- ChimeraX-users - RBVI Mailing Lists

Right click bond rotation help
by Raneem Akel 16 Mar '23

16 Mar '23

Hello, I am trying to adjust some bonds in my protein model, however, I want to also be able to control which segment of the protein I’m rotating (i.e. C-terminus vs N-terminus). Is there a way to do that? I’m using ChimeraX 1.5 on Mac. Thank you! Raneem

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Importing pdb structures from OPM
by Prathvi Singh 15 Mar '23

15 Mar '23

Hi Elaine, I was wondering where it is possible to use the "open" command to import PDB structures of membrane proteins from OPM. I see in: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#fetch that we can fetch data from various sources but OPM was not listed there. If this were possible, we could directly import membrane protein structures from OPM which have dummy residues that can be used to define membrane boundaries via the *define plane *command. Thank you -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Re: [chimerax-users] [Chimera-users] Selecting planes using command line
by Elaine Meng 13 Mar '23

13 Mar '23

Hi Prathvi, I believe you would have to use ChimeraX to do this, not Chimera. So this answer is for ChimeraX only: You can select the plane models with Ctrl-click in the graphics window, or you can use the selection checkboxes in the Axes/Planes/Centroids tool (ChimeraX) or in the Model Panel, where you may need to use the disclosure triangles to see the submodels and their numbers. Or you can just look in the Model Panel to find out the number to specify that model directly in commands without using selection. You can move them separately from other models in the same was as any other models in ChimeraX. I.e. with "models" keyword of move/turn commands, or with mouse modes that move only the selected and/or clicked models. <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004945.html> Of course, if you do this with the planes defined from the membrane "atoms" from the OPM database, you are no longer using their predicted membrane locations. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 13, 2023, at 5:24 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > I see that after defining a plane, it gets listed in the "Axes/Planes/Ellipsoids" section with each plane having a unique ID. However, I am unable to use these IDs to select planes individually via command line. Moreover, when I hover my mouse over a plane, it displays: #0:? > > How to select the planes using the command line? And, can I move these planes independent of the protein model? > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Possible to read a trajectory "lazily" or in the background?
by Ben Webb 13 Mar '23

13 Mar '23

Am I right in thinking that when reading a trajectory (e.g. .dcd file), all requested frames from that trajectory are first read in, after which the "coordset" command can be used to work with the trajectory? I am reading frames from an RMF file (using the RMF plugin, the "rmf readtraj" command) which is quite slow, perhaps a second per frame - because RMF stores local coordinates which must be transformed to make the global coordinates ChimeraX is using. So if the user asks to read 100 frames, ChimeraX becomes unresponsive for ~100s, which is not a great user experience. One possible solution would be to read the 100 frames "lazily", e.g. just create 100 copies of the active coordset, then when the user writes "coordset #1 N" for the first time or scrolls to frame N with "coordset slider", read in frame N from the RMF file and overwrite coordset N. That way there would be a 1s delay only the first time that frame is shown. Is this possible? I see there is an "active coordset changed" trigger - perhaps I could attach to that? Alternatively, is there an API for tools to run long-running processes in the background so that the user can work on other things in the meantime, or cancel it if it takes too long? Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Interface residue plot.
by Amber Smith 10 Mar '23

10 Mar '23

I want to save the 2D image of the residue plot (the gray circles with the interacting residues outlined and numbered by residue number). When I left click I can see the menu but save plot as is not an option. Is there a way for me to save that window as an image? -- ammariesmith(a)gmail.com Amber.Smith(a)ucsf.edu Amber M. Smith, Ph.D Department of Biochemistry and Biophysics Yifan Cheng Lab, Genentech Hall University of California, San Francisco 600 16th Street, San Francisco CA 94158-2517 Lab: 415.514.9708

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Showing atoms of select residues while also showing the remainder of the model
by McClean, Phillip 09 Mar '23

09 Mar '23

Hi Everyone, I would like to show the atoms for just a few of the amino acid residues in a protein model will displaying the remainder of the model using the default format. Here is what I did: 1. Opened the model from my working directory 2. Selected a subset of residues using the select command: sel /A:102,105,106 3. Then used this command: show target a This command gives me the atoms for all of the residues. Is there a way to just show the atoms for the selected residues while also leaving the remainder of the model in the standard format. Thanks for any advice. Phil McClean

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circular balls instead of residue
by Revan Katte 09 Mar '23

09 Mar '23

Hello sir/Madam, I'm labeling (or marking) the residues of my protein structure with Chimerax. So I want to use circular balls instead of residue, but he doesn't have that option. Could you please assist me with this? Thank you! Revan -- Revan Katte, Ph.D. Postdoctoral Research Associate, Prof. Maolin Lu Laboratory, Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, Texas 75708, USA. E-mail: *Revansiddha.Katte(a)uthct.edu <Revansiddha.Katte(a)uthct.edu>* Professional Website: Google Scholar <https://scholar.google.com.tw/citations?user=phuOXjgAAAAJ&hl=en> LinkedIn <https://www.linkedin.com/in/dr-revan-katte-3b53a788/>

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Virtual Crash Course - Understanding PDBx/mmCIF | May 3rd | REGISTER NOW!
by Brian Hudson 09 Mar '23

