- ChimeraX-users - RBVI Mailing Lists

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

2 2

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

3 3

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

2 4

electrostatic surface of docking model
by Citterico, Matteo 23 Jan '23

23 Jan '23

Hello everyone, I am trying to visualize the electrostatic potential surface of a docking model generated with ClusPro2.0 (job: https://cluspro.bu.edu/models.php?job=898454) When I click on the electrostatic button on ChimeraX 1.3 to visualize the charge, it gives the error: "Using Amber 20 recommended default charges and atom types for standard residues. Hydrogen copy of model.000.00.pdb #/A PHE 244 H1 bonded to atom that should not have hydrogens (copy of model.000.00.pdb #/A PHE 244 C)." How can I solve this problem? Thank you for the help and always a big up to the Chimera staff! Matteo

2 6

Coot view in ChimeraX
by Cryo EM 23 Jan '23

23 Jan '23

Hi everyone, Does anyone know of a command for getting a coot view of map in ChimeraX? I remember seeing it in chimera, so I guess there should be something of such sort in ChimeraX too? Regards and thanks

2 1

Error in opening Chimera
by Ashfaque Rahman 22 Jan '23

22 Jan '23

Why is this error showing? What is the solution? [image: image.png]

2 1

Non contiguous residues selection from command line
by LEONARDO SORCI 22 Jan '23

22 Jan '23

Hello there! I wondered if there is a way to quickly select noncontiguous residues from the command line (useful, for example, when selecting a set of residues defining an active site, a template for docking, etc.). In standard chimera, I would use the command SELECT with numbers, commas, and hyphens (e.g., SELECT: 172,192,193,208:214). Thanks, Leonardo Polytechnic University of Marche, Ancona, Italy

2 2

How to select best pose from docking model?
by Luigi Marongiu, PhD 22 Jan '23

22 Jan '23

Dear all, I am new to docking analysis. I have obtained a list of poses from VINA analysis, but what of them shall I choose? Is the first the best choice? The problem is that, according to the pose, the ligand binds the protein in a different position. Different ligands might or might not bind on the same position, thus choosing the right pose is essential to determine whether there is a position that allows binding of multiple molecules. What is the procedure to determine whether such a multiple binding site exists? What is the protocol to choose the right pose? Thank you

2 1

Re: [chimerax-users] overwrite session aliases from the startup options
by Helge Paternoga 20 Jan '23

20 Jan '23

Hi Elaine, Thanks for the tip with "alias delete all", I had not considered that one. My solution so far was to open the startup screen and copy all new aliases, then paste them in the command line and hit enter which overwrites everything with the newest ones. So a toggle option to "re-run startup script upon session loading" or something similar could alleviate the issue. Best, Helge Am 18.01.23 um 21:00 schrieb chimerax-users-request(a)cgl.ucsf.edu: > Dear Helge, > I don't have an elegant solution, but faced with this problem I would > > (1) open old session > > (2) use "alias delete" to get rid of the old versions of the aliases (or "alias delete all" if you are OK with getting rid of all of them) > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alias.html> > > (3) re-save session > > I understand that it is a pain to do this if you have a large repertoire of saved sessions, however. > I hope this helps, > Elaine

2 4

ChimeraX image saving automation
by Attana, Fedaa 19 Jan '23

19 Jan '23

Hi all, I have started to use Chimera recently and found it very cool. I liked the way I can edit all of my structure with one command when no model is selected. However, to save images, I have to manually show each structure (model) and run the same saving command with a new name. I wonder if there is an easier way to do this or if somebody did automate this process so one can save images of individual models with a script? Thanks in advance, Fedaa

