- ChimeraX-users - RBVI Mailing Lists

Install ChimeraX on Linux without sudo
by Roden Deng Luo 10 Jul '24

10 Jul '24

Dear ChimeraX Team, The install notes for all the current distributions for the Linx system require sudo. I wonder is it possible without sudo? On Rocky Linux VERSION 9.4 (Blue Onyx), I tried the following. $ flatpak --user install ChimeraX-1.8.flatpak error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/23.08 which was not found $ rpm -ivh ucsf-chimerax-1.8-1.el9.x86_64.rpm error: Failed dependencies: fftw-libs-single is needed by ucsf-chimerax-1.8-1.el9.x86_64 mesa-libOSMesa is needed by ucsf-chimerax-1.8-1.el9.x86_64 sqlite is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-cursor is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-image is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-keysyms is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-renderutil is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-wm is needed by ucsf-chimerax-1.8-1.el9.x86_64 Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Morphing of different surfaces
by Leonardo Talachia Rosa 10 Jul '24

10 Jul '24

Dear ChimeraX community, I hope you are well. I have a set of models for which I want to show the exposure of specific regions as protein changes conformation through morphing. I can do a morphing between atoms or ribbons, and that looks ok, but the presentation would benefit from a morphing between surface representation coloured by electrostatic potential of each state. I scavenged the youtube tutorials and chimeraX documentation but could not find a way to do it. Would anyone know how to produce this? All models have identical sequence and I calculated the surface for all of them. Thank you for your time, Kind wishes, Leonardo -- ************************* Leonardo TALACHIA ROSA, PhD Associated professor Department of Biochemistry and Tissue Biology (DBBT) Biology Institute Universidade Estadual de Campinas - UNICAMP Rua Monteiro Lobato, 255 - Campinas - SP - Brasil - CEP 13083-862 **************************

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Re: ChimeraX Coloring Single Residues
by Elaine Meng 09 Jul '24

09 Jul '24

Hi Colorado (CC'ing the chimerax-users list), This page in the User Guide covers how to specify models, chains, residues, etc. in commands: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> Besides commands ("color" "show" "style" etc.) you can use the menu and other graphical interfaces. E.g. Select menu or drawing boxes in the Sequence Viewer to select atoms/residues and then the Actions menu to act on the selection. All these commands and tools have help pages in the User Guide. <https://www.rbvi.ucsf.edu/chimerax/docs/user/index.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/selection.html> You may also want to look at the tutorials, e.g, "protein-ligand binding sites" for general structure analysis <https://www.rbvi.ucsf.edu/chimerax/tutorials.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> ...and many example images on our website with links to the command scripts (.cxc files) to generate them, <https://www.rbvi.ucsf.edu/chimerax/gallery.html> <https://www.rbvi.ucsf.edu/chimerax/features.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 Jul 9, 2024, at 11:07 AM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > Hi Colorado, > Happy to hear you like ChimeraX images! In general it would be best to send these kind of general usage questions (that don't include proprietary information) to the chimerax-users list (chimerax-users(a)cgl.ucsf.edu) ChimeraX is developed by a team of people with varying roles, so some questions may best be answered by one team member whereas other questions might better be answered by another. The answer to a question might also benefit other users this way. > To actually answer your question :-), you add :residue-number to the specifier, so if it was residue 53 then "#1/T:53". Also, you only need to include the model number if you have multiple models open. This is all documented of course. To find that documentation you could type "help color", which would bring up the color help page. That page shows the syntax of the command, including "spec", which is a link to another page that explains command-line specifiers in detail. > > --Eric > >> On Jul 9, 2024, at 9:33 AM, Colorado Wilson <colorado(a)neurosnap.ai> wrote: >> >> Hello Dr. Petterson, >> >> Our company has recently swapped from PyMol to ChimeraX for creating images as ChimeraX provides some beautiful image generation scenes. However, for the life of me and a number of colleagues we cannot figure out how to color a single residue in a chain / structure. >> >> I am able to color a chain like so: >> >> color #1/T#ffffff (color hexcode) >> >> Would you be able to provide any guidance? Thank you for your time and the tool you've made! >