09 Mar '23

Use PDB data to their full extent: Understanding PDBx/mmCIF Wednesday, May 3rd 2023 | 1:00 PM EDT Registration: go.rutgers.edu/u3vpwjet <https://go.rutgers.edu/u3vpwjet> * This RCSB Protein Data Bank (PDB) virtual course will be broadcast on Zoom. Please fill out the registration form to receive the Zoom link. Registration will be available online from March 1, 2023 to May 3, 2023. LEARNING OBJECTIVES Understand the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined three-dimensional biostructures in the PDB. Learn about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data. Main topics: * PDBx/mmCIF format description and examples * PDBx/mmCIF data model * Software tools for generating, editing, and visualizing PDBx/mmCIF files * PDBx/mmCIF dictionary extensions, including ModelCIF for computed structure models (CSM) from AI/ML * Parsing data from PDBx/mmCIF files for your research WHO SHOULD ATTEND Professionals and graduate students interested in learning about strategies to take full advantage of PDB data in the fields of: * Structural biology * Cheminformatics and computational chemistry * Bioinformatics and computational biology PROGRAM | Download Printable Program <https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-cras…> 1:00–1:10 PM Welcome Stephen K. Burley, M.D., D.Phil. Director, RCSB PDB and Founding Director, Institute for Quantitative Biomedicine, Rutgers University 1:10–1:25 PM Introduction and course objectives Gregg Crichlow, Ph.D., RCSB PDB, Rutgers University 1:25–1:45 PM PDBx/mmCIF format - Not your parents’ legacy PDB format Ezra Peisach, Ph.D., RCSB PDB, Rutgers University 1:45–2:05 PM PDBx/mmCIF data files - Lifting the lid off the black box Brian Hudson, Ph.D., RCSB PDB, Rutgers University 2:05–2:50 PM Programmatic data access and analysis using PDBx/mmCIF files Irina Persikova, Ph.D. and Chenghua Shao, Ph.D., RCSB PDB, Rutgers University 2:50–3:00 PM Closing remarks and acknowledgements Stephen K. Burley, M.D., D.Phil. Development and management of the PDBx/mmCIF data dictionary is a collaborative effort involving RCSB PDB, Worldwide Protein Data Bank (wwPDB, wwPDB.org <http://www.wwpdb.org/>) partners, and members of the wwPDB PDBx/mmCIF Working Group (wwpdb.org/task/mmcif <https://www.wwpdb.org/task/mmcif>). CO-ORGANIZERS RCSB PDB Biocurators: Gregg Crichlow, Justin Flatt, Sutapa Ghosh, Brian Hudson, Yuhe Liang, Ezra Peisach, Irina Persikova, Monica Sekharan, Chenghua Shao, Jasmine Young (Rutgers, The State University of New Jersey). QUESTIONS Contact Michelle Sanghera msanghera(a)iqb.rutgers.edu CO-SPONSORS RCSB Protein Data Bank rcsb.org <https://www.rcsb.org/> RCSB PDB is managed by Rutgers, UCSD/SDSC, and UCSF. RCSB PDB is supported by grants from the NSF (DBI-1832184), the US DoE (DE-SC0019749), and the NIH (R01GM133198). RCSB PDB is a founding member of the wwPDB. Institute for Quantitative Biomedicine iqb.rutgers.edu <https://iqb.rutgers.edu/>

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Mutated several residues (amino acids or nucleotides) at the same time
by Vorländer,Matthias Kopano 08 Mar '23

08 Mar '23

Hi there, I wondered if it would be possible to change several residues at the same time using the “swapna” and “swapaa” commands in order to change the model file so that it matches a target sequence. This would be extremely helpful for model building purposes. Many thanks, Matthias

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Re: [chimerax-users] Some beginner's questions
by Elaine Meng 07 Mar '23

07 Mar '23

Hi Boaz, Glad you're getting acquainted with ChimeraX! Now I find it easier to use than Chimera. (1) no, it is not necessary to name the selection. The "save" command for PDB has an option to include selected atoms only, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> (2) do you mean the Side View tool? (ChimeraX does not have a per-model clipping gui currently). There is an icon in the Graphics tab of the toolbar across the top to show the Side View, or you can open it from the menu: Tools... General... Side View (3) if the surfaces are different, yes, that would be the reason for different min/max values found at surface vertices (4) Chimera's ~longbond command just hides the "missing segments" pseudobond group. In ChimeraX, you can look in the Model Panel (may need to use disclosure triangle on the model that contains it) to find the "missing structure" model. In that tool, you can just un-check the display box in the column under the eye icon to hide the whole model, or see what the model number is to use in a hide command, e.g. open 1www hide #1.1 (5) I would need more information: Are you trying to show isopotential surfaces, or to color the molecular surface by the potential value? If the latter, are you coloring the molecular surface of the protein or of the ligand? Do you have your own dx file already or do you just want to calculate Coulombic ESP and color by that? Coloring the protein surface by Coulombic ESP is as simple as clicking the icon in the Molecule Display tab of the toolbar. It is also covered in several tutorials, e.g. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#e…> <https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-channel.html#esp> <https://www.youtube.com/watch?v=FEIJ0lmybXo> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 7, 2023, at 9:12 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi, > > I checked the commands-user guide but couldn't find answers: > • To write out a selection of atoms to a PDB, do I need to name the selection first? > • I couldn't find the clipping tool (after setting a pivot I see only small part of the model). > • The min/max values of a potential from APBS (.dx) seem to be different in Chimerax than they are in Chimera. I'm working on a tetramer and while in Chimera the whole tetramer surface is covered by the potential, in Chimerax it' shown for each monomer. Is that the source of the difference? > • What's the Chimerax equivalent of ~longbonds of Chimera? > • Just wondering, is there a demo for electrostatic potential surface around a ligand? I seem to be making progress on that but a demo would be most helpful. > Thanks, > > Boaz

