April 2024 - ChimeraX-users - RBVI Mailing Lists

Lighting options in ChimeraX
by Elaine Meng 23 Apr '24

23 Apr '24

> On Apr 20, 2024, at 7:36 PM, Friedman, Simon <friedmans(a)umkc.edu> wrote: > > I am working on mol graphics for a figure. I'm using both chimera-x and chimera. I'm trying to figure out if chimera-x has a set of functionality that chimera has. Specifically in chimera I was able to move light sources around, change intensity, shinyness etc. Also I was able to use ray tracing in the output. In chimera-x I can't find any menu for moving light sources around etc. One very cool thing that is there is the 'soft' lighting option which gives a very cool surface to the carbon atoms. So I was wondering if there were more options for messing with lighting etc in chimera-x? > Thank you! > > Cheers, > Simon > > Simon H. Friedman, Ph.D. > UM Curators' Distinguished Professor > Division of Pharmacology & Pharmaceutical Sciences > University of Missouri, Kansas City Hey Simon! ChimeraX does not have ray-tracing, but as you discovered with the ChimeraX "soft" lighting (sugar cube icon in the toolbar), it does have ambient-occlusion lighting simulated by multiple multidirectional light sources, which Chimera does not have. The rest of this description pertains to ChimeraX: When you try the different lighting icons in the toolbar, the corresponding command is shown in the Log. So that should help you learn some of the common options. However, there are lots more options available with the commands than are represented by toolbar icons. (1) the "lighting" command has the presets including soft, but also options for intensities, colors and directions of the directional lights (key light and fill light), depth cueing, and shadows, among many other things. There is no GUI for changing the direction interactively, however. See the "lighting" manpage and many options explained therein. It also shows pictures of the relevant icons from the toolbar. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> (2) the "graphics" command has options for background color, silhouette edges (the outlines that are usually black), and triangulation fineness of atom/bond/ribbon representations, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> (3) the "material" command has control over shininess of objects <https://rbvi.ucsf.edu/chimerax/docs/user/commands/material.html> 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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Running AlphaFold through Chimerax vs. Colab directly
by Coyle, Maxwell C 22 Apr '24

22 Apr '24

Hello! I’ve been predicting structures recently using the AlphaFold tool through ChimeraX (which directs to the alphafold21_predict_colab.ipynb notebook), but I’ve noticed I get often quite different results when I run the same prediction through the AlphaFold.ipynb notebook directly in Colab. I was wondering if anybody could point me to the major differences between these two implementations? Are they searching different libraries to generate a multiple sequence alignment? Are they using different numbers of iterations or energy minimization strategies? Thanks for any guidance, Max Max Coyle, PhD Postdoctoral Fellow, Bellono Lab Dept of Molecular and Cellular Biology Harvard University mcoyle(a)fas.harvard.edu

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transform coordinates of an atomic model
by Engeholm, Maik 22 Apr '24

22 Apr '24

Hi Tom, hi Eric, thanks a lot for answering my previous question so comprehensively! Hope it's OK to bother you again. This is about something completely unrelated. I would like to apply a transformation (rotation plus translation) to an atomic model. I need to change the coordinates of the model relative to the overall coordinate system. Changing the scene or camera coordinates is not an option, since in the end I want to place multiple copies of my model (in this case a nucleosome) in a specific orientation relative to each other (i.e. within the same coordinate system) to model an array of nucleosomes. If I remember correctly, back in Chimera this could be achieved with "model.openState.global/localXform(transformation)" where transformation was an chimera.Xform object. But as far as I can see this is not supported in chimeraX. Here is a reproducible example of the simplest case, in which I define the center and two (roughly) orthogonal axes of my atomic model (i.e. the normal of the DNA superhelix and the dyad axis) and try to map those onto the origin of the coordinate system and two unit vectors. """ from chimerax.core.commands import run import numpy as np from numpy import cross, dot np.set_printoptions(suppress = True) run (session, 'close session') run (session, 'windowsize 360 360') target_centre = np.array((0, 0, 0)) target_normal = np.array((0, 1, 0)) target_dyad = np.array((0, 0, 1)) target_3rd_axis = cross(target_normal, target_dyad) run (session, 'open 3lz0 name 3lz0') pdb3lz0_DNA_plane = run (session, 'define plane #1/I,J:-56-56') pdb3lz0_DNA_centre = run (session, 'define centroid #1/I,J:-56-56') pdb3lz0_dyad_base_pair = run (session, 'define centroid #1/I,J:0') pdb3lz0_dyad_axis = run (session, 'define axis #1.4 #1.5') pdb3lz0_centre = session.models[3].xform_center pdb3lz0_normal = session.models[3].xform_normal pdb3lz0_dyad = session.models[6].xform_direction pdb3lz0_3rd_axis = cross(pdb3lz0_normal, pdb3lz0_dyad) rotation_inverse = np.c_[pdb3lz0_3rd_axis, pdb3lz0_normal, pdb3lz0_dyad] rotation = np.linalg.inv(rotation_inverse) translation = -pdb3lz0_centre transformation = np.c_[rotation, translation] print(session.models[0].position.matrix) """ At this point I have tried to modify the position.matrix with "session.models[0].position.matrix = transformation" but this gives me an "AttributeError: property 'matrix' of 'Place' object has no setter". I'm sure there must be a way to transform an atomic model in this way and would be really grateful for your help. Thanks a lot in advance, Maik