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Alter method of distance calculated for "closest" command
by Alexander Lee 09 Jul '24

09 Jul '24

Currently, I have these commands to calculate the closest 5 :SIA out of 45 to a binding site each frame parm ../2_md/CPLX_Neut_Sol.parm7 trajin ../2_md/10.1.produ.nc rms :1-1469 first # align receptor closest 5 :132-134 solventmask :SIA closestout SIA2ChainA_Binding_sites.dat name SIA run exit The output file contains Frame Molecule Distance FirstAtom# which to my understanding, the distance is from the :SIA atom closest to the center of mass of the residues :132-134. 1. Is there some way to do the distance from center of mass :SIA to center of mass residues instead? * ex: [distance of closest :SIA atom to residues] > [distance of :SIA center of mass to residues] 2. Is there a way to do RMSD calculation of those selected closest ligands to a pdb reference? I was thinking along the lines of "for FRAME in" maybe? Thank you, Alex

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Label “check_interface” residues in ChimeraX
by Gupta, Arun 09 Jul '24

09 Jul '24

Hello ChimeraX team, I came to know this fabulous ChimeraX custom “check_interface” command to instantly identify interface residues between chains A and B of protein complex model #1. It works nicely with any number of protein complex models for e.g. #1, 2, 3, 4 with chains A and B However, when I am trying to “label” the identified interface residues using the below mentioned ChimeraX command for the various protein complex models #1, 2, 3, 4. It doesn’t seem to work. I am interested to identify and label the interface residues for the related set of various protein complex models #1, 2, 3,4. label sel text "{0.label_one_letter_code}{0.number}" Can somebody suggest what I am doing wrong with the ChimeraX “label” command ?? Thanks a lot ! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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ChimeraX for mobile platforms
by Schäfer, Christian 05 Jul '24

05 Jul '24

Hello I was wondering if you are planning to release a ChimeraX version for mobile platforms such as iOS for iPad? Best, Christian

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markers radius
by Yanhe Zhao 05 Jul '24

05 Jul '24

Dear ChimeraX community, I thought the radius of marker is in angostrom, right? And is that possible to set the transparency of the marker? Thanks and cheers, Yanhe

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Announcing chimerax-emacs
by Zach Pearson 05 Jul '24

05 Jul '24

Hi ChimeraX Users, Over the holiday, I wrote a package that will let you use the command line from Emacs, leveraging ChimeraX’s rest server. https://github.com/zjp/chimerax-emacs This should be helpful if you use Emacs as your main editor and you want to debug your bundles without leaving your editors. Contributions from other emacs users welcome. — Zach

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Doubt about sequence visualization after real.space.refinement in phenix
by Leyre Marin Arraiza 04 Jul '24

04 Jul '24

Dear UCSF ChimeraX, I have a practical question regarding model sequence visualization after real.space.refinement in phenix. After I worked on my model in ISOLDE and Coot, I deleted some residues that were out of the map density. Then, a dashed line appeared in my model, connecting the gap between the remaining residues (example, ALA97------GLN110). When I visualize the model sequence in ChimeraX, the deleted residues appear boxed with a rectangle, to indicate they are missing in the structure. Once I get the results back from the phenix real.space.refinement, and I visualize the model sequence in ChimeraX again, the deleted residues do not appear boxed anymore, but they are gone instead from the visualized sequence, keeping their corresponding numbers but not showing a boxed gap (in the example I mentioned they jump from 97 to 110 directly). I would like to keep the deleted residues boxed in the sequence when I visualize it. Is that possible? Hope I am explaining myself. Thanks and best regards, Leyre Leyre Marin Arraiza PhD fellow University of Copenhagen Novo Nordisk Foundation Center for Protein Research Taylor Group Blegdamsvej 3B, Building 6, 6-1-10 2200 København N leyre.arraiza(a)cpr.ku.dk<mailto:leyre.arraiza@cpr.ku.dk> [CvwfJbQuv4S75bEAAAAASUVORK5CYII=] How we protect personal data<https://informationssikkerhed.ku.dk/english/protection-of-information-priva…>