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Build Structure - peptide
by Jeffrey D. Hartgerink 06 Mar '23

06 Mar '23

Hello, I’m trying to build a series of related peptides with ChimeraX’s Build Structure - peptide tool. The way it currently works is simple and easy to use. However it is cumbersome to input phi/psi angles repeatedly, especially if the peptide sequences is anything more than very short. I am wondering if there is a way for this tool to take in either a text file list containing (Amino Acid, Phi, Psi), to paste in the same data into the input window, or any other related way to more efficiently generate peptide structures for starting points. This would greatly reduce the time needed to compare a variety of related sequences and conformations. Thank you very much for your time and consideration! -Jeff ---------------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University jdh(a)rice.edu / 713-348-4142 https://hartgerink.rice.edu

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Fwd: Request for Help with Chimerax and Protein Visualization
by Eric Pettersen 02 Mar '23

02 Mar '23

> Begin forwarded message: > > From: Ratchanont Viriyakitkosol <ratchanont.vir(a)gmail.com> > Subject: Request for Help with Chimerax and Protein Visualization > Date: March 2, 2023 at 12:26:42 AM PST > To: pett(a)cgl.ucsf.edu > > Dear Eric Pettersen, > > I hope this email finds you well. I am a medical school undergraduate student, and I have been using Chimerax to visualize protein structures that I predicted using AlphaFold. I am reaching out to you as I have encountered some difficulties with visualizing chemical bonding interactions in Chimerax, and I was hoping you could provide some guidance. > > Firstly, I have been using the "contacts" command in Chimerax to visualize chemical bonding interactions that interact with a single amino acid. However, I am not sure if this is the correct command to use. The visualization only shows blue dashlines, which I assume are hydrogen bonds. However, I am not sure if it is showing all direct interactions, including polar and nonpolar, favorable and unfavorable (including clashes). I want to know what is meant by "favorable and unfavorable" interactions in this context. > > Secondly, I have been unable to find a command to show disulfide bonds within a protein in Chimerax. I know that Pymol can show disulfide bonds in the same model, but I find Chimerax easier to use. Could you please let me know how to visualize disulfide bonds in Chimerax? > > As an undergraduate student with limited knowledge of structural analysis, I want to ensure that the bonding I use in my manuscript is shown correctly. I would greatly appreciate any advice or guidance you could provide. > > Thank you for taking the time to read my email, and I look forward to your reply. > > > > Best regards, > > James >

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Inquiry about bond type generated by the "contacts" command with default settings for AlphaFold-generated protein structure
by stomp.pumped0g＠icloud.com 02 Mar '23

02 Mar '23

Dear UCSF ChimeraX team, I hope this email finds you well. I am writing to inquire about the bond type generated by the "contacts" command with all default settings in UCSF ChimeraX for a protein structure that was generated using AlphaFold. I am particularly interested in understanding the nature of the blue line that is generated after running this command. As a reminder, my protein structure was generated using AlphaFold, and I would like to know if the bond type is a hydrogen bond, salt bridge, disulfide bond, or another type of bonding. Any information or insight you could provide on this matter would be greatly appreciated. Thank you for your time and assistance. Best regards, James

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Discrepancies in SASA values between chimera and chimeraX
by Prathvi Singh 01 Mar '23

01 Mar '23

Hi Elaine, I compared the SASA values generated by chimera and chimeraX for a few PDB files and I noticed that whenever the SASA value of a residue is reported to be zero by chimera, the same residue's SASA value is reported to be -1.42 by chimeraX. Few examples are 18.A and 38.A of the PDB ID 1A62. *Method used to calculate SASA of residues in chimera: *Tools > Structure analysis > Render by attribute *Method used to calculate SASA **of residues** in chimeraX: *I ran the following commands: measure sasa protein;info residues attribute area Why is this happening? Kindly help. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Ring fill color
by Luca Pellegrini 01 Mar '23

01 Mar '23

Is it possible to color differently the ring fill for sugar and base in DNA? When I select just the bases or just the riboses and then apply color using the ‘ring fill’ option, they both change to the new color. Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Update pdb model in cxs session
by 张一小 28 Feb '23

28 Feb '23

Hi, I'm using ChimeraX to prepare figures. I saved a session containing several pdb files and maps. (The pdb files were saved in the CXS file right?) Now, I manually adjusted one of the models in Coot. Is there a way to update the old model with the new one in the session so that all the settings, such as colors, views, showing residues, hidden ribbons can be kept and applied?" Thanks, Yixiao

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Rotating/moving a chain to a different site
by Lohry, David 27 Feb '23

27 Feb '23

Hello! I am working with a protein dimer with DNA from a crystal structure. The dimer is composed of 2 chains (chain A and chain B) I would like to be able to place one of the chains on a different region of DNA and at a slightly different position. The only tool that I could find was the Movement Mouse Mode in Chimera original. Is there a way to do this a bit more mathematically (keeping the chain in tact)? Move 50 angstroms in the x direction, rotate chain by 30 degrees, etc . Also, I need it to update the actual coordinates in the PDB when saved so it can't be something that just affects the visual output. Thank you!

