- ChimeraX-users - RBVI Mailing Lists

Problem with Chimerax on Ubuntu 20.04
by svle＠tiscali.it 26 Jan '24

26 Jan '24

Hi, I've installed Chimerax 1.7.1 using the .deb. When launching the application from the icon It appears the Chimerax window along with another error panel and after one or two seconds these are closed. If I call Chimerax from a shell I receive the following: $ chimerax NOTE: available bundle cache has not been initialized yet [48347:48390:0126/183239.131894:ERROR:skia_output_surface_impl.cc(927)] surface_size=1224x615 format=6 color_type=4 backend_format.isValid()=0 backend_format.backend()=5 backend_format.asGLFormat()=0 backend_format.asVkFormat()=0 backend_format.asVkFormat() vk_format=0 surface_origin=1 willGlFBO0=0 Segmentation fault (core dumped) If this can be useful on my laptop: $ uname -a Linux xxxx-Lenovo-IdeaPad-S340-15API 5.4.0-74-generic #83-Ubuntu SMP Sat May 8 02:35:39 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux $ glxinfo -B name of display: :0 display: :0 screen: 0 direct rendering: Yes Extended renderer info (GLX_MESA_query_renderer): Vendor: AMD (0x1002) Device: AMD RAVEN (DRM 3.40.0, 5.4.0-74-generic, LLVM 11.0.1) (0x15d8) Version: 20.3.4 Accelerated: yes Video memory: 2048MB Unified memory: no Preferred profile: core (0x1) Max core profile version: 4.6 Max compat profile version: 4.6 Max GLES1 profile version: 1.1 Max GLES[23] profile version: 3.2 Memory info (GL_ATI_meminfo): VBO free memory - total: 866 MB, largest block: 866 MB VBO free aux. memory - total: 5689 MB, largest block: 5689 MB Texture free memory - total: 866 MB, largest block: 866 MB Texture free aux. memory - total: 5689 MB, largest block: 5689 MB Renderbuffer free memory - total: 866 MB, largest block: 866 MB Renderbuffer free aux. memory - total: 5689 MB, largest block: 5689 MB Memory info (GL_NVX_gpu_memory_info): Dedicated video memory: 2048 MB Total available memory: 7928 MB Currently available dedicated video memory: 866 MB OpenGL vendor string: AMD OpenGL renderer string: AMD RAVEN (DRM 3.40.0, 5.4.0-74-generic, LLVM 11.0.1) OpenGL core profile version string: 4.6 (Core Profile) Mesa 20.3.4 OpenGL core profile shading language version string: 4.60 OpenGL core profile context flags: (none) OpenGL core profile profile mask: core profile OpenGL version string: 4.6 (Compatibility Profile) Mesa 20.3.4 OpenGL shading language version string: 4.60 OpenGL context flags: (none) OpenGL profile mask: compatibility profile OpenGL ES profile version string: OpenGL ES 3.2 Mesa 20.3.4 OpenGL ES profile shading language version string: OpenGL ES GLSL ES 3.20 The same problem also with Chimerax 1.7.0 but not 1.6. Thanks. Saverio

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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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