- ChimeraX-users - RBVI Mailing Lists

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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Download issue for Realsense plugin
by Casey Eubanks 12 Apr '24

12 Apr '24

Hey guys, I am trying to download the realsense plugin for Chimerax but I am getting this error on the download page [cid:image001.png@01DA8CC9.5111D810] Can you help me with this? Thanks, Casey Eubanks Service Desk Specialist MOBILE (205) 617-0581 time zone United States, Central Time Zone (CST) [cid:image002.png@01DA8CC9.5111D810]<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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hide silhouettes for pseudobonds and mesh
by Daniel Larsson 11 Apr '24

11 Apr '24

Hi all, Is it possible to specifically hide silhouettes? The “graphics silhouettes” command unfortunately does not take a spec argument. One example is to hide it for the mesh when you want to show the model and the map at the same time. Silhouettes around the mesh can make the scene look very cluttered. For this particular case, my colleague showed me a trick to use the selection command instead of “graphics silhouettes” and change the appearance of the selection, e.g. “graphics selection color black width 1”. But it gives slighly different apperance with far clip planes, where silhouettes are truncated while selections are enclosing clipped elements, removing some of the depth illusion from the mist. Another scenario is for pseudobonds, e.g. when displaying cartoon and mainchain atoms at the same time using the trick with “cartoon suppress false; cartoon tether opacity 0” given in this thread https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… I like to have the cartoon visible to guide the eye where the main chain goes, but I do not want the pseudo bonds to be visible since that adds clutter and is confusing. But the silhouettes command will outline the connections to the ribbon for the C3’ and C4’ atoms in nucleic acids. Regards, Daniel 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 download for academic research
by Muhammad Tahir 11 Apr '24

11 Apr '24

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 <https://www.springer.com/journal/12539/editors>* *Google Scholar: https://www.springer.com/journal/12539/editors <https://www.springer.com/journal/12539/editors>* *ORCID ID:*https://orcid.org/0000-0003-1158-2133

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chimeraX silhouette look spotty
by kellychen52071＠gmail.com 11 Apr '24

11 Apr '24

Dear ChimeraX support team, I'm experiencing an issue with ChimeraX silhouette showing dark spots. I’m using ChimeraX version 1.7.1. Please see the picture attached. Could you please help me resolve this? I’m using the latest version of macOS Sonoma 14.4.1 (graphics: intel iris plus graphics; processor: 2GHz Quad-core Intel core i5) Is this a graphic issue, this may be a ChimeraX bug for the newest version of mac as my peers who are using an older version of mac do not have this ChimeraX issue.

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chimeraX silhouette show dark spots
by Kelly Chen 11 Apr '24

11 Apr '24

Dear ChimeraX support team, I'm experiencing an issue with ChimeraX silhouette showing dark spots. I’m using ChimeraX version 1.7.1. Please see the picture attached. Could you please help me resolve this? I’m using the latest version of macOS Sonoma 14.4.1 (graphics: intel iris plus graphics; processor: 2GHz Quad-core Intel core i5) Is this a graphic issue? This could be a ChimeraX bug for the newest version of mac as my peers who are using an older version of mac do not have this ChimeraX issue. Thank you for your help, Kelly

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Mesh settings in ChimeraX
by Matthew Hancock 11 Apr '24

11 Apr '24

Hello, I have a density map I am visualizing as a mesh in ChimeraX. If I recall there are settings to manipulate the mesh visualization (line width, antialiasing, etc.) but I cannot them. If they exist, where might I find them? Thank you. Best Matthew

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Dealing with netcdf trajectories
by Enrico Martinez 11 Apr '24

11 Apr '24

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

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Not able to sign up to start a thread in RBVI mailing list
by Kelly Chen 10 Apr '24

10 Apr '24

Hi, I signed up using my email address, but I don’t receive an email confirmation in the inbox with steps for finishing an account creation. I checked my spam folder as well. Could you please help me sign up an account? Thank you, Kelly

