmsd attribute across all of the chains in the superposition that I want. My current models (same protein, but different states and slightly altered built sequences) have chains A/B/C/D/E/F separated over two domains of A/B/C and D/E/F, for example. My problem is that domain D/E/F is much larger than the former and when I run a matchmaker command such as this: matchmaker #1/A/B/C/D/E/F to #2/A/B/C/D/E/F pairing ss show true I get the resulting superposition favoring the /D/E/F domain (larger RMSD values on A/B/C). This would be fine, however, I want to investigate RMSD variation in D/E/F relative to a fixed position of A/B/C. If I run the following command I only get pairwise RMSDs (seq_rmsd header) for the specified chains but lack those of the larger D/E/F domain as they are not included. matchmaker #1/A/B/C to #2/A/B/C pairing ss show true I look to Calculate the RMSD between paired residues of chains /A/B/C/D/E/F without moving the current structures (after ‘mmaker’ alignment to A/B/C) with the ‘align’ command but the ‘move’ option set to nothing: align #1/A/B/C/D/E/F toAtoms #2/A/B/C/D/E/F move nothing matchNumbering (or matchAtomNames also tested) true I believe the above is what I want with regards to superposition for the RMSD calculations, but the ‘align’ job does not appear to give a seq_rmsd header attribute once run, even though the log seems to suggest it does a pairwise residue alignment to calculate the RMSDs. (Possibly because it does not just look at the CA like matchmaker does?) Is there a way to generate seq_rmsd attributes from the ‘align’ command, or is there a way to have an equivalent ‘move nothing’ in ‘mmaker’? I am looking to use seq_rmsd information to color the model and I am using v1.6.1. Any help is much appreciated! Dan.

2 2

Chimerax
by François Ferron 15 Sep '23

15 Sep '23

Hi I am making a figure using a pdb and a density map in chimeraX1.6.1. each time I do that I have coloured arrows representing an axis that is in the middle. how do I get rid of them. I am sure it is trivial but I just could not find the answers in the manual. thanks François -- François Ferron, Ph.D. francois.ferron(a)univ-amu.fr @F2erron@fediscience.org Laboratoire CNRS - UMR 7257 (AFMB) AFMB - POLYTECH Case 925 163, Av de Luminy 13288 Marseille Cedex 09 France & European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany ######################################### Success is not final, failure is not fatal; it's the courage to continue that counts.

2 2

Request to Resolve the Issue of Modifying Surface Dot Size in ChimeraX
by 18802001045＠163.com 14 Sep '23

14 Sep '23

Dear ChimeraX Maintenance Team, I hope this email finds you well. I am writing to seek assistance regarding an issue I have encountered while working with protein models in ChimeraX. After performing MPL calculations on protein models, I have found that I am unable to modify the dot size of the resulting surface representation. In Chimera, this task was easily accomplished through the "Model Panel" by adjusting the "MSMS Model Attributes". However, I have not been able to find a similar option or command in ChimeraX. I would greatly appreciate it if you could provide guidance or suggest a solution to address this matter. Being able to adjust the dot size of the surface representation is crucial for my current research project, and I rely heavily on the functionalities provided by ChimeraX. Thank you very much for your attention to this matter. I look forward to your kind assistance and prompt response. Best regards, Zhuangwei Zhang, Ph.D. State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Centre of Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University E-mail: dg21240166(a)smail.nju.edu.cn

5 4

Monitor distance angle and torsion angles along trajectoty
by CUNIASSE Philippe 14 Sep '23

14 Sep '23

Dear all, I am wondering if there is a mean in ChimeraX to monitor distances, angles and torsion angles along a MD trajectory. The ideal would be to export a vector containing the frame id (a number) and the value measured for the distance or torsion angle. At the moment I can only built a distance histogram (which is already very usefull) after having created a pseudobond. But doing this, you lose the time evolution along the trajectory. Thanks in advance for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:philippe.cuniasse@cea.fr> Web: http://biodev.cea.fr/rasmot3d/ [signature_575242473][signature_2653780937][signature_3407707164] -----------------------------------------------