3 2

scalemol extension not working
by André Graça 19 Jan '23

19 Jan '23

Hi everyone, I hope to at least get a reply from Tom, but this may need a bit of troubleshooting (?). I looked into a very old post of yours, Tom, about rescaling an atomic model (see it at the end of my email). I put everything in place but I get an error and I wonder if anything has changed with the PDB format since 2005, or some incompatibility with new chimera versions... If there is actually a way of doing the same with ChimeraX, that would be incredible =) Cheers! André Error and forwarded message comes now: __________________________________________________ AttributeError Exception in Tk callback Function: <bound method MidasUI.processCommand of <Midas.midas_ui.MidasUI instance at 0x00000000079092C8>> (type: <type 'instancemethod'>) Module: <module 'Midas.midas_ui' from 'C:\Program Files\Chimera 1.16\share\Midas\midas_ui.pyc'> (line: 618) Args: (<Tkinter.Event instance at 0x00000000198D8AC8>,) Event type: KeyPress (type num: 2) Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\share\Midas\midas_ui.py", line 628, in processCommand midas_text.makeCommand(cmdText) File "C:\Program Files\Chimera 1.16\share\Midas\midas_text.py", line 69, in makeCommand f(c, args) File "C:\Program Files\Chimera 1.16\share\scalemol\ChimeraExtension.py", line 23, in scale_molecule x, y, z = a.coord().xyz.data() AttributeError: '_chimera.Point' object has no attribute 'xyz' ================================================ Event contents: char: delta: 0 height: ?? keycode: 13 keysym: Return keysym_num: 65293 num: ?? serial: 14638 state: 8 time: 154527203 type: 2 widget: .121252488L.126915336L.428746824L.428747592L.428747720L width: ?? x: 228 x_root: 288 y: -22 y_root: 941 ______________________________________________________________________ ------- Start of forwarded message ------- Date: Wed, 27 Apr 2005 11:05:55 -0700 (PDT) From: Thomas Goddard <goddard at cgl.ucsf.edu<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> Hi Jinghua, By "virus cage pdb file" I guess you mean you placed atoms at icosahedral positions, and want to show them connected up to show some icosahedral pattern. I think the easiest approach is to open your old session, run a command to change the diameter of the cage, then save a new session. Below is some Python code that provides a "scalemol" Chimera command. Make a directory chimera/share/scalemol in your Chimera distribution and put the code below in file chimera/share/scalemol/ChimeraExtension.py. Then start Chimera, open the cage PDB model, use menu entry Favorites/Command line, and type a command: scalemol 0 1.5 to make model number 0 bigger by a factor of 1.5. If you have more than one model open you can see the model numbers using Favorites / Model Panel, the model number is shown in the left hand column. Tom - ---- scalemol/ChimeraExtension.py code follows: # ----------------------------------------------------------------------------- # def scale_molecule(cmdname, args): from Midas.midas_text import error fields = args.split() try: model_num = int(fields[0]) factor = float(fields[1]) except: error('Syntax error: scalemol <model-number> <factor>') return import chimera mlist = chimera.openModels.list(id = model_num) if len(mlist) == 0: error('scalemol: No model number %d' % model_num) return for model in mlist: for a in model.atoms: x, y, z = a.coord().xyz.data() c = chimera.Coord() c.x, c.y, c.z = (factor*x, factor*y, factor*z) a.setCoord(c) # ----------------------------------------------------------------------------- # import Midas.midas_text Midas.midas_text.addCommand('scalemol', scale_molecule) ------- End of forwarded message -------

2 1

missing or invalid sequences
by Liang, Junyi 19 Jan '23

19 Jan '23

I would like to predicate interaction between two proteins, and tried chimerax version 1.5 after noticing a youtube video https://www.youtube.com/watch?v=6lXeCPuTePs. [https://www.bing.com/th?id=OVP.95Ygyv4AXQTgCS0WB9iXtgHgFo&pid=Api]<https://www.youtube.com/watch?v=6lXeCPuTePs> Running AlphaFold to Predict Protein Complexes from ChimeraX<https://www.youtube.com/watch?v=6lXeCPuTePs> How to predict the structure of a photoreaction center complex of 3 proteins from ChimeraX using AlphaFold-Multimer. Requires a ChimeraX daily build newer than December 2, 2021 or version 1.4. It is not in ChimeraX version 1.3. Web page describing steps https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html www.youtube.com I input the two protein sequences in same way as shown in the video and hit predict. But your software says "missing or invalid sequences". How come? Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

2 5

Is RR Distance Maps implemented in ChimeraX?
by Michael Bruist 19 Jan '23

19 Jan '23

I use RR Distance Maps in Chimera for my teaching. I want to switch to ChimeraX, but I have not bee able to find this tool. Is it available in ChimeraX? Mike Bruist Michael F. Bruist Professor of Biochemistry Department of Chemistry and Biochemistry St. Joseph’s University 215-596-8530 mbruist(a)sju.edu