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Central path for bundles on shared computing environment?
by Ricardo Righetto 09 Apr '24

09 Apr '24

Hi, We are setting up a new cluster at our university, and I stumbled upon the following problem: our nodes used for remote visualization don't have access to the internet. Therefore, users running an interactive graphical session won't be able to install bundles by themselves, which was the case in our old cluster. One workaround is to start ChimeraX either without GUI or with X forwarding over SSH on one of the normal login nodes (no high-end visualization capability) just for the purpose of downloading and installing bundles from the toolshed. This is however inconvenient to most users. Another approach is to install using the 'toolshed' command with a pre-downloaded wheel, but also not ideal. My thought would be to preinstall the most common plugins we use (like ArtiaX and ISOLDE) into a shared location, and ChimeraX would then find the bundles installed there upon startup. Therefore, my question is: is any other path other than the user's home folder supported for installing bundles? If yes, what is the order of search paths? Alternatively, is there some environment variable or other setting that I can use to tell ChimeraX where to find installed bundles? Thanks in advance, -- Ricardo Diogo Righetto

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Morphing Protein/NA Complex
by Shawn Rumrill 09 Apr '24

09 Apr '24

Hello All, I am trying to create an animation morphing between two states of a protein/nucleic acid complex (one binary, one with an incoming nucleotide). Excluding the nucleotide, the corresponding chain IDs between structures are the same and the sequences are the same. In both ChimeraX and PyMol, I am able to create the morphing animation however, only the protein appears (nucleic acid just does not appear in the animation). Am I missing something obvious? I appreciate any insights. Thanks, Shawn R

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Opening chimera within MS powerpoint
by Prathvi Singh 09 Apr '24

09 Apr '24

Hi Elaine, I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)? This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation. Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Transparency of cartoon and surface
by Enrico Martinez 09 Apr '24

09 Apr '24

Dear ChimeraX users, I am trying to add transparency on the cartoon representation of the protein that have additionally transparent surface in the same session. hide protein target a surface protein rainbow protein target c palette paired-12 rainbow protein target s palette paired-12 transparency 90 transparency protein 10 target c The last command hides all cartoons. I've also tried adding the transparency option directly to the rainbow command: rainbow protein target c palette paired-12 transparency 20 But it had the same effect as the total disappearance of the cartoons. Is it possible to have two different levels of the transparency on both cartoon and surface representation ? Thank you in advance ! Enrico

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About surface representation
by Enrico Martinez 08 Apr '24

08 Apr '24

Dear ChimeraX users! I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation. 1- I've found that the quality of the surface could be mainly controlled using two options gridSpacing and probeRadius so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ? 2- Setting different degrees of transparency of different selections. In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using # first color the entire membrane in blue color ~protein blue surface transparency 40 # color only the headgroups in red setting less transparency color :PC red surface transparency 80 This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ? Thank you very much in advance Best regards Enrico

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Suggestions for optimizing movie quality when working with file size limits?
by Vorländer,Matthias Kopano 08 Apr '24

08 Apr '24

Dear ChimeraX team, Making movies in ChimeraX is my favorite way of communicating my research, but unfortunately many journals have strict file size limits for supplementary movie files (30 MB in my case). I am wondering if there are suggestions for settings that give relatively small files with good visual appearance, i.e a specific format that works better then others. I am currently encoding in .mp4. Is it preferable to set qscale rather than quality/bitrate? I assume both bitrate and the windowsize scale linear with data size? Or are there recommendations for external software that efficiently compresses high-quality ChimeraX movies? Many thanks, Matthias

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How to download prepared molecule as pdb file in chimera X
by Mokshith Dg 07 Apr '24

07 Apr '24

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Visually filtering out unstructured regions
by David S. Fay 06 Apr '24

06 Apr '24

Hi, I was looking for a way to filter out (hide) low scoring pLDDT regions of proteins so my models have less red "spaghetti strands" in my ribbon diagrams. I tried looking in the documentation for a command or pulldown option, but maybe missed it. Thanks in advance! David