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Question!
by Matthew Wengler (TSL) 26 Feb '23

26 Feb '23

Hello, I am a PhD student studying the downstream signalling events of a kinase in a fungal plant pathogen. We have differential phosphopeptide data of the kinase itself over a time course during plant infection (i.e., four residues on this kinase are differentially phosphorylated during stages of infection). I had a vision of showing a movie that incorporated the phosphorylated residues x phosphorylation abundance x time on the kinase’s tertiary structure and was wondering if this could be possible with Chimera X: * The tertiary structure would be displayed in grey * The phosphorylated residues would be highlighted in blue * A movie would be played and the highlighted residues would change colour based on phosphopeptide abundance over a time course (ranging from 0-100% abundance = blue -> red) I was wondering if this was currently possible. Alternatively (and maybe this is really the easiest way), because we only have ~6 time points, I could have 6 different stills of the protein with the residues highlighted corresponding to the phosphopeptide abundance values (blue-red 0-100%) and then piece them together in a 6 frame video that will loop…? I think I would prefer the colours to blend slower together dynamically than 6 harsh frames. Would there be a way to do this in Chimera? Thank you, Matt Wengler

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some question about the use of chimera x 1.4
by 游宠昭 24 Feb '23

24 Feb '23

Dear developers, Sorry to bother you. Recently, I notice that chimera x display the DNA/RNA in a different way from that in chimera, and I find that there is a option in chimera called ribbon spline containing two options:B-spline and cardinal which explain why DNA/RNA is displayed in different ways in two softwares. However, I can not find the related actions in chimera x: "ribbon spline" in chimera refers to what in chimera x and how can I adjust this parameter. Sincerely, Chongzhao You

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Help Generating a Volume to use for 2D classification template generation
by Joshua Denson 22 Feb '23

22 Feb '23

Hi, I’m trying to take an alpha fold model of my complex, generate a low resolution map of the model using molmap, and then use it for 2D template generation in CryoSparc. I am able to generate the low resolution map just fine, but the resulting map is in a rectangular volume (48x64x51) and I need it to be a cubic volume for CryoSparc to accept it. Ideally it would have dimensions of 64x64x64. Is there a way to generate a low resolution map in a cell with specific dimensions while maintaining the protein complex dimensions? (eg. I don’t want to simply scale it into a cube) I am using ChimeraX 1.5. Best Josh Joshua M. Denson PhD Candidate (Johnson Group) Dept. of Chemistry and Biochemistry Utah State University

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Matchmaker on a subset of residues
by McClean, Phillip 22 Feb '23

22 Feb '23

Is it possible to use the Chimerax Matchmaker command to obtain the RMSD value between a subset or residues between two different proteins. Phil McClean

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Custom Toolbar Button
by Dominik Sordyl 22 Feb '23

22 Feb '23

Hi, Is there a possibility to add a button to the "File" section on the toolbar? I have installed custom plugin and it can be run from Tools --> General section, but I am wondering if there is a way to add a shortcut button to the toolbar. Best, Dominik

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Making a movie from a group in PDB file
by Aleksandar Donev 21 Feb '23

21 Feb '23

Hi, I am trying to create a simple animation of a demo molecular dynamics program https://github.com/stochasticHydroTools/DemoMD using either chimerax or chimera. The code creates a .pdb file that has multiple time frames in it, which show up in chimerax as a "group". How do I make chimera show the frames one by one and then make a movie out of that or save each frame as an image? I used to be able to do that in chimera but either the interface has changed or I have forgotten. I found lots of instructions about how to make movies by manipulating one data set (say rotating a molecule) but could not find anything about animation in time. Thanks, Aleks -- Aleksandar Donev, Professor of Mathematics Courant Institute of Mathematical Sciences Office: 1016 Warren Weaver Hall, New York University E-mail: donev(a)courant.nyu.edu Phone: (212) 992-7315; Fax: (212) 995-4121 Mailing address: 251 Mercer St, New York, NY 10012 Web: http://cims.nyu.edu/~donev

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Distance maps and all atom distances
by André Graça 17 Feb '23

17 Feb '23

Hi everyone! Does ChimeraX have a tool to calculate distance maps in the same fashion as Chimera does with RRDistMaps? I believe Chimera's RRDistMaps only calculates intermodal distances between C-alpha atoms. Does anyone know a tool or have a script that could calculate all atom distances from two sequence identical models? Cheers, André

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Image saving/exporting options
by Matthew Graneri 16 Feb '23

16 Feb '23

Hi there, I was wondering if there was an option to set the resolution of an image you want to export? In the older Chimera application, there were many more options open to you when you wanted to save an image (I’ve attached a screenshot of the old and new image saving screens for comparison). If not, is there any chance of implementing a resolution specification option sometime in the future? I was also wondering if it was possible to save images from ChimeraX as PDF files? I find that they usually maintain a high resolution without being particularly big, in terms of memory. Apart from that, really enjoying ChimeraX! Regards, Matthew

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Loading MTZ data - volume is restricted to a small sphere within the protein model
by Lewis James martin 15 Feb '23