2 1

Reasign secondary structure for back-bone trace
by Enrico Martinez 19 Jan '23

19 Jan '23

Dear Chimera-X users! I am working on the visualization of a trajectory containing only back-bone atoms of the protein obtained from the PCA. When I load this multi-pdb ensemble to Chimera-X I can see only back-bone traces without any secondary structure information. I've tried to use dssp command to re-assign the secondary structure but it did not change the visualization state. Would it be possible to do it in some automatic fashion via some built-in command? Many thanks in advance Cheers Enrico

2 4

incomplete output from matchmaker embedded in python script
by Borchert, Milan 19 Jan '23

19 Jan '23

Hello ChimeraX community, I have been trying to use the Chimerax tool to sequentially check one query pdb against multiple (later up to 10000) pdb files. For this I have been working with the python scripting functionality. With the following code I was able to get the resulting data (number of matched atoms and resulting RMSD) saved as a html log file: import os from chimerax.core.commands import run as rc # change to folder with data files os.chdir("/home/ubuntu/Desktop/Chimerax_search/N_crassa_pdb") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # give path to query file to be searched against pdb library query = "/home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb" # open the query file as #1 in ChimeraX rc(session, "open /home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb") # loop through the files for fn in file_names: # open first target pdb as #2 rc(session, "open " + fn) # match both structures rc(session, "match #1 to #2") # save log with ID matching input filename, close #2 and clear log rc(session, "log save " + fn.split(".")[0] + ".log") rc(session, "close #2") rc(session, "log clear") Instead of trying to gather the relevant data from thousands of rather large html output files I instead would prefer to only get then resulting values from matchmaker. I learned that the command actually has all the values I wanted as return values, so I tried to write a modified script, that saves these values in a variable and collects the values for every target pdb file in a dict: import os from chimerax.core.commands import run as rc # change to folder with data files os.chdir("/home/ubuntu/Desktop/Chimerax_search/N_crassa_pdb") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # give path to query file to be searched against pdb library query = "/home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb" # open the query file as #1 in ChimeraX rc(session, "open /home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb") # create empty dict to collect matchmaker output output = {} # loop through the files, opening, processing, and closing each in turn for fn in file_names: id = fn.split("/")[-1].split(".")[0] rc(session, "open " + fn) match = rc(session, "match #1 to #2") output.update({id : match}) rc(session, "log save " + fn.split(".")[0] + ".log") rc(session, "close #2") rc(session, "log clear") # display dict print(output) For now I just used 4 target pdbs with my query and only tried printing the result to quickly check if it fits. However the result is a bit baffling to me. I do get the RMSD values, but not the other data: {'NCU01382': [{'full match atoms': <chimerax.atomic.molarray.Atoms object at 0x7f1944492130>, 'full ref atoms': <chimerax.atomic.molarray.Atoms object at 0x7f194448f610>, 'final match atoms': <chimerax.atomic.molarray.Atoms object at 0x7f1946694430>, 'final ref atoms': <chimerax.atomic.molarray.Atoms object at 0x7f1946694550>, 'full RMSD': 63.065617285514556, 'final RMSD': 1.365365439813019, 'transformation matrix': <chimerax.geometry.place.Place object at 0x7f194669c130>, 'aligned ref seq': <chimerax.atomic.molobject.Sequence object at 0x7f19f7b8f8b0>, 'aligned match seq': <chimerax.atomic.molobject.StructureSeq object at 0x7f19f7b8f610>} here is one of the resulting hits, for my first target pdb (NCU01382). As you can see, the RMSD scores are correctly given, but for other values the internal object names and no resulting value are displayed. Any help with figuring this out would be greatly appreciated. Best Wishes Milan Borchert

2 2

select displayed atoms via command line / transfer saved views
by Helge Paternoga 18 Jan '23

18 Jan '23

Dear ChimeraX users, I have to unrelated questions: 1) Is there a way to select displayed atoms via the command line? 2) Is it possible to transfer saved views from one session to another one? Many regards and thank you for reading, Helge