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ChimeraX becomes the default HTML viewer on Linux
by Guillaume Gaullier 05 Apr '24

05 Apr '24

Hello, I encountered an annoying behavior of ChimeraX on Rocky Linux 9.3, installed with the RPM package: ChimeraX seems to have declared itself the default application to open local html files. When I need to open an html file in ChimeraX's browser, I do it from within ChimeraX. But when I double-click on an html file, I want it to open in my default web browser (which is already running most of the time, and if not it still starts faster than ChimeraX). I could revert this behavior. I also checked that this doesn't happen on a Mac. If it is intended, in my experience it's been mostly getting in the way when doing tasks unrelated to ChimeraX, so maybe it is worth reconsidering. Cheers, 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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Two-sided surface coloring in ChimeraX?
by Elaine Meng 03 Apr '24

03 Apr '24

> On Mar 31, 2024, at 7:59 PM, Krishnan Raman <RKrishnan(a)BIOCRYST.com> wrote: > > https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/pocket/pocket_2zcp.ht… > Hi Elaine, > How can I mimic this image with chimerax? > Thanks > Krish > > Krishnan Raman > Executive Director, Structural Biology > BioCryst Pharmaceuticals Hi Krish, That Chimera example includes a Chimera command script that uses a "measure contactArea" command with a "slab" option to draw a surface. <https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/pocket/pocket_2zcp.ht…> However, I can't think of a way to do it in ChimeraX, since as far as I know there is no analogous command in ChimeraX currently. ChimeraX has "measure buriedArea" but it does not have an option to create a surface model of just the contact region. Maybe others have ideas? Sorry about that, 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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Re: ChimeraX question
by Tom Goddard 03 Apr '24

03 Apr '24

Hi Amita, Google Colab can predict sequences of about 2000 amino acids with a free google account -- the limit is set by the GPU memory which tends to be 12-16 Gbytes on the old Nvidia GPUs free Google Colab gives you (K8, T4, V100). You can also pay Google Colab to get GPUs with more memory that can handle up to about 5000 amino acids, but such a prediction can take 24 hours and cost about $50. I don't know anything about cosmic2 alphafold. Tom > On Apr 3, 2024, at 11:03 AM, Amita Mohan <amimohan(a)sas.upenn.edu> wrote: > > Is there a limit on amino acid used for prediction? > > Also does cosmic2 alpha fold is different from google Colab alpha fold prediction? > > Best, > > Amita > > > Sent from my iPhone > >> On Apr 3, 2024, at 1:52 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Amita, >> >> The Google Colab connection will time out if your computer goes to sleep. Google Colab is an interactive service, so if Colab doesn't hear from the web browser window because your computer is sleeping it will disconnect and kill your alphafold prediction. So you may want to turn off sleep on your computer. >> >> Tom >> >> >>> On Apr 3, 2024, at 7:08 AM, Amita Mohan <amimohan(a)sas.upenn.edu> wrote: >>> >>> Thank you Tom for your quick reply. The Colab works but terminate without reaching to the point of downloading results. It shows the connection fails and if I try to reconnect it gives me error message. >>> >>> I do also get response from Elaine. I will work on the recommendation and contact you if I will still have issues. >>> >>> >>> Best, >>> >>> Amita >>> >>>> On Apr 2, 2024, at 4:17 PM, Tom Goddard <goddard(a)sonic.net> wrote: >>>> >>>> Hi Amita, >>>> >>>> You would need to give a more detailed explanation of what you mean by "Google Colab keep on termination". Does Google Colab disconnect? Does an error message from AlphaFold appear? Does it finish and say "Downloading results..."? >>>> >>>> Tom >>>> >>>> >>>>> On Apr 2, 2024, at 12:58 PM, Amita Mohan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>> >>>>> 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 >>>>> _______________________________________________ >>>>> 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 question
by Tom Goddard 03 Apr '24