15 Feb '23

Hi folks, I recently installed Clipper, and on loading some example PDB and MTZ data, I'm seeing just a sphere of density data that does not cover the full protein model. This behaviour is not restricted to a single example. Is it expected? The example files I used are in 6DIL <https://www.rcsb.org/structure/6DIL>. I downloaded "PDB Format" and "Map Coefficients (MTZ Format)" from the drop-down menu. Loading the PDB by drag-and-drop into ChimeraX works as expected (coordinates do show). On loading the MTZ by drag-and-drop, and selecting the PDB model to import data into, I see the below representation. The density does not cover the full set of protein coordinates - it's limited to a sphere within the protein. Curiously, I saw this on coot too - so maybe I'm just getting the options incorrect? I did try shifting the cutoffs in the "Volume Viewer" Tool, and the mesh does change but it's still limited to this sphere. Changing from a mesh surface to "Maximum" shows that the available data is limited to a cube that does not cover the protein. Is there a way to view the full density? Out of interest, I also tried generating the mesh myself, but only got halfway. This at least shows that the data does cover the whole protein: import gemmi import numpy as np import meshplot as mp from skimage.measure import marching_cubes #run 'gemmi mtz2cif 6dil_phases.mtz 6dil_phases.cif' first doc = gemmi.cif.read('/Users/ljmartin/Desktop/6dil_phases.cif') rblocks = gemmi.as_refln_blocks(doc) rblock = rblocks[0] size = rblock.get_size_for_hkl(sample_rate=2.6) full = rblock.get_f_phi_on_grid('pdbx_FWT', 'pdbx_PHWT', size) array = np.array(full, copy=False) complex_map = np.fft.ifftn(array.conj()) scale_factor = complex_map.size / full.unit_cell.volume real_map = np.real(complex_map) * scale_factor v,f,n,_ = marching_cubes(real_map, 0.05) mp.plot(v, f)

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move models relative to each other
by Raik Grunberg 14 Feb '23

14 Feb '23

Dear ChimeraX developers and users, I would like to move to different proteins that I have opened separately into a particular position relative to each other. In the old Chimera, this is possible by going to the Model panel, then selecting one of the two models as "Active" and the other one not and then making the normal rotation and translation moves which will now only happen on the "active" model. However, this "Active" column is missing in the ChimeraX Model panel and I cannot find any alternative way of doing this. Any suggestions? Thanks a lot in advance Raik -- 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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Re: [chimerax-users] Transparency with soft lighting
by Tom Goddard 10 Feb '23

10 Feb '23

Hi Scott, I made a ChimeraX recipe web page to show this transparency and shadows trick. https://rbvi.github.io/chimerax-recipes/shadows/shadows.html That's amazing Esther refound it in that long fitting video. Tom > On Feb 10, 2023, at 12:23 PM, Scott Stagg <sstagg(a)fsu.edu> wrote: > > Thanks, Tom. That’s exactly what I was looking for! Esther Bullit found the video. It’s this one > https://www.youtube.com/watch?v=v3jI43YJQMg > Fitting an atomic model in an electron microscopy map with ChimeraX > youtube.com > Scott > > >> On Feb 10, 2023, at 3:09 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Scott, >> >> I'm not sure what video that is in. But there is some obscure ChimeraX magic involved. If you use the "soft" lighting (shadows cast from all directions) with a transparent surface it looks horrible because transparent surfaces by default don't cast shadows in ChimeraX. The reason for that default is often you are showing a molecule inside a transparent surface and then the molecule is dark (black actually) and hard to see. Because the transparent surface doesn't cast shadows it does not shadow itself so you don't get any of the darkened cavities that help 3D appearance. To make transparent surface cast shadows use ChimeraX command >> >> material transparentCastShadows true >> >> If you have an atomic structure (#2) inside the surface it will look black (shadowed), but you can tell it not to accept shadows >> >> lighting model #2 multishadow false >> >> The model inside can look pretty horrible and flat with soft lighting and you might try full lighting that adds a spot light, and also use silhouette edges. >> >> Here is an example of all these tricks. >> >> open 1080 from emdb >> light soft >> volume level 0.6 >> open 1grl >> preset cylinders >> fitmap #2 in #1 >> transparency #1 80 >> material transparentCastShadows true >> lighting model #2 multishadow false >> graphics silhouettes true >> set bgColor white >> light full >> >> Thanks for asking! >> >> Tom >> >> Opaque map, and transparent map, and transparent map with shadows with soft lighting. >> >> <image1.png><image2.png><image3.png> >> Atomic model is dark inside transparent map casting shadows. Can make atomic model not accept shadows. "Full" lighting instead of soft can make the atomic look less flat. >> >> <image4.png><image5.png><image6.png> >> >> >>> On Feb 10, 2023, at 6:48 AM, Scott Stagg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Hi everybody, >>> >>> I’m writing because I saw in a YouTube video that you used “soft” lighting with transparency for an EM density map. It looked great. I can’t find the video again or the right documentation on how to do it. There was some command with the lighting that you typed in the command line. Do you know what I’m talking about? >>> >>> Thanks, >>> Scott >>> >>> Scott Stagg >>> Professor >>> >>> Institute of Molecular Biophysics >>> Department of Biological Sciences >>> Florida State University >>> Tallahassee, FL 32306-4380 >>> w: 850-645-7872 >>> f: 850-644-7244 >>> sstagg(a)fsu.edu >>> https://www.stagglab.com <https://urldefense.com/v3/__https://www.stagglab.com__;!!PhOWcWs!3QUvw8SGqe…> >>> >>> >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chim…> >> >

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Transparency with soft lighting
by Scott Stagg 10 Feb '23