3 3

Clipper's strange behaviour
by André Graça 16 Jan '23

16 Jan '23

Hi everyone! Is there any known issue with Clipper plugin for ChimeraX? After installing clipper and restarting ChimeraX, the software is not responding after I execute the Open command. I expect that it takes some time to open an .mtz file as the map needs to be calculated, however I have waited more than 45 minutes and ChimeraX keeps unresponsive... I am using Chimera 1.5 and I installed the (hopefully compatible) version of Clipper 0.19.0 Did anyone faced the same problem? Let me know if you have a fix or trick ;) Thanks for any feedback in advance, André ____________________ [cid:image001.png@01D9272E.120B2740]

2 2

Movie clipping planes in chimera x
by Greg Martin 13 Jan '23

13 Jan '23

Hi, I’m trying to make a movie where I highlight different parts of a large complex. For one scene, I’m trying to interpolate between a zoomed out view of the whole complex (view p1), and then a zoomed in view of an interface (view p2), which shows a series of interactions. What I want is a smooth transition of both the view and clipping plane from p1 to p2. However, when I give the command: view p1 p2 100 it interpolates the two positions/zooms fine, in 100 frames, but then after the movement adjusts the clipping plane all at once. Is there a way to have the plane adjusted smoothly during transition between p1 and p2? I’ve also tried fly, but this disregards clipping planes altogether. Views are saved with view name p1 view name p2 Thanks in advance, Greg -- Gregory Martin, PhD. Staff Scientist Lab of Andrew Ward Department of Integrative Structural & Computational Biology The Scripps Research Institute La Jolla, CA 92037

3 3

Inquiry: Map sequence conservation onto a protein structure
by Gomez Barillas, Andrea 13 Jan '23

13 Jan '23

Dear ChimeraX developers, I am trying to map sequence conservation onto a protein structure. I am using ChimeraX version (version 1.4 (2022-06-03). For this purpose, I was trying to use a tutorial from 2014 for Chimera for Mapping Sequence Conservation onto Structures (Showing Sequence Conservation in Chimera (ucsf.edu)<https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html>). It seems that some the tools mentioned in this tutorial are no longer available, or maybe work differently. Specifically, the tutorial's "Case 4" (calculating values outside of Chimera but showing them in Chimera) has you set an attribute, and then render/color the structure based on the attribute. The Tools > Structure Analysis > Define attribute mentioned in the tutorial is no longer available. I was as able to assign values directly to structure residues in a text file and read it in using the command defattr instead. The next step would be to use the tool Render by Attribute for coloring but I cannot find this option anymore. Is there a different command I can use for this step, or a new functionality built into ChimeraX I could use for my purpose of mapping sequence conservation onto the structure? One relevant point is that I already have my sequence identify values calculated from another program, and I want to import those values. Thank you in advance for your help, Andrea Showing Sequence Conservation in Chimera<https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html> Example 2B Chimera session: ConSurf-1hd2-chimera19.py [show this last!] (result of submitting 1hd2 to the ConSurf server and choosing to show results in Chimera; alignment has 150 sequences including that of the query, 1hd2) . Given a protein structure, the ConSurf server estimates the evolutionary conservation of amino acid positions based on the phylogenetic relations between homologous ... www.cgl.ucsf.edu

2 1

Inquiry: Map sequence conservation onto a protein structure
by Gomez Barillas, Andrea 13 Jan '23

13 Jan '23

Dear ChimeraX developers, I am trying to map sequence conservation onto a protein structure. I am using ChimeraX version (version 1.4 (2022-06-03). For this purpose, I was trying to use a tutorial from 2014 for Chimera for Mapping Sequence Conservation onto Structures (Showing Sequence Conservation in Chimera (ucsf.edu)<https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html>). It seems that some the tools mentioned in this tutorial are no longer available, or maybe work differently. Specifically, the tutorial's "Case 4" (calculating values outside of Chimera but showing them in Chimera) has you set an attribute, and then render/color the structure based on the attribute. The Tools > Structure Analysis > Define attribute mentioned in the tutorial is no longer available. I was as able to assign values directly to structure residues in a text file and read it in using the command defattr instead. The next step would be to use the tool Render by Attribute for coloring but I cannot find this option anymore. Is there a different command I can use for this step, or a new functionality built into ChimeraX I could use for my purpose of mapping sequence conservation onto the structure? One relevant point is that I already have my sequence identify values calculated from another program, and I want to import those values. Thank you in advance for your help, Andrea