03 Apr '24

Hi Amita, The Google Colab connection will time out if your computer goes to sleep. Google Colab is an interactive service, so if Colab doesn't hear from the web browser window because your computer is sleeping it will disconnect and kill your alphafold prediction. So you may want to turn off sleep on your computer. Tom > On Apr 3, 2024, at 7:08 AM, Amita Mohan <amimohan(a)sas.upenn.edu> wrote: > > Thank you Tom for your quick reply. The Colab works but terminate without reaching to the point of downloading results. It shows the connection fails and if I try to reconnect it gives me error message. > > I do also get response from Elaine. I will work on the recommendation and contact you if I will still have issues. > > > Best, > > Amita > >> On Apr 2, 2024, at 4:17 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Amita, >> >> You would need to give a more detailed explanation of what you mean by "Google Colab keep on termination". Does Google Colab disconnect? Does an error message from AlphaFold appear? Does it finish and say "Downloading results..."? >> >> Tom >> >> >>> On Apr 2, 2024, at 12:58 PM, Amita Mohan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> 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 >>> _______________________________________________ >>> 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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Missing Vina on ChimeraX
by Luigi Marongiu 03 Apr '24

03 Apr '24

Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

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Re: Can α-carbon trace and bond be adjust for PBC?
by qizan chen 02 Apr '24

02 Apr '24

Thanks, I tried to update Eric’s script to do it by my own as attached. It works well for my system.

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About Uninstall
by 김재욱 02 Apr '24

02 Apr '24

Hello. I installed chimera uscf on the server using mobaxterm, and even if I delete all the chima related files after installation, chima uscf will run when using juppter notebook, what can I do?

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question about pb file
by Renee Garza 02 Apr '24

02 Apr '24

Hi there! I've been saving pb files and see that the colors are of varying shades and transparency. I have looked at the link regarding the color key however some colors in the pb files are not in the list. I'm wondering if there's a place to look at the degree of confidence based on color somewhere or a way to have the output with the general color like red, blue, orange, yellow, etc. instead of very specific shades. Thanks, Renee

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Range selection dose not work.
by 洪冉 02 Apr '24

02 Apr '24

Dear Users and Developers of ChimeraX, I am attempting to make a selection of a range of atoms by their numbers in ChimeraX. However, the command I have used does not seem to work in my case. The command in question is sel #1:@1-3. Could anyone assist me with this issue? For screenshots, please see below. Many thanks in advance! Ran

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Can α-carbon trace and bond be adjust for PBC?
by qz.chen＠tamu.edu 01 Apr '24

01 Apr '24

Hi, I want to use ChimeraX to visualize the protein slab simulation in the condensed phase as the link below. Unlike typical protein simulations, simulations of the condensed phase slab often need to keep the atoms inside the box for more accurate visualization. This means that particles between proteins may be jumping, leading to unreasonable lines appearing in the visualization. I have not found a way to adjust this in ChimeraX. https://www.biorxiv.org/content/10.1101/2020.08.05.237008v1.full Is there a way to limit the maximum distance between carbon and bond among particles? Thanks!

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Define axis along z?
by Oliver Clarke 01 Apr '24

01 Apr '24

Hi, For symmetric EM volumes, it would be useful to be able to easily create an axis corresponding to the molecular symmetry axis - generally coincident with a vector parallel to the Z-axis of the box, directly through the center. Is there an easy way to create such an axis in ChimeraX for an arbitrary map? It would be useful to have such an axis in order to rotate a volume around the molecular symmetry axis, even in the absence of a model (this is fairly easy to do if a model is present using define axis). This might be a useful generic extension to "define axis", if there isn't already an easy way to do so. Cheers Oli

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Difficulty with Z-translation - bug?
by Oliver Clarke 01 Apr '24