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Re: ChimeraX license and download
by Elaine Meng 20 Apr '24

20 Apr '24

Hi Asma, It is recommended to send ChimeraX questions to chimerax-users(a)cgl.ucsf.edu CC'd here, if the questions do not include any information that needs to be private (i.e. do not include your license key or proprietary data). I don't know all technical aspects of the program. I'm not sure exactly what this error is but the first thing to try is to get a newer version of ChimeraX. As the message says, you are running an extremely old version and probably if you download and use the current version 1.7 this error message will not appear. However, if it does, then you can ask again, or use the usual bug reporting mechanism (ChimeraX menu Help... Report a Bug). 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 Apr 16, 2024, at 8:19 AM, Asma Rehman <ARehman(a)Novavax.com> wrote: > > Hi Elaine, > > Good morning, > Hope you’re doing well! > > I was reaching out to ask about the following error that I’m seeing on ChimeraX software- Please suggest! > > Many thanks, > Asma >

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Fwd: ChimeraX Chain Transparency
by Elaine Meng 19 Apr '24

19 Apr '24

Hi Matt, The address for ChimeraX questions is chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here, as mentioned in the "contact us" page: <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html>> Yes, of course you can make some of the atoms transparent and others not. I say "atoms" because at least in your image, you are displaying the atoms in the sphere style. You just need to specify that set of atoms in the transparency command, for example, for atoms of B chain only to be 70% transparent: transparency /B 70 target a ...or you could use menu: Select... Chains... [choose the one that you want] ...and then use command: transparency sel 70 target a The "target a" part means atoms. The default is to change transparency of only molecular surface (target s), so if you omit "target a" nothing happens to the atoms. Of course you can use a different % value than 70. 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 > > From: Matthew Bubak <Matthew-Bubak(a)omrf.org> > Subject: ChimeraX Chain Transparency > Date: April 18, 2024 at 12:48:22 PM PDT > > Hello, > > I am trying to make specific chains of mitochondrial complexes more or less transparent. I am able to make the entier complex transparent, but not individual chains. For example in the figure below (mitochondrial complex I), I would like to make the purple chains approximately 50% transparent, and the blue chain 90% transperent, and leave the rest untouched. Is this possible? > > > > Thank you for your help, > > Matt Bubak, PhD. > Post-Doctoral Fellow > Aging and Metabolism Program > The Oklahoma Medical Research Foundation

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import from local file in chimerax-python script
by Engeholm, Maik 18 Apr '24

18 Apr '24

Hi there, I'm running a python script either from within ChimeraX (with "open http://myScript.py") or from the command line (using "chimerax http://myScript.py"). As the script gets longer and longer, I would like to store some class definitions in a separate file (http://classDefinitions.py within the same directory as http://myScript.py and then import those into the main script with some command like "from classDefinitions import testClass". This, however, gives me an "ModuleNotFoundError: No module named 'testClass'". What is the correct way to do this? Any help would be much appreciated! Cheers, Maik

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Volume flip issue
by Luca Pellegrini 18 Apr '24

18 Apr '24

Hi, if I flip a map with ‘volume flip #ID', save the flipped map and then open it, the saved copy is noticeably shifted by a small amount relative to the original flipped map. This doesn’t happen if I save and reopen the map without flipping. Can you please explain what causes this and if it can be avoided? Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Color accuracy in ChimeraX / flat lighting
by Élie Lambert 17 Apr '24

17 Apr '24

Hi all, I wrote a script to color code individual chains of a structure based on fold change values. When I plug the resulting rgb values in ChimeraX, the colors that are rendered are off by quite a bit in some cases. Attached is an example demonstrating such a difference. On the left is shown the color provided for the selected chain, which shows correctly in the 'Select color' window as rgb(196,216,214). However the resulting structure rendered has a different actual color (rgb(227,251,248), as measured with eyedropper tool in Illustrator). This variation is not consistent, colors with higher saturation are not impacted as much, but can still be a bit off. I am using flat lighting with depthcue off, which I believe should mean that no shadows could affect the rendering. I have tried providing colors in other formats such as hex with no difference. I just updated to ChimeraX version 1.7.1 which also did not help (Windows). Please let me know if I am missing anything obvious. Thanks in advance! Regards, Elie