2 2

Setting default volume step and rms level
by Samuel Haysom 13 Sep '23

13 Sep '23

Hello, Is it possible to change the default step and level that ChimeraX uses when it opens maps? My data (cryoEM) mostly opens at step 2 with the level set too low for useful viewing, necessitating adjusting these settings for every map I open. Is there a global setting that I can change (for instance by specifying it in a startup script) to change this behaviour so my maps always open at step 1 and at a specified level (say rmsLevel 8)? KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

4 5

Advice on handling cofactor-protein electrostatic interactions
by Boaz Shaanan 12 Sep '23

12 Sep '23

Hi, I would like to present effects of mutations around cofactors (TDP derivatives) on the protein - cofactors electrostatic interactions. I use APBS and chimerax to display the electrostatic surface potential of the protein, but since PDB2PQR eliminates the cofactor from the pqr file I need a tool for the cofactor surface potential. I'm wondering what tool I should use for this. Is it Antechamber+chimerax or something else? Is there by chance a demo for such scenario? I'd appreciate your advice. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

2 7

ChimeraX "Fly" Command
by Kayla Deuter 12 Sep '23

12 Sep '23

Good afternoon, I am emailing you to try and troubleshoot the ChimeraX software I am currently using. I just recently downloaded ChimeraX 1.1.1 and I am operating on a Macbook Pro with High Sierra 10.13.6 software. I am currently teaching myself the program by watching tutorials and referencing the User Guide. Everything seems to work fine except for the "fly" command. I am trying to record movies for practice and examples but every command works except for the "fly" command. I went into the user guide, I've tried researching the issue, and I've done about all I can do to try resolving this issue on my own. After I create my view points, I attempt to create transitions by typing "fly view 1 view 2" but every time I try typing fly it always says command unknown and gives me error messages. When I try to further investigate the error code, it is useless and I get no answers. If there is anything I can do to fix this, please let me know. The fly command is crucial for creating a smooth animation. Best, Kayla Deuter

2 1

Re: Trouble installing plugin
by Eric Pettersen 12 Sep '23

12 Sep '23

Hi Barry, We continue to work on this issue, but have not yet succeeded in getting installation as a source dependency to work. We hope to get it resolved soon, but it's hard to say exactly how long it will take, so in the interest of allowing you to make progress I suggest using an alternate approach -- include mdtraj as an additional package in your bundle. In your bundle_info.xml you would use an AdditionalPackages tag with a child tag of "Package" which has a "name" attribute of "mdtraj" and a "folder" attribute of wherever mdtraj got installed. Since mdtraj is not pure Python, you would also have to use a "platform" attribute of mac/linux/windows. If you also built mdtraj on other platforms you could copy it over to the machine you're building the bundle on and include additional Package tags with different platform/folder values. You also have to have a DataFiles tag with a "package" attribute of "mdtraj" and an appropriate "platform" attribute, with child DataDir/DataFile tags enumerating what to copy from the installation. One thing to keep in mind is that the installation has to be compatible with the version of Python ChimeraX is using, which is Python 3.9 for ChimeraX 1.6.1 and Python 3.11 for the daily build. So you would want to include the corresponding dependency on ChimeraX-Core. Also, a binary version of mdtraj is available for Mac (Python 3.9) so you could conceivably include that directly as a dependency (i.e. in a Dependency tag rather than a Package tag) with a "mac" platform attribute and a ChimeraX-Core dependency of ==1.6.1. For reference, SEQCROW uses the AdditionalPackages tag in its bundle_info.xml, which you can see here. <https://github.com/QChASM/SEQCROW/blob/master/bundle_info.xml> --Eric Eric Pettersen UCSF Computer Graphics Lab > OK. So, we decided to wipe some computers and start fresh to install our plugin. And using the daily build from a couple days ago and a daily build from 7-15 and always on a freshly built linux 20.04 system we are unable to install my plugin. However, it somehow installed in the past on my coworker's system (using 7-15 chimerax) and my system (using 6-6 chimerax). He and I can both repeatedly install and uninstall my plugin. But any clean system will not "devel install" the plugin. Below is the latest log output using the daily build from 7-15 (because we have one user successfully using it). I am at a real loss as to what is going on. FWIW the clean systems do also have python 2.7. I know recently you fixed a problem of installing a plugin on a system that has python 2.7 on it. Please let me know what I can do. Our plugin is alpha ready and if I can't get it easily installable then our project is at a standstill.

