- ChimeraX-users - RBVI Mailing Lists

Question about visualisation of DNA structure
by Enrico Martinez 26 Apr '24

26 Apr '24

Dear Chimera-X users, I have a question about the visualisation of the DNA structure obtained after tleap processing for Amber. As I have noticed, due to the renaming of the DNA residues, some of the sugar parts are not correctly recognised by Chimera-X (see the attached screenshot) and so these elements are only displayed as organic ligands. Would it be possible to change its style using some commands, assuming that the names of the residues located at the terminal parts of the DNA helix are DC5, DG3 and DT5, DT3 (so that Amber adds numbers to them)? Would it be possible to change the style of all the residues e.g. showing them ass ring fills or like a color bricks (default vizualisation which looks very cool!) using selection expressions like :DT*,DG*,DC*,DA* ? Many thanks in advance ! Enrico

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Add options to snapshot command
by Jaremko, Matt Joseph 26 Apr '24

26 Apr '24

Hello ChimeraX Team, Can you add option to snapshot command like transparentBackground and height to allow more customization of this convenient tool? Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 126 E Lincoln Ave | 80B 1012 | Rahway, NJ 07065 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.

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palette command
by Cairns, Claudia Anna 26 Apr '24

26 Apr '24

Dear sir or madam, I try to apply the palette command to change the color range of the mlp command. Unfortunatelly i always get an error. For "palette rainbow" for example I get: rainbow Unknown command: palette rainbow Can you please help me? Sincerely, Claudia Cairns M.Sc. (Biotechnology) Department 'Applied and Molecular Microbiology' Institute of Biotechnology - TIB 4/4-1 Technische Universität Berlin Gustav-Meyer-Allee 25 D-13355 Berlin Phone: +49-(0)30-314-72827 E-mail: c.feurstein(a)tu-berlin.de<mailto:carsten.pohl@tu-berlin.de> Web: <http://www.mikrobiologie.tu-berlin.de> https://www.tu.berlin/mikrobiologie/

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Reconstruction of missed loop fragments
by Enrico Martinez 26 Apr '24

26 Apr '24

Dear Chimera-X user! I am preparing a model of GPCR protein for the molecular dynamics simulation. In this structure there is a loop fragment of 10-20 residues which is missed. Is it possible to reconstruct it (e.g. based on the sequence information or alternatively just add manually the missing fragment) using some tool of Chimera-X e.g. combining with the bond command ? Many thanks in advance ! Enrico

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Greek characters
by Marta Martinez 25 Apr '24

25 Apr '24

Hi guys, I just downloaded a pdb file from AlphaFold DB (AF-P69905-F1-model_v4.pdb). After modifying it with ChimeraX (version 1.6.1 (2023-05-09)) I've saved the modified atomic structure as a cif file. The original pdb file contains this line: COMPND 2 MOLECULE: HEMOGLOBIN SUBUNIT ALPHA; After saving the file as cif format ALPHA is not longer a string but a GREEK character: _entity.pdbx_description "hemoglobin subunit α" Is there any flag in the save command that disables this conversion from plain ASCII to UTF-8? Thank you very much for the answer in advance: MARTA -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

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atom serial_number is inconsistent with PDB serial numbers in multi-chain structure
by Daniel David Richman 25 Apr '24

25 Apr '24

Hi all, I’ve been debugging an off-by one error in a ChimeraX script I’m working on, which I’ve traced to a apparent inconsistency between the serial_number reported by ChimeraX for an atom and the actual serial number of that atom read/written in PDB format. To reproduce: open 5MJ7 select #1/B:6@CA info atoms sel attribute serial_number ==> atom id /B:6@CA serial_number 2548 but the correct serial number for this atom in 5MJ7.pdb is 2549. Maybe this is because the TER record for chain A takes up one serial number in the PDB file, but ChimeraX doesn’t include it as a numbered atom? Regardless, how can I query ChimeraX for the actual serial number that will be written if I write out a PDB file? Thanks, Daniel

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How to make an MD template for ISOLDE?
by Guillaume Gaullier 25 Apr '24

25 Apr '24

Hi Tristan and chimerax-users, Some time ago I asked the list about modeling PTM and got several helpful answer, including this one: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… Now, I am working on a structure containing chlorophyll A molecules (residue code CLA) and realized that it won’t work for MDFF in ISOLDE because there is no MD template for it. After trying to manually fit one of these molecules rigidly, I concluded that I would rather spend the rest of the month learning how to make an MD template for it (than next month painstakingly fitting every single molecule manually rigidly). From the message linked above, I think this should be doable because this time it is not a covalent modification on an otherwise parameterized residue, but simply a new ligand (ok, maybe the coordinated Mg2+ makes it a bit more complicated?). I looked up ANTECHAMBER, and also some documentation from OpenMM, but that got me nowhere, mostly because I have little clue what the task really entails. My guess is that I need some program to take the CLA residue in PDB or mmCIF format (which I can easily save from a previous PDB entry) and write out an OpenMM XML file like the one you sent me back then for KCX. Is this correct? The ANTECHAMBER documentation mentions many programs and formats, and I got totally confused. If you have time to elaborate a bit on the specific practical steps to take (including how to supply the final XML file to ISOLDE), that would be super helpful! I can do with pointers to documentation, not afraid to read, but I need help getting oriented. 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