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show 5% or 10% Z-axis of a fibril density
by Binh Nguyen 03 Jul '24

03 Jul '24

Dear all, Is there a way to display say 10% on the Z-axis of a fibril density map? Or maybe save 1 or 2 layers of the map? [cid:11c579f0-867a-4136-b817-27e4c071e57e] I know 2 ways to do it but they both take a long time, and I wonder if we have an easier way to do it. 1. Use volume eraser with a big diameter sphere 2. Build a rough backbone carbon model in 1 layer, and do zone selection. Thanks, B ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Doubt about chimera
by DIEGO ANGOSTO BAZARRA 03 Jul '24

03 Jul '24

Hello, My name is Diego. I’m a beginner user of ChimeraX (1.8) and I was wondering if there is an option to check the % of similarity between two structures after making the matchmaker. I mean, I make a matchmaker with two structures, can I see the % of similarity between these two structures? Not between the sequences, but between the structures. Thank you very much for your time and attention. Best regards Dr. Diego Angosto Bazarra Molecular inflammation and experimental surgery group. IMIB. University Hospital Virgen de la Arrixaca

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ChimeraX workshop
by Jisoo Hwang 03 Jul '24

03 Jul '24

To whom it may concern, Good afternoon! I hope this email finds you well. I'm a student doing research at Johns Hopkins and was wondering if it'll be possible for us to set up a zoom meeting to ask some questions about the software. It's my first time using the software and it would be incredibly helpful if we can have a short workshop going over the features of ChimeraX. We're trying to include a 3D structure in a paper that we're planning on publishing soon. Please let me know if there's any other resource that you can point us to if we can't do a zoom meeting. Thank you so much for your help! Best, Suzie Hwang

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Request for Assistance: Selecting and Visualizing Interacting Residues in UCSF ChimeraX
by Rashmi Aggarwal 30 Jun '24

30 Jun '24

Dear UCSF ChimeraX Support Team, My name is Rashmi, and I am currently working on molecular docking studies as part of my research. I have been using UCSF ChimeraX version 1.8 for visualizing and analyzing protein structures. I am facing difficulties in performing the following tasks related to identifying interacting residues between chains A and B within 4 angstroms, similar to what I have previously done in PyMOL: 1. Select residues in chain A that are within 4 angstroms of chain B: select interactA, byres ((chain A) within 4 of (chain B)) 2. Select residues in chain B that are within 4 angstroms of chain A: select interactB, byres ((chain B) within 4 of (chain A)) 3. Combine the selections for interacting residues: select interaction_residues, interactA or interactB 4. Show interacting residues in stick representation and color them yellow: show sticks, interaction_residuescolor yellow, interaction_residues Despite attempting various commands and exploring the graphical user interface, I have been unable to achieve the desired results using UCSF ChimeraX. Could you please provide guidance on the correct commands or steps to accomplish this task in ChimeraX? Any assistance or advice would be greatly appreciated, as I have a pending deadline for my project. Thank you very much for your attention to this matter. I look forward to your prompt response. Best regards, Rashmi

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Aligning small molecules in Chimera
by Prathvi Singh 30 Jun '24

30 Jun '24

Hi Elaine, Is it possible to superimpose/align small molecules in chimera/chimeraX? I have isolated a very small part of a polypeptide chain from a PDB file (it contains a CO and NH group engaged in peptide bond formation and both the groups are flanked by C-alpha atoms such that the structure's formula becomes CH3-CO-NH-CH3). I have 10 such PDB files. I want to extract this fragment from each PDB file and superimpose them to know the differences. Thank you Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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RMSD does not make sense in a few cases
by Roden Deng Luo 30 Jun '24

30 Jun '24

Hello ChimeraX Team, In the attached screenshot, #1 and #3 are almost overlapping, but get an RMSD as 57. I occasionally encounter this. The session and log files are attached. In short, to reproduce, open 5nl2.cif and emd_3658.map; fitmap #1 in #2 search 1000; rmsd #1 to #3. This happened rarely, but in this case, it happened twice. It might be that I fit other structures first. But I indeed click "Clear List" and "close session" after each fitting. The second top hit's RMSD seems to make sense in the attached session (screenshot attached too). Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Where has the ribbon style editor gotten to?
by Dearborn, Altaira (NIH/NIAID) [E] 28 Jun '24