10 Feb '23

Hi everybody, I’m writing because I saw in a YouTube video that you used “soft” lighting with transparency for an EM density map. It looked great. I can’t find the video again or the right documentation on how to do it. There was some command with the lighting that you typed in the command line. Do you know what I’m talking about? Thanks, Scott Scott Stagg Professor Institute of Molecular Biophysics Department of Biological Sciences Florida State University Tallahassee, FL 32306-4380 w: 850-645-7872 f: 850-644-7244 sstagg(a)fsu.edu https://www.stagglab.com

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About plotting independent component analysis vectors
by Tianming Qu 09 Feb '23

09 Feb '23

Dear all, Is there any way I can display the eigenvectors I got from the independent component analysis on ChimeraX, which is calculated from the protein MD trajectory. Best, Tianming

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Show palette range scale
by Gomez Barillas, Andrea 08 Feb '23

08 Feb '23

Dear ChimeraX developers, I've mapped sequence conservation into my protein structure by defining a specific attribute and I colored it using a specific palette. I was wondering how I can show in my model the scale of colors for the range I've stablished in my map. Maybe there is a command I can use to show the range I used for mapping and what the colors represent. Thank you for your help, Andrea

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Re: [chimerax-users] Help getting rmsd value per residue of 2 similar structures.
by Elaine Meng 08 Feb '23

08 Feb '23

Hi Binh, This is almost the same question as asked yesterday on chimerax-users(a)cgl.ucsf.edu, so I have the same answer: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html> That answer assumes you are using Matchmaker to superimpose these structures first, which has an option to display the pairwise sequence alignment with RMSD values per column, which can then be written out, used for coloring, etc, as detailed in that answer. Note that this RMSD is only using CA atoms so for two structures, it is simply the distance between the 2 CA atoms. You can use the Sequence Viewer settings to make it use the 4 backbone atoms per residue instead (N,CA,C,O): <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html> Secondarily, remember that Chimera and ChimeraX are two different programs and if you are viewing help/answers for Chimera they may not pertain to ChimeraX. Finally, for the best chance of getting a good answer to ChimeraX questions in the future, please use chimerax-users(a)cgl.ucsf.edu unless you are including private data. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 8, 2023, at 12:39 PM, Binh Nguyen <AnBinh.Nguyen(a)UTSouthwestern.edu> wrote: > > Dear Elaine, > > Is there a way to generate the rmsd per residue of 2 similar structures using chimeraX? I have searched through but I can only manage to get the overall RMSD. > > I have found this too but I have no idea how to get such information. > https://www.rbvi.ucsf.edu/pipermail/chimera-users/2019-February/015415.html > > Please help, thank you. > > B

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Questions about MultiAlign Viewer
by Beate Aftret 06 Feb '23

06 Feb '23

Hi, I have some issues accessing the Multiaglin Viewer in ChimeraX. I’ve tried to look at this response: https://www.rbvi.ucsf.edu/pipermail/chimera-users/2019-February/015415.html . However, I’m unable to access it. I’m trying to access the multialign viewer so I can get individual RMSD values on structures compared using Matchmaker. Thank you in advance. Let me know if I need to give more detail. Kind regards, Beate Aftret

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No Access to Personal Files
by Anna Popa 02 Feb '23

02 Feb '23

Good afternoon, I am a college student using your ChimeraX software to complete an assignment in my biochemistry course. I have downloaded your app to my HP Chromebook using the most recent Ubutun version. Despite being on my personal computer, ChimeraX cannot open the files needed from my computer. When I tried to find out why this is happening, I concluded that it might be a software issue because I wasn't even able to set up the ChimeraX app completely. I would greatly appreciate some guidance and assistance. Thank you, Anna Popa

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Fwd: Your message to ChimeraX-users awaits moderator approval
by Eric Pettersen 02 Feb '23

02 Feb '23

> Begin forwarded message: > > From: Krishnan Raman > Subject: RE: Your message to ChimeraX-users awaits moderator approval > Date: February 2, 2023 at 9:47:12 AM PST > To: "chimerax-users-owner(a)cgl.ucsf.edu" <chimerax-users-owner(a)cgl.ucsf.edu> > > Hi guys > > is there a way to get structures + other numerical data into chimerax? > I get the structures using a sdf file. I want to get in someother data associated each structure. > > How to start multiple instances of chimerax from a html-commands file? > 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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Obtain electrostatic potential from PQR/DX via script
by Lohry, David 02 Feb '23

02 Feb '23

Hi everyone, I'm performing an analysis where I want to select different regions on a molecule and obtain a list of all of the electrostatic potentials from that region. My input is a PQR file with a DX file. These were generated from a PDB and APBS. The electrostatic potential can be viewed when the option "Report value at mouse position" is selected in the Surface Color tool (Tools...Volume Data...Surface Color...Options button) In the status bar at the bottom, it will show the value along with the coordinates. Is there a way to obtain this information via a ChimeraX command that I could script? Thank you!