1 0

ChimeraX Log window remains blank
by Scott White 13 Jan '23

13 Jan '23

Hi, Sorry if this is a dumb question, but recently when starting ChimeraX the Log window is not on Display. Opening the Log window (Tools> log) opens it as a separate window, and whether docked or free-floating the Log window remains blank no matter what I do. Even just "open 1nov" on the command line will download and open the PDB entry 1NOV, but no text appears in the Log window. I've tried a fresh install of ChimeraX 1.5 to no avail. I've tried opening an older version of ChimeraX, which despite having worked countless times before, now shows the same behaviour regarding the Log window as my abberant ChimeraX 1.5. I've tried rebooting the computer - no fix. I've tried "log clear" and "log show". It's a Windows 10, university owned PC. I don't have the issue on other computers. Is it a software clash? Thanks in advance for any help or advice. Scott _______________________________________ Dr Scott A. White SFHEA School of Biosciences, Room T716 University of Birmingham, B15 2TT E: s.a.white(a)bham.ac.uk<mailto:s.a.white@bham.ac.uk> T: +44-(0)121-414-7534 Office Hours Generally Tues 10am - 11am, Wed 3 pm - 4 pm Please contact me for an appointment. ______________________________________

2 2

Changing MD trajectory default frame rate
by Visvaldas K. 12 Jan '23

12 Jan '23

Dear all, Is there a way to change frame rate when I hit that red "record" button when playing MD trajectory? I could do "movie record", but then it becomes interactive (I hit triangle "play", and then "movie encode /Users/visvaldas/Desktop/movie.mp4 framerate 5"), so inadvertently can record some undesired frames. Of course I probably can reduce framerate using external programs, but how to that non-interactively in ChimeraX? Best regards, Vis

3 3

How to integrate ChimeraX with phenix
by Suresh K 12 Jan '23

12 Jan '23

Hi, We integrate pymol and coot with phenix but unable to integrate ChimeraX. In internet we found that you using ChimeraX with phenix. Could you help us with way to integrate ChimeraX with phenix? Thanks and regards, Suresh K

2 1

Select complelementary of range
by Pranav Shah 12 Jan '23

12 Jan '23

Hi Team, How do I go about selecting everything that does NOT lie between a given range of residues? For instance I want to select everything that is NOT r.410420. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 1

Smooth MD trajectory during moovie making
by Enrico Martinez 12 Jan '23

12 Jan '23

Dear Chimera-X users! I am trying to make a movie using MD trajectory (in multi-model pdb file) by means of the Molecular Dynamics Viewer (v 1.2). is it possible to introduce smooth effects on the snapshots transition in the same way like it could be done via V*D ? Many thanks in advance Cheers Enrico

3 10

Trouble displaying missing structure dashed lines in cartoon mode
by Jonathan Jih 11 Jan '23

11 Jan '23

Hello ChimeraX team, I'm having quite a bit of trouble displaying missing structure dashed lines when my models are shown in cartoon mode. This is despite the "missing structure" sub-model box being ticked in the model panel. I recall finding a workaround for this nearly a year ago on ChimeraX 1.3, but I cannot for the life of me remember how I did so (now using ChimeraX 1.5). Interestingly, old sessions that I saved in 1.3 and 1.4 with whatever workaround I applied back then display the missing structure dashed lines properly in 1.5. However, opening the exact same pdb files from those older sessions in 1.5 yields no dashed lines in cartoon mode. Full atom mode appears fine. I also found this thread ( https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html) which seems to indicate the issue has been fixed, so not sure if I'm just doing something wrong? My OS is Windows 11 if that matters. Thanks in advance for the help! Jonathan -- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles

2 6

Saving .mrc volume as coordinates
by Joshua Jenkins 10 Jan '23

10 Jan '23

Hi, I've segmented a tomogram using EMAN2 neural network workflow. I then use the segger function to extract regions of interest within the segmented volume, and save these to .mrc. I wondered if there is a way in chimera, or chimeraX, to convert/extract/save the .mrc volume as a simple 3