1 1

Lock model(s) to rotation/translation?
by Oliver Clarke 08 Sep '23

08 Sep '23

Hi, I know that in ChimeraX the preferred way to manipulate models with respect to one another is using the mouse modes. This works, but is still (in my experience) less precise/ergonomic than deactivating selected models in Chimera and freely manipulating the remaining active models using the trackpad/mouse. Is there any possibility in the future (or present) of adding the capacity to “lock" selected models to rotation/translation, to allow free manipulation of the remainder? Cheers Oli

2 14

Add model number to pop up balloon?
by Oliver Clarke 08 Sep '23

08 Sep '23

Hi, Currently the info in the pop up balloon that appears when one hovers over a residue is of the following format: res-name res-num.chain atom-name. Would it be possible to add the model number at the start? The model number is in the pop up balloon for maps, but not atomic models, and it would be convenient to have it to avoid having to bring up the model panel when typing commands. Cheers Oli

2 2

Re: Trouble installing plugin
by Zach Pearson 08 Sep '23

08 Sep '23

Per https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8927 which broke on the same dependency (mdtraj), dealing with recursive pip was such a nightmare that ChimeraX’s pip command searches for the python executable _next to_ ChimeraX.exe and uses that instead of ChimeraX; toolshed_utils will have to do the same to fix this error. — Zach > On Aug 30, 2023, at 14:40, Tom Goddard <goddard(a)sonic.net> wrote: > > Hopefully Zach or Greg can help you with this pip install error. > > Tom > > >> On Aug 30, 2023, at 2:19 PM, BARRY E DEZONIA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> OK, so we have now installed chimerax-daily on another system that already had it on there. We were getting similar errors as detailed in my earlier email. After carefully cleaning the system and removing and reinstalling the July 14 daily build we are still getting install errors for my plugin. Instead of the python 3.9 complaints they are now python3.11 complaints. So that part of the earlier problem was fixed by my cleanups. But it is still broken. We still have pip running problems. Even with upgrading chimerax's python's pip and making sure that the chimerax's pip's bin dir is in the path. The error message is basically "AssertionError: Cannot run __pip-runner__.py as a non-main module". I will post the (lengthy) log output of my plugin install process below. Please let us know what might be causing this. We were just going to install a new daily build but your website has been down today. >> >> ==================================================== >> >> UCSF ChimeraX version: 1.7.dev202307150241 (2023-07-15) >> © 2016-2023 Regents of the University of California. All rights reserved. >> How to cite UCSF ChimeraX >> devel install /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qtrunning build >> running build_py >> running bdist_wheel >> installing to build/bdist.linux-x86_64/wheel >> running install >> running install_lib >> creating build/bdist.linux-x86_64/wheel >> creating build/bdist.linux-x86_64/wheel/chimerax >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt >> copying build/lib/chimerax/tut_tool_qt/tool.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt >> copying build/lib/chimerax/tut_tool_qt/__init__.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/zncc.sh -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/zncc.jar -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/simCC.com <http://simcc.com/> -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/simNC.com <http://simnc.com/> -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable >> copying build/lib/chimerax/tut_tool_qt/Installable/install_traj2nmr.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/README.md -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/setup.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/session.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/ucsf.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/__init__.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/resonance.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/shifts.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/utils.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/LICENSE -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> running install_egg_info >> running egg_info >> writing ChimeraX_BphonTool.egg-info/PKG-INFO >> writing dependency_links to ChimeraX_BphonTool.egg-info/dependency_links.txt >> writing requirements to ChimeraX_BphonTool.egg-info/requires.txt >> writing top-level names to ChimeraX_BphonTool.egg-info/top_level.txt >> reading manifest file 'ChimeraX_BphonTool.egg-info/SOURCES.txt' >> writing manifest file 'ChimeraX_BphonTool.egg-info/SOURCES.txt' >> Copying ChimeraX_BphonTool.egg-info to build/bdist.linux-x86_64/wheel/ChimeraX_BphonTool-0.4-py3.11.egg-info >> running install_scripts >> creating build/bdist.linux-x86_64/wheel/ChimeraX_BphonTool-0.4.dist-info/WHEEL >> creating 'dist/ChimeraX_BphonTool-0.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it >> adding 'chimerax/tut_tool_qt/__init__.py' >> adding 'chimerax/tut_tool_qt/tool.py' >> adding 'chimerax/tut_tool_qt/Installable/install_traj2nmr.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/LICENSE' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/README.md' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/setup.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/__init__.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/resonance.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/session.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/shifts.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/ucsf.