01 Apr '24

Hi, I can't seem to get the mousemode "Z-translate selected models" to work properly. I have "translate selected" set to Alt+left-drag, so per the docs ("assigned button + Ctrl (in that order) switches to Z-translation instead"), Alt+Ctrl+left-drag should translate the selected model in Z. It does not, or at least in any reproducible manner. Watch the selected yellow marker in the side view here on the right hand side: https://www.dropbox.com/scl/fi/vds0cwu0zizclg64vlxqc/z_translate_bug.mov?rl… 1. Initially I translate in x-y using Alt-drag - works fine. 2. I try to translate in z using alt-ctrl-drag - nothing happens 3. I keep trying translate in z, and eventually it "works" - but if you look closely you will see that the movement of the marker is not synced up with the direction/speed of the mouse cursor. Is this a bug? I remember testing this when it was initially implemented and I thought it worked fine so I suspect so...? Cheers Oli

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*.mdb files from MOE (chemcomp)
by Krishnan Raman 29 Mar '24

29 Mar '24

how to convert docking poses from MOE software to be read into chimerax? thanks Krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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pTM and ipTM Score Access
by Haley V Goodwin 27 Mar '24

27 Mar '24

Hello! I am using ChimeraX to use AlphaFold Multimer. I have read from a couple of places that AF provides pTM and ipTM scores to evaluate the quality of the models. I was wondering how I access these values from ChimeraX. I have looked through the results zip file, but can’t seem to find where these values may be stored. Thank you so much for your help! Best, Haley Goodwin

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Re: isolde write phenixRsrInput (how to restrain ions?)
by Shahid, Taha (Dr.) 27 Mar '24

27 Mar '24

Hi Tristan, That worked perfectly - many thanks for your help! Phenix.metal_coordination didn’t like for_phenix.cif file created by Isolde write phenixRsrInput, but I was able to create the edits file by saving the model file as a PDB from ChimeraX directly. Cheers and happy Easter, Taha On 25 Mar 2024, at 16:15, Tristan Croll <tcroll(a)altoslabs.com> wrote: You don't often get email from tcroll(a)altoslabs.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> ***CAUTION:*** This email was sent from an EXTERNAL source. Think before clicking links or opening attachments. Hi Taha, I'm very glad you find ISOLDE useful! Regarding magnesium (and metal ions in general): ISOLDE itself doesn't currently try to write extra Phenix restraints for these, but you can use the program phenix.metal_coordination to generate an edits file that you can add to the phenix.real_space_refine input. That should automatically create a set of bond and angle restraints for all metals in the model. Best, Tristan On Mon, Mar 25, 2024 at 3:46 PM Shahid, Taha (Dr.) via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear Tristan, I find ISOLDE invaluable for my work. Not only has it enabled me to build models of the highest quality, but been hugely instructive in giving me an instinctive ‘feel' for protein structure. I am having a minor problem with magnesium ions moving out of density when I run phenix.real_space_refine with settings output by isolde write phenixRsrInput. I typically specify restrainPositions true and includeHydrogens true as well. Is there a way to restrain these ions as well (perhaps an edit I could make to the real_space_refine.eff file)? Many thanks, Taha _______________________________________________ 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/ 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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change chain description
by Joshua Arribere 27 Mar '24

27 Mar '24

Hello, When I load a pdb into chimerax, a table appears with the chain IDs and associated descriptions. I would like to change the chain descriptions. How do I do that? Thank you, J

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Apple's cpus for trajectory visualisation
by Enrico Martinez 26 Mar '24

26 Mar '24

Dear ChimeraX users ! I wonder about the performance on the modern Apple CPUs: using several Apple's models as a benchmark, I tested Chimera-X on the 2015 and 2017 iMacs equipped with the i7 8 cores and then on the 2023 Macbook Pro equipped with the Apple m2pro chip. In the end, although the modern hardware was much more stable (never mind when loading large netcdf trajectories, as I reported in the case of the 2015 iMAC), I only noticed a slight increase in performance during film editing. As a benchmark, I took a very large model containing the membrane with an embedded oligomer and loaded a trajectory of 5500 frames in Chimera-X. I used surface rendering with 0.4 grid spacing for everything. While everything worked fine, I was able to produce a short 30-second film of 750 frames in about 1h30 on the m2pro, which was almost the same as on my imac 2015. Is there any way to improve the performance of film-making on modern Apple CPUs? Many thanks in advance Enrico