28 Jun '24

I tried the NIH3D presets to prepare my structure for 3D printing. The large size of the complex, however, makes those settings still too lacey for the NIH 3D printing service. I need to edit the ribbon sizes. The youtube tutorials from the NIH 3D Printing Exchange are 7-10 years old and their instructions to open the Ribbon Style Editor no longer match chimerax. Has this feature been renamed and moved? Thank you, Altaira Dearborn

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NICE DCV graphics error
by georg.kempf＠fmi.ch 28 Jun '24

28 Jun '24

Dear ChimeraX developers and users, we would like to use ChimeraX in a virtual session using the “NICE DCV” software. We verified that OpenGL hardware rendering is working in the virtual session (glxinfo, glxgears, nvidia-smi) but when opening a structure in ChimeraX, we get the below error. We tried it with different versions of ChimeraX (1.8.dev202311220127, 1.6.1 stable) on Ubuntu 20.04.6 LTS. Since the error doesn’t appear when using ChimeraX on the physical display of the same workstation(s) (where the DCV server is running) it must be related to the virtual session context. I was wondering if anyone knows what could be the cause of the error and in which direction to look regarding debugging? This is the traceback from ChimeraX: An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_NONE,) ) Traceback (most recent call last): File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84, in draw_new_frame view.draw(check_for_changes = False) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188, in draw self._draw_scene(camera, drawings) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 226, in _draw_scene shadow, multishadow = self._compute_shadowmaps(opaque_drawings, transparent_drawings, camera) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 626, in _compute_shadowmaps multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1628, in use_multishadow_map self._start_rendering_multishadowmap(center, radius, size) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1711, in _start_rendering_multishadowmap fb = r.start_depth_render(self._multishadow_map_framebuffer, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1356, in start_depth_render if not fb.activate(): ^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2309, in activate fbo = self.framebuffer_id ^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2305, in framebuffer_id self._fbo = fbo = self._create_framebuffer() ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2141, in _create_framebuffer fbo = self._create_fbo(self.color_texture or self._color_rb, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2169, in _create_fbo GL.glDrawBuffer(GL.GL_NONE) File "src/errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_NONE,) ) Many thanks! Kind regards, Georg

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ChimeraX install problems
by Alexander Hung Lee 28 Jun '24

28 Jun '24

I tried to install ChimeraX daily build on a fresh install of Ubuntu 24. When I launch the program, the log says "Available bundle cache has not been initialized yet." Another oddity I"ve noted is that tying to run a python script w/ "chimerax --nogui --silent --offscreen --script path/to/script" works but "chimerax --script path/to/script" doesn't. I just get a black screen. There also isn't a stable build for Ubuntu 24, only daily builds. Should I downgrade my OS? Alex

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induce mutations in protein structure
by Mamadou Sangare 27 Jun '24

27 Jun '24

Dear, I'm new in chimera and I wouldlike to know how to induce mutations in protein structure, in other words, how to replace one residue by another in the protein structure. Kind regards! Mamadou SANGARE, PhD student ACE-B,Mali

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Feature suggestions for the Segmentations tool
by Ricardo Righetto 27 Jun '24

27 Jun '24

Hi, Thanks a lot for adding the Segmentations mode in v1.8, this is very much welcomed for cryo-ET data! Are there any plans for expanding the capabilities of this tool? If possible, I would like to suggest some features for manual segmentation: * Segment contiguous density in 3D by clicking on it (akin to the blob selector in the "Right Mouse" options, which operates on surfaces) * Related: threshold-based segmentation i.e. segment in 3D all contiguous density between selected minimum and maximum density thresholds * 2D/3D Lasso-based segmentation * Dilation, erosion and smoothening of segmentations Some of these things are already possible by combining volume and surface operations or with external tools, but it would be very nice to have everything streamlined in one click (or a few) through the GUI. Alternatively, I would appreciate pointers on how to implement these features as a ChimeraX plugin. Happy to discuss more. Thank you and have a nice weekend! -- Ricardo Diogo Righetto