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/utils.py' >> adding 'chimerax/tut_tool_qt/Runnable/simCC.com <http://simcc.com/>' >> adding 'chimerax/tut_tool_qt/Runnable/simNC.com <http://simnc.com/>' >> adding 'chimerax/tut_tool_qt/Runnable/zncc.jar' >> adding 'chimerax/tut_tool_qt/Runnable/zncc.sh' >> adding 'ChimeraX_BphonTool-0.4.dist-info/METADATA' >> adding 'ChimeraX_BphonTool-0.4.dist-info/WHEEL' >> adding 'ChimeraX_BphonTool-0.4.dist-info/top_level.txt' >> adding 'ChimeraX_BphonTool-0.4.dist-info/RECORD' >> removing build/bdist.linux-x86_64/wheel >> Distribution is in /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> [toolshed install](help:user/commands/toolshed.html#install) >> /home/crow/bphon/bphon/chimerax- >> plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> >> [toolshed install /home/crow/bphon/bphon/chimerax- >> plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none- >> any.whl](cxcmd:toolshed install /home/crow/bphon/bphon/chimerax- >> plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl) >> >> Traceback (most recent call last): >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 517, in _pip_install >> results = _run_logged_pip(command, logger) >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 583, in _run_logged_pip >> raise RuntimeError(s) >> RuntimeError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ >> Processing /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> Requirement already satisfied: ChimeraX-Core~=1.1 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.7.dev202307150241) >> Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.30.2) >> Collecting mdtraj (from ChimeraX-BphonTool==0.4) >> Using cached mdtraj-1.9.9.tar.gz (2.2 MB) >> Installing build dependencies: started >> Installing build dependencies: finished with status 'error' >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> [22 lines of output] >> ERROR: >> Traceback (most recent call last): >> File "<frozen runpy>", line 198, in _run_module_as_main >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 1044, in <module> >> exit_code = init(sys.argv) >> ^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 801, in init >> runpy.run_path(opts.run_path) >> File "<frozen runpy>", line 291, in run_path >> File "<frozen runpy>", line 98, in _run_module_code >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/pip/__pip- >> runner__.py", line 49, in <module> >> assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main >> module" >> ^^^^^^^^^^^^^^^^^^^^^^ >> AssertionError: Cannot run __pip-runner__.py as a non-main module >> >> >> [end of output] >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> See above for output. >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> >> >> During handling of the above exception, another exception occurred: >> >> Traceback (most recent call last): >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/devel.py", line 174, in _run >> unbound_method(bb, *args, **kw) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder.py", line 154, in make_install >> run(session, cmd) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 38, in run >> results = command.run(text, log=log, return_json=return_json) >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897, in run >> result = ci.function(session, **kw_args) >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/toolshed.py", line 301, in toolshed_install >> ts.install_bundle(bundles, logger, **kw) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 916, in install_bundle >> _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 252, in _install_bundle >> results = _pip_install( >> ^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 520, in _pip_install >> raise UserError(str(e)) >> chimerax.core.errors.UserError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ >> Processing /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> Requirement already satisfied: ChimeraX-Core~=1.1 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.7.dev202307150241) >> Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.30.2) >> Collecting mdtraj (from ChimeraX-BphonTool==0.4) >> Using cached mdtraj-1.9.9.tar.gz (2.2 MB) >> Installing build dependencies: started >> Installing build dependencies: finished with status 'error' >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> [22 lines of output] >> ERROR: >> Traceback (most recent call last): >> File "<frozen runpy>", line 198, in _run_module_as_main >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 1044, in <module> >> exit_code = init(sys.argv) >> ^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 801, in init >> runpy.run_path(opts.run_path) >> File "<frozen runpy>", line 291, in run_path >> File "<frozen runpy>", line 98, in _run_module_code >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/pip/__pip- >> runner__.py", line 49, in <module> >> assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main >> module" >> ^^^^^^^^^^^^^^^^^^^^^^ >> AssertionError: Cannot run __pip-runner__.py as a non-main module >> >> >> [end of output] >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> See above for output. >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> >> From: Tom Goddard <goddard(a)sonic.net> >> Sent: Thursday, August 24, 2023 9:49 PM >> To: BARRY E DEZONIA <barry.dezonia(a)wisc.edu> >> Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> >> Subject: Re: [chimerax-users] Trouble installing plugin >> >> The ChimeraX daily build is using Python 3.11 and your error message includes paths to Python 3.9. It will probably cause havoc if you have both in your same ChimeraX installation. >> >> ChimeraX developers Greg or Zach who know more about Linux would have to comment on whether it is even possible to install ChimeraX over another ChimeraX without the original copy being deleted. And they also work on the "devel install" command. >> >> Tom >> >> >>> On Aug 24, 2023, at 12:08 PM, BARRY E DEZONIA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> It is possible that on my home machine I installed the latest daily build over an earlier daily build. >>> From: BARRY E DEZONIA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> >>> Sent: Thursday, August 24, 2023 6:33 AM >>> To: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> >>> Subject: [chimerax-users] Trouble installing plugin >>> >>> I am having trouble installing a plugin I am developing. It works on one system I am using at work and fails on my system at home. The home system has the latest daily build on it. The work system has an earlier daily build on it. >>> >>> This is what I try to do inside chimerax: >>> >>> devel install ~/dev/bphon/chimerax-plugin/tut_tool_qt >>> >>> And this is the installation error: >>> >>> open /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.pyTraceback (most recent call last): >>> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py", line 49, in <module> >>> assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main module" >>> AssertionError: Cannot run __pip-runner__.py as a non-main module >>> >>> Error opening python file /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py >>> >>> Any idea what is happening? I may have run into this problem some time ago on the work computer and fixed it but I honestly don't know. >>> >>> Please forward this to the bugs email list of it should go there instead. Thanks. >>> >>> Sorry for yet another question. You guy seems very busy with mail recently. >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >> _______________________________________________ >> 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> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >

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Coloring of trajectory using mpl command
by Alexander Hung Lee 08 Sep '23

08 Sep '23

Hello everyone, I'm sorry for bothering all of you so often these past few days... but I ran into another issue. I opened a pdb and corresponding trajectory .nc file, and I ran "mlp #1 key true". Lipophilicity coloring showed up, but when I played the trajectory, the mpl colors went away and the default colors came back. I noticed the same happened for "coulombic" command. For now, I'm making due with a custom attribute file and "color byattribute name palette lipophilicity" from this tutorial https://www.cgl.ucsf.edu/chimerax/docs/user/formats/defattr.html#examples. It does stay throughout the trajectory but doesn't look as good, and the colors aren't blended. I have also tried doing "mlp map true" and "color sample #1 map #2" with #1 being the pdb with trajectory and #2 the resulting map from mlp. It looked really bad. The protein is now one color. "mlp map true" command [cid:41c39c60-61c8-47ff-b996-f063b013d319] [cid:d2f10dad-4f81-40e6-99cc-407b2d96a17f] [cid:ec390e08-8756-45ce-af0d-8e8a03992457] Alex

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Selection syntax for atomic models vs surfaces/volumes?
by Oliver Clarke 06 Sep '23

06 Sep '23

Hi, Is there anything in the ChimeraX selection syntax to select by model type? For example, I would like to select only atomic models, excluding surfaces and volumes, and do something to them in a script or an alias - is there an efficient way of doing that? Right now, I can do this using "sel @*”, which selects everything is an atom, but I have the feeling that this is not so efficient (it is quite slow for large models). Cheers Oli