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ChimeraX_question
by 杜博文 26 Mar '24

26 Mar '24

hello,  Chimerax will have an error when we want to use the ribbon inside color white command, please guide me to correct this mistake,Thx. 杜博文南方科技大学/研究生/研究生2021级广东省深圳市南山区学苑大道1088号  

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Re: Chimera X Matchmaker RMSD
by Elaine Meng 25 Mar '24

25 Mar '24

(CC-ing chimerax-users(a)cgl.ucsf.edu since that is the recommended address for ChimeraX questions as long as they do not include private data. Email sent to me directly has more chance of falling through the cracks.) Dear Dr. Sharyn Endow, The Matchmaker algorithm in ChimeraX is the same as in Chimera. So everything I said before about Chimera's Matchmaker is also the case in ChimeraX. If you have the "iteration" option turned on it doesn't use all aligned columns but instead prunes residue pairs for a better fit of the core. If you are showing the sequence alignment, it shows what set of positions were used for the final fit as a light orange colored box. As before, it uses only the CA-CA pairs within those columns, not the side chains. These overall RMSD values are reported in the Log. "pruned" refers only to the fit iteration process, where iteration prunes away some pairs so that they are not used in the final fit. See "Fitting" at the bottom of the "Matchmaker" help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#fitting> Or, if you are using the "matchmaker" or "mmaker" command, see the "cutoffDistance" option for the description of iteration and pruning: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> If you mean the RMSD header across the top of the sequence alignment, that is a different thing calculated per column (not for the whole structures overall), and you can control in the Sequence Viewer Settings whether this RMSD histogram is calculated CA-only or backbone-only. Neither of them uses the sidechains. If a pairwise alignment, "CA RMSD" boils down to just the CA-CA distance. Simply selecting some range of residues on the sequence alignment doesn't change anything. See help for Sequence Viewer, its header lines, and its Settings: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings> Finally as mentioned in my previous answer about Chimera, you can use the "rmsd" command to calculate RMSDs over any sets of atoms that you choose (with or without sidechains) without changing the current positions of the structures. The more tricky part is that you have to specify in the command which atoms to pair with which atoms, since it is not calculated automatically like it is in Matchmaker. The syntax is a little different than in Chimera: there is a "to" between the two sets of atomspecs, and in ChimeraX the slash symbol "/" is used to indicate chains. "rmsd" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> ChimeraX atomspec including many examples: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.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 Mar 23, 2024, at 8:09 AM, Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> wrote: > > Dear Dr Elaine Meng, > > We wrote to you a few years ago regarding Chimera RMSD and you were kind enough to send the information below. We now have a few Q's regarding Chimera X Matchmaker, which displays RMSD values, e.g., when all beta-strands are selected in the Sequence Viewer window. > > • We would like to know what the RMSD values correspond to after aligning two protein sequences using Matchmaker Iwhich uses only only one point per residue for fitting) and selecting all b-strands in the Sequence Viewer window. Is a single RMSD value calculated for each residue to obtain the average RMSD for the "pruned" or all atom pairs and, if so, is the RMSD value between the single point per residue that was used for fitting? > > • Is there some way to obtain the C-alpha RMSD values but not the side chain values, after aligning two protein chains in Matchmaker in Chimera X? > > • What does "pruned" atom pairs mean in this context? > > T > hank you in advance for your help - > > Sincerely, > > Sharyn A. Endow, PhD > Professor of Cell Biology, DUMC > DUS, Cell Biology > PO Box 3709 / 245/247 Sands Bldg / 303 Research Drive > Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 > > > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: January 25, 2021 at 4:26:34 PM EST > To: "Sharyn Endow, Ph.D." <sharyn.endow(a)duke.edu> > Cc: Chimera <chimera-users(a)cgl.ucsf.edu> > Subject: Chimera RMSD > Reply-To: Chimera <chimera-users(a)cgl.ucsf.edu> > > > From: "Sharyn Endow, Ph.D." <sharyn.endow(a)duke.edu> > Subject: Chimera RMSD > Date: January 23, 2021 at 11:27:17 AM PST > > Thank you for your work in developing Chimera. We are trying to use Chimera RMSD to quantitate twisting of a beta-sheet and would like to know what the syntax is to list rmsd values for specified residues corresponding to a beta-strand, not just for single residues. Is it possible to list these values using RMSD? If so, we would greatly appreciate knowing how to get started. > > Sincerely, > Sharyn > > Hi Sharyn, > You can specify any sets of atoms/residues that you like in the RMSD command, as long as there are equal numbers of atoms in the two sets that you specify (from two different models). They will be paired in the order specified. We have a command-line "atom specification" syntax for that kind of thing. There is a longish page with lots of examples here: > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html > > > In your case, you may need to specify residue numbers, chain ID, and possibly atom names if you just want to use alpha-carbons or backbone as opposed to all atoms of the residues. E.g. something like > > rmsd #0:12.A,57-63.A #1:14.A,59-65.A > > ... for all atoms of model 0 residues 12 and 57-63 in chain A vs. all atoms of model 1 residues 14 and 59-65 in chain A. Or to use CA-only or backbone only: > > rmsd #0:12.A,57-63.A@ca #1:14.A,59-65.A@ca > rmsd #0:12.A,57-63.A@n,ca,c,o #1:14.A,59-65.A@n,ca,c,o > > Of course the numbers could be the same in the two models, I just was trying to give a more general example. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > P.S. the chimera-users(a)cgl.ucsf.edu address CC'd here is recommended for general Chimera how-to or is-it-possible types of questions