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Re: Dealing with netcdf trajectories
by Enrico Martinez 17 Apr '24

17 Apr '24

Hello Eric, just one question. When I load a netcdf trajectory using: open ./trajectory_part1.nc structureModel #1 Would it be possible to additionally precise the range of the loaded frames e.g. to load the first 5000 frames or in range of 500 to 5000 etc? I also noticed that the maximal number of frames is 9999, isn't it ? Many thanks in advance ! Enrico Il giorno gio 11 apr 2024 alle ore 19:49 Eric Pettersen <pett(a)cgl.ucsf.edu> ha scritto: > Happy to help. :-) > > —Eric > > On Apr 11, 2024, at 12:52 AM, Enrico Martinez via ChimeraX-users < > chimerax-users(a)cgl.ucsf.edu> wrote: > > Thank you very much Eric !! > > Il giorno mer 10 apr 2024 alle ore 18:24 Eric Pettersen <pett(a)cgl.ucsf.edu> > ha scritto: > >> Hi Enrico, >> Add "replace false" to the open command you use when opening the second >> set of coordinates and it will append those coordinate to the current ones. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> On Apr 10, 2024, at 2:34 AM, Enrico Martinez via ChimeraX-users < >> chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Dear Chimera-X users ! >> >> Typically having loaded pdb of the system I use the following command to >> load the netcdf file, which replaces current pdb with the trajectory: >> open ./trajectory_part1.nc structureModel #1 >> >> would it be possible to load in the same section the second part of the >> same trajectory and merge the both into the same ensemble ? >> E.g. if I run subsequently the same command with another trajectory, it >> will produce another ensemble related to the second trajectory (and not >> merge the both together): open ./stripped_*part2.nc structureModel #1 >> >> Many thanks in advance! >> >> Enrico >> _______________________________________________ >> 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 > 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/ > > >

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Re: ChimeraX download for academic research
by Guillaume Gaullier 17 Apr '24

17 Apr '24

Click on one of the download links for a specific installer (I don't know which operating system you use, but choose the correct one). Only then will you see the license text. And please keep the list in CC when replying. I hope this helps, Guillaume ________________________________ From: Muhammad Tahir <tahirmicrobiologist(a)gmail.com> Sent: Friday, April 12, 2024 9:41:38 AM To: Guillaume Gaullier Subject: Re: [chimerax-users] Re: ChimeraX download for academic research After clicking the link, I did not see the academic link. On Fri, Apr 12, 2024 at 3:39 PM Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se<mailto:guillaume.gaullier@kemi.uu.se>> wrote: Hello, Did you try clicking on the download link Elaine sent? It takes you to a list of installers, and when you click on one of these download links you will be shown the text of the academic/teaching/personal use license (there is even a button to print it). Cheers, Guillaume ________________________________ From: Muhammad Tahir via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Friday, April 12, 2024 4:46:45 AM To: ChimeraX Users Help Subject: [chimerax-users] Re: ChimeraX download for academic research Dear Elaine, Thank you for your kind reply. Sorry to say but it did not help me. I need it for academic purposes but I do not have license information. How to get academic/research purpose ChimeraX please On Wed, Apr 10, 2024 at 11:56 PM Elaine Meng <meng(a)cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: See "Download" quick link on the left side of the ChimeraX home page. Here is the ChimeraX home page, the quick links are on the left <https://www.rbvi.ucsf.edu/chimerax/index.html> Or if you still don't see it, the direct link to the download page is <https://www.rbvi.ucsf.edu/chimerax/download.html> 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 Apr 10, 2024, at 3:25 AM, Muhammad Tahir via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: > > > Dear management > Have a good day. I did not see the link for subject download please. COuld you help > -- > > Warm Regards: > Dr Muhammad Tahir Khan > PhD Bioinformatics > YOUTH EDITORIAL BOARD MEMBERS > Springer; Interdisciplinary Sciences: Computational Life Sciences > https://www.springer.com/journal/12539/editors > Google Scholar: https://www.springer.com/journal/12539/editors > ORCID ID:https://orcid.org/0000-0003-1158-2133 -- Warm Regards: Dr Muhammad Tahir Khan PhD Bioinformatics YOUTH EDITORIAL BOARD MEMBERS Springer; Interdisciplinary Sciences: Computational Life Sciences https://www.springer.com/journal/12539/editors Google Scholar: https://www.springer.com/journal/12539/editors ORCID ID:https://orcid.org/0000-0003-1158-2133 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 -- Warm Regards: Dr Muhammad Tahir Khan PhD Bioinformatics YOUTH EDITORIAL BOARD MEMBERS Springer; Interdisciplinary Sciences: Computational Life Sciences https://www.springer.com/journal/12539/editors Google Scholar: https://www.springer.com/journal/12539/editors ORCID ID:https://orcid.org/0000-0003-1158-2133 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.

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