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inquiry
by Talha Shafi 06 Sep '23

06 Sep '23

hi I am using chimerax for model visualization. i wanted to inquire how can drag and rotate a selected model to manually overlap with my density may. in chimera1.13 version in model panel i could just uncheck the action option and perform my task. i can not figure this in chimerax to move my model over the density. fit in map is not able to align the models. may be manually aligning them and then perform fit to map works better. looking forward to hearing from you talha -- Talha Shafi Postdoc Scholar York Structure Biology Laboratory. University of York United Kingdom

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Dealing with artefact bonds
by Enrico Martinez 06 Sep '23

06 Sep '23

Dear Chimera-X users ! I am performing visualisation of the protein-protein complex obtained from md trajectory. The issue is that the pbd lacks the TER record between two different chains so Chimera-X recognises it as a bound complex and consequently adds a long unusual bond (>30A) between C term of one unit and N term on the another. Are there any commands that could be useful to omit such an artifact (e.g. to hide all bounds > 5 A etc) ? I found only a solution to hide several residues from the both units that will remove the long bond automatically. Many thanks in advance Enrico

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Aligning residue/ligand to foreground
by Alexander Hung Lee 05 Sep '23

05 Sep '23

Hello everyone, In old Chimera, I was able to center the ligand to the foreground of view using "align ligand ~ligand" no matter the orientation, if the ligand is in view or not. Is there a comparable way in ChimeraX? The same command gives "expected a keyword" and using "view ligand" or "view sel-residues zalign sel" does not bring it to foreground if it's behind something else. Thanks, Alex

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Predict a large protein structure with Alphafold2 and Chimerax
by Sara Qubisi 05 Sep '23

05 Sep '23

Hello Chimerax team. I am a postdoc at SICKKIDS hospital, and I am currently working on a project that involves large protein (~5400 aa). I am new to Alphafold and Chimerax and I want to perform a structure comparison between the wild type protein and a set of frameshift mutation (result in protein truncation) versions of the protein. I learned online and from your YouTube videos that I cannot enter more than 1200aa per assay request. Is there a way to overcome this where I can use the full protein sequence. Regards, Sara Qubisi. ________________________________ 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.

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[AMBER] Converted PSF file (prmtop > psf) failed to open in ChimeraX but did in old Chimera
by Alexander Hung Lee 05 Sep '23

05 Sep '23

Hello, I converted prmtop to psf to use with ChimeraX by just editing the suffix as suggested http://archive.ambermd.org/201902/0118.html and also converted it a second way with ParmEd. ChimeraX couldn't read either version and gave me the error "list index is out of range." I successfully opened the original prmtop and the two psf versions in the old Chimera with trajectory .nc file. What do I need to do? Alex

2 2

save "side view" settings
by vincent Chaptal 05 Sep '23

05 Sep '23

Hi, I opened the side view dialog window and adjusted the view planes for a nice figure. I would like to save the parameters so I can go back and modify the figure at a later stage, but the setting are not stored in the "view matrix" command. Could you tell me which command can save these settings? (I'm using chimeraX 1.5). Thank you. Best 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/

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Zone map around center of rotation?
by Oliver Clarke 02 Sep '23

02 Sep '23

Hi, Surface zone allows one to carve the map in a sphere around a selected atom (with “nearAtoms”). When navigating around the map, it would be convenient to be able to use the center of rotation as a reference point instead. Would it be possible at some point to add a “nearCofR” option to surface zone to facilitate this? In Chimera, I had kind of a hack-y way to do this, by placing a marker atom at the center of rotation and using that as the reference, but this option is not yet available in ChimeraX. Cheers Oli

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Set defaults for molecule display?
by Oliver Clarke 01 Sep '23

01 Sep '23

Hi, Is there anyway to set default preferences for molecule display? Currently it seems to vary (I think?) based on the number of atoms in the model - so relatively small proteins will load as ribbons, while larger ones will load in sphere representation. I would rather set a default such that all molecules load as ribbons, rainbow colored by chain. Is this possible? Cheers Oli

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