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Re: ChimeraX does not Support .stl files?
by Zach Pearson 26 Jun '24

26 Jun '24

Hi Kevin, Please direct questions about ChimeraX to our mailing list, chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> — others on the team or even in the community may have more experience or more recent experience in a given subject than I or any other developer has at the moment. Eric (CC’ed) has been working on the NIH 3D pipeline; part of that pipeline is adding struts to delicate objects for 3D printing. He may be able to help you better than I can. — Zach > On 26 Jun 2024, at 14:55, Maroney, Kevin James <kmaroney(a)uab.edu> wrote: > > Hello Dr. Pearson, > Despite doing more Immunology research and really no proteomics, I have had a hobby interest in fooling around with Pymol and ChimeraX. I just recently got a very nice 3D Printer and was hoping to print out a model of the epitope of my PhD complexed between HLA-B57 and TCR that is publically available. I was going to use UCSF Chimera, but it does not seem like it is capable of representing space-filling diagrams and only gives me errors. I obviously can’t print the complex and delicate ribbon or atomic representations and like ChimeraX better anyway. But the guide from the NIH suggests passing PDB models through Chimera to generate .stl files which I can easily then pop into my Studio software to 3D print and resize etc. Problem is, I don’t see that there is any way to actually export as .stl in ChimeraX. Is there any way you could add this feature? Thank you very much. Lovely program. > > Sincerely, > Kevin Maroney > M.S. Biotechnology > University of California, Irvine > PhD Student > University of Alabama at Birmingham

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transparency using in movie making
by Yanhe Zhao 26 Jun '24

26 Jun '24

Dear ChimeraX team, I have a map with model docking and am making movie. My plan is to fade away the map to show the docked model for next step. I tried the crossfade which works. But I want to use the transparency command for this purpose because I want to keep the map at specific transparency level, like 80%. The chimera has command like 'surftransparency 80 #1 50'. I was wondering what is the similar command in ChimeraX? Thanks and cheers, Yanhe

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Sequence based selections
by Kumpula, Esa-Pekka 26 Jun '24

26 Jun '24

Dear ChimeraX team, Two selection-related questions: 1. I'm looking for a way to combine multiple sequence based selections into one selection but I wasn't able to find a way to do this. The use case is, I have a lot of models that have these two proteins and I would like to use them together for superposition (via align command against Calphas). I would normally refer to them by chain ID, but here these are not consistently assigned so I need to use the sequence for selection. 1. Is it possible to have a named, sequence-based selection that, when called, would perform the selection? This would save a lot of pain when writing scripts for sequence based selections. Cheers, EP -- Esa-Pekka Kumpula, PhD Senior Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb>

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Generic Linux installation package for ChimeraX 1.8
by Kumpula, Esa-Pekka 26 Jun '24

26 Jun '24

Dear ChimeraX team, I noticed that version 1.8 no longer comes with a "Generic Linux" installation package (unlike 1.7). I have been using this for a centralised installation on a network drive that has so far worked very well. Is this coming to 1.8 or is it discontinued? Cheers, Esa-Pekka -- Esa-Pekka Kumpula, PhD Senior Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb>

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Bundles with dependencies
by Vincent Mallet 24 Jun '24

24 Jun '24

Hello, Thanks for the tool and the tutorials. I have a machine learning tool based on pytorch to analyse cryo-EM data. I was hoping to package (bundle) it for Chimerax and started to follow tutorials, but I don't think you mention the right way to set up a code environment with depencies. I see a numpy import in the save_new_format tutorial, but it's not listed in the "dependencies" section of the xml file. I guess my question is : can I add arbitrary packages in a bundle ? Is there a way to install pip packages only ? Should I copy all source code in the folder and deal with my imports like that ? In particular, I am thinking of torch that is not so easy to replace... I am hoping you can help me, thanks in advance for the help ! Best, Vincent

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