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Multi-chain single macromolecule .pdb file read as two molecules
by Lenye Dlamini 31 Jan '23

31 Jan '23

Hello, I have a homo-oligomeric model that I've refined using phenix and the ISOLDE tool in ChimeraX that's read during deposition as 2 separate molecules, a larger 14mer and a smaller tetramer. It's read as one molecule in Coot, Chimera and Pymol but read as two distinct molecules in ChimeraX exactly like the deposition. I found this curious and thought that perhaps you might have some idea of what's wrong with the file. There is nothing that appears obviously incorrect to me in the text of the .pdb file, all TER cards follow the chains and all amino acids and their identifiers are in sequence and correct. I'd appreciate any ideas you may have and I'm happy to send the file to you if you prefer. Thank you, Kind regards, Lenye Dlamini Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

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Fwd: EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection
by Eric Pettersen 30 Jan '23

30 Jan '23

> Begin forwarded message: > > From: Tom Goddard <goddard(a)sonic.net> > Subject: Re: [chimerax-users] EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection > Date: January 30, 2023 at 11:54:02 AM PST > To: Paul Korir > Cc: Martin Schorb > > Hi Paul, > > ChimeraX does not specify what distance units the open models use. For atomic structures and cryoEM map it is usually Angstroms. For light microscopy images it is often microns. For medical image scans (MRI, CAT) it is I think meters. The file formats for the data define the physical distance units, not ChimeraX. So if EMDB SFF provides a segmentation for say an MRC or CCP4 density map file the scaling of that density map in the ChimeraX graphics is taken from the file header which has a field "cell dimensions in Angstroms". If a segmentation of that density map is made that is say a bounding surface it might use x,y,z coordinates in Angstroms or it might use grid index units when it writes out a file, that would depend on the segmentation file format and the software that is writing the segmentation. In ChimeraX it always tries to scale the data into physical units so that different data sets, like an atomic structure and 3D image data have the correct relative scale. So ChimeraX never displays images using grid index units. > > So from what you say about EMDB SFF the first transform goes from grid index units to physical units and ChimeraX should apply that transformation to the segmentation data so that it has the same scaling as the map data that the segmentation was derived from. I see there is a function in the ChimeraX EMDB SFF file reader called "guess_scale_and_shift" that is trying to figure out what transform to apply, but it is just a hack and looks for any non-identity transform. > > https://github.com/RBVI/ChimeraX/blob/da72f2cd9b23c0c35a66122b7edc453d593ea… <https://github.com/RBVI/ChimeraX/blob/da72f2cd9b23c0c35a66122b7edc453d593ea…> > > And another comment in the code suggests it is doing that hack because it was needed for EMDB SFF test data EMDB 1547. > > If I understand you correctly ChimeraX should instead always apply the first transform from transforms_list. I can make that change. The main thing will be to test it on pairs of EMDB SFF segmentations and corresponding maps to make sure it produces the correct alignment. > > Tom > > >> On Jan 30, 2023, at 2:20 AM, Paul Korir via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hi Tom/ChimeraX admin, >> >> Just to clarify: what are the units of physical space in ChimeraX: Å or nm? >> >> Kind regards, >> >> Paul K. Korir, PhD >> 3D Visualisation Lead >> CS3DB >> EMBL-EBI >> >> On 30/01/2023 08:51, Paul Korir wrote: >>> Hi Tom, >>> >>> To the best of my understanding, ChimeraX displays images and associated segmentations in physical space not image space. However, segmentations are performed in image space. EMDB-SFF uses the first transform in the transforms_list field (with id=0) as the image-to-physical transform. (https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html… <https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html…>) >>> >>> I've tested with two files having the same segmentation but different values for transform 0 and they render the same. >>> >>> Could you please implement this feature in ChimeraX? >>> >>> Kind regards, >>> >>> -- >>> Paul K. Korir, PhD >>> 3D Visualisation Lead >>> CS3DB >>> EMBL-EBI >>> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >

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EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection
by Paul Korir 30 Jan '23

30 Jan '23

Hi Tom, To the best of my understanding, ChimeraX displays images and associated segmentations in physical space not image space. However, segmentations are performed in image space. EMDB-SFF uses the first transform in the transforms_list field (with id=0) as the image-to-physical transform. (https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html… <https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html…>) I've tested with two files having the same segmentation but different values for transform 0 and they render the same. Could you please implement this feature in ChimeraX? Kind regards, -- Paul K. Korir, PhD 3D Visualisation Lead CS3DB EMBL-EBI

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How to license AlphaFold with ChimeraX
by Asma Rehman 28 Jan '23

28 Jan '23

Hi, I'm currently a chimeraX user and would like to also use AlphaFold along with it. I was wondering if you could help us with directions. I appreciate your support. Thanks, Asma

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Isolde in with VR Headset ?
by Thibault TUBIANA 27 Jan '23

27 Jan '23

Dear all, I tried to use my Occulus Quest with ChimeraX Isolde Pluggin, while it works amazingly, the "tugging" function doesn't work. I thought that maybe it is the mouse mode that is node configured, so I tried "vr button trigger select" or 'vr button trigger "isolde tug atom"' but nope... It is not a request of course, just a question to know if someone already tried it ^^ Best regards, Thibault Tubiana. -- Thibault Tubiana, PhD Postdoctoral Fellow @ [ https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism… | IMAPP ] Institute for integrative biology of the cell ( [ https://www.i2bc.paris-saclay.fr/ | I2BC ] ) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: [ http://www.tubiana.me/ | http://www.tubiana.me/ ]

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Select ring atoms of ligand using python in chimerax
by Dr. Vijay Masand 26 Jan '23