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Realsense issues
by Casey Eubanks 24 Apr '24

24 Apr '24

Hey guys, You all helped me a week or so ago getting the Realsense package updated to the new version of chimerax, which I can now download so thats great! But I am now having an issue with running its command "Realsense on" I receive the following errors attached to this email It is having errors processing the trigger and it says it cant resolve the requests. Let me know if I am doing anything wrong or need to make any changes! Thanks, Casey Eubanks Service Desk Specialist MOBILE (205) 617-0581 time zone United States, Central Time Zone (CST) [cid:image001.png@01DA9660.03D4DE80]<https://www.biocryst.com/> "Go Fast, Patients are waiting" If you need immediate IT support please submit a ticket to ITsupport(a)biocryst.com<mailto:ITsupport@biocryst.com> 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.

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Finding unmodeled blobs in a map
by Guillaume Gaullier 24 Apr '24

24 Apr '24

Hello, With `volume zone` I can show the parts of a map close to an atomic model. Is there a way to do the opposite, i.e. show only the parts of a map that don’t enclose any atoms? This would be already very helpful only as a visualization. But even better would be a way to build a list of markers at the centroids of such unmodeled blobs, to easily navigate to them. Or maybe this is too narrow in scope and better left to ISOLDE? (Sorry Tristan… more feature suggestions…). Thank you, 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

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Adding missing atoms of the DNA structure
by Enrico Martinez 24 Apr '24

24 Apr '24

Dear Chimera-X users I am preparing the structure of the protein-DNA complex for molecular dynamics simulation with Amber. This is the original pdb: https://www.rcsb.org/structure/5FKW When I try to parametrize it the tleap shows the following error because of the absence of some atoms from the phosphate: FATAL: Atom .R<DG5 733>.A<P 32> does not have a type. FATAL: Atom .R<DG5 733>.A<OP1 33> does not have a type. FATAL: Atom .R<DG5 733>.A<OP2 34> does not have a type. FATAL: Atom .R<DG5 758>.A<P 32> does not have a type. FATAL: Atom .R<DG5 758>.A<OP1 33> does not have a type. FATAL: Atom .R<DG5 758>.A<OP2 34> does not have a type. Would it be possible to use some commands of the Chimera-X to automatically repair this part of the DNA by adding missing atoms ? Thank you in advance ! Enrico

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Cutting out an asymmetric unit from the map
by Das, Abhinaba 23 Apr '24

23 Apr '24

Hi! I was wondering if there is a sequence of commands one could use to extract an asymmetric unit from the original map after roughly fitting the model into it. The positions of these extracted maps should of course be preserved and should on the same grid. One can then better fit the model in this extracted ASU density. Thanks in advance for any guidance. Abhi

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Lighting options in ChimeraX
by Elaine Meng 22 Apr '24

22 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 19 Apr '24

19 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 16 Apr '24

16 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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Fwd: Rotating bonds chimeraX
by Eric Pettersen 16 Apr '24

16 Apr '24

> Begin forwarded message: > > From: "Leonardo BETANCURT ANZOLA" <leonardo.betancurt-anzola(a)pasteur.fr> > Subject: Rotating bonds chimeraX > Date: April 16, 2024 at 5:49:03 AM PDT > To: ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> > > Hello, > > I was wondering if in ChimeraX it is possible to choose which side of a bond moves and which stays still when using the right mouse feature “bond rotation”. > > Thank you and have a nice Tuesday, > > Leo B. >

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ChimeraX question
by Amita Mohan 16 Apr '24

16 Apr '24

Hello, I would appreciate if you please answer the following questions: 1. I am using chimeraX, and I have a trouble getting results from Alphafold. The Google Colab keep on termination without saving results. Could you please help? 2. I am using hydrogen bond tool, how can I save all the H-bonds in the protein as file containing all the information for the paired residues involved in the H bond. Similarly, I also would like to save the information of residues involved in the protein-protein interactions. I hope to hear from you. Best, Amita Department of Biology University of Pennsylvania

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align the atoms
by 化工化工 16 Apr '24

16 Apr '24

Dear Professor： Hello, I have aligned the atoms #1 of different models with the command "align #1:1 toAtoms #2:1", but I found that the atoms #1 don't overlap very well, which affects the aesthetics of the publication. So, I would like to ask you if there is a way to align the green atoms in the center, thank you very much (see Figure 1)! 化工化工 1366924572(a)qq.com  

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ModuleNotFoundError: No module named 'chimerax'
by Antony Merlin Jose 15 Apr '24

15 Apr '24

Hello, I am a relatively new user of ChimeraX. I would like to be able to run commands on chimerax 'headless' by passing them from python. When I used 'from chimerax.core.commands import run' within the python program, I get the error 'ModuleNotFoundError: No module named 'chimerax''. I am using a MacOS 13.5 and the version of Chimera I have installed is 1.7.1 Any help is much appreciated. Thank you Antony -- Antony M Jose [he/him/his] Associate Professor, Department of Cell Biology & Molecular Genetics, Director, MOCB Concentration Area - Biological Sciences Graduate Program University of Maryland, Rm 2136, Bioscience Research Building, 4066 Campus Drive, College Park, MD - 20742. Website: https://science.umd.edu/cbmg/joselab/

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