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isolde write phenixRsrInput (how to restrain ions?)
by Shahid, Taha (Dr.) 25 Mar '24

25 Mar '24

Dear Tristan, I find ISOLDE invaluable for my work. Not only has it enabled me to build models of the highest quality, but been hugely instructive in giving me an instinctive ‘feel' for protein structure. I am having a minor problem with magnesium ions moving out of density when I run phenix.real_space_refine with settings output by isolde write phenixRsrInput. I typically specify restrainPositions true and includeHydrogens true as well. Is there a way to restrain these ions as well (perhaps an edit I could make to the real_space_refine.eff file)? Many thanks, Taha

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ISOLDE query - non crystallographic symmetry?
by Oliver Clarke 25 Mar '24

25 Mar '24

Hi Tristan, I've been using the latest version of ISOLDE with ChimeraX 1.7.1 and it is working beautifully - very smooth simulation and very helpful for fixing up problem areas! One query - is there any support for non crystallographic symmetry in ISOLDE, or if not is this on the roadmap? Thinking both in terms of NCS restraints, but also in terms of propagating edits from one subunit of an oligomer to all the others - this would be very helpful to have for a lot of folks I think, as so many proteins are oligomeric. Thanks for the wonderful piece of software! Cheers Oli

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Difficulty unsubscribing
by BARRY E DEZONIA 24 Mar '24

24 Mar '24

I am trying to leave this email list and currently am unable to. I send email to: chimerax-users-leave(a)cgl.ucsf.edu And it processes and says my email barry.dezonia(a)wisc.edu is not a list member. That is because I signed up with bdezonia(a)wisc.edu.. My mail service treats them as equivalent but it only sends out on the incorrect email address. Can someone unsubscribe ndezonia(a)wisc.edu? I can't figure out how to get my email client to use my other email address as the sending address.

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