26 Jan '23

Dear all I am looking for an efficient method to select ring atoms of ligands using python in chimeraX. Also, is there any python code/method to get the sum of charges on ligand atoms only? Thanks in advance. From Vijay With Warm Regards *Dr. Vijay H. Masand* Department of Chemistry, Vidya Bharati College, Amravati, 444 602 Maharashtra, India. Phone number- +91-9403312628 https://sites.google.com/site/vijaymasand/

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Re: [chimerax-users] recent query
by Rangarajan, Amith 26 Jan '23

26 Jan '23

Dear Eric, thanks for taking time to answer my query. It was very detailed and i am beginning to understand how bundles work on chimerax. i am working on a methods paper that uses sidechain center of masses as a representation of mutation position and generates clusters to intrepret the impact of the mutations. i tried scripting this, but i realised that pandas library is not present in chimerax (?) and i did not proceed further. is there a way to include scikit learn , pandas libraries in chimerax script? thanks once again for all your support ! best amith

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Macbook Pro, fans, and ChimeraX
by Lewis James martin 26 Jan '23

26 Jan '23

Hi all, Ever since I got my Macbook Pro (16-inch, 2019, 2.3GHz 8‑core Intel Core i9) I noticed the fans can go full bore for seemingly small tasks. ChimeraX is one of those - swinging a protein view around is enough to set them off, and Activity Monitor reports around 200% usage for the "UCSF ChimeraX" process. I can see that GPU usage on the inbuilt AMD Radeon Pro 5500M can get up to about 50%, too. The bottom can get quite hot - it's Summer here now, but this happens in Winter too. A couple of questions: - Is this expected (for ChimeraX, not generally)? Do other people experience this? - Does ChimeraX use the GPU for rendering? If so, what's driving the CPU spike when I move the protein on screen? Is it just from calculating the coordinate rotations? Thanks, Lewis

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Re: [chimerax-users] [Chimera-users] Rotation along symmetry axys
by Tom Goddard 25 Jan '23

25 Jan '23

Hi Leonardo, As Elaine said, rotating the view in ChimeraX does not change what is saved in the map (*.mrc) file. The data needs to be rearranged in the 3D array. That can be done with the ChimeraX "volume resample" command (in Chimera it is called vop resample) but that interpolates the data on a new grid, and it would be better to just rotate the 3D data array so you don't get interpolation errors. I made a ChimeraX command to do that "volume rotate_90" available on the ChimeraX Recipes web site. https://rbvi.github.io/chimerax-recipes/rotate_90/rotate_90.html We no longer develop Chimera so I provide this for ChimeraX. Tom > On Jan 25, 2023, at 6:14 AM, Leonardo Talachia Rosa via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera team, > I hope you are well. > > I am processing a phage dataset which presents D5 pseudossymetry. The C5 axys is aligned to the z axys. I would like to rotate the map 90 degree in the z axys, so that Z axys now separate the molecule in a C2 pseudosymmetry, in order to play with some symmetry relaxation features to refine differences in the two map vortexes. > Is there a way in chimera to rotate the map in relation to the xyz axys? The way I see, all rotate commands I know rotate the axys themselves alongside the map. > > Thank you for your time, > Kind wishes, > Leonardo > > -- > ************************* > Leonardo TALACHIA ROSA, PhD > PostDoctoral Researcher > Microbiology and Structural Biology > Instituto de Química, Universidade de São Paulo - IQ-USP > Av. Prof. Lineu Prestes, 748 - Butantã, São Paulo - SP > ************************** > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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color palette in transprency ?
by vincent Chaptal 25 Jan '23

25 Jan '23

Hi, I'm rendering a series of models using this command line (which works very well): rainbow #1 structures palette cyan:blue I would like to do the same but in a series of transparent models, with a range from 0 to 80 (or similar). Is there a command for this, I couldn't find it? Thanks a lot. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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vector
by Dr.S.Somasundaram 25 Jan '23

25 Jan '23

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Pseudobonds change style
by Samo Lešnik 25 Jan '23

25 Jan '23

Dear ChimeraX developers, I am wondering if it is possible to change the style of pseudobonds, specifically "Distances", from "dotted disks" to "whole undotted lines"? It is very easy to do this in Chimera, with just changing the style in the graphical interface of Distances. Thank you very much, dr. Samo Lešnik

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Re: [chimerax-users] downloading pdb files from another webserver
by Rangarajan, Amith 24 Jan '23

24 Jan '23

hi, i mostly resort to using the resource from dunbrack's lab to download structures renumbered as per uniprot numbering. i currently do it using a simple .py script: [cid:14eb2e7f-deaa-4341-92eb-3f9c56db264b] i want to make this as a chimerax script that i can call from command line with open {scriptname.py} { pdbid} wondering if some one has tried to do similar things and some tips regarding which modules to use might be helpful. thanks a lot , best amith

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Memory problems with Orbital Viewer
by Michael Patzschke 24 Jan '23

24 Jan '23

Dear colleagues, I am using ChimeraX mostly for small molecular complexes, typically up to 100 atoms. I am running the code on a MacBook Pro with 16 GB of memory under macOS 11.8.8. When I try to render molecular orbitals from an orca calculation I get even for very small molecules the warning message: Estimated peak memory usage (0.0GB) is above or close to the available memory (0.0GB). Exceeding available memory might affect the stability of your computer. You may attempt to continue, but it is recommended that you lower your resolution, decrease padding, or use fewer threads. Press "Ok" to continue or "Abort" to cancel Is there any way to fix this problem? Kind regards, Michael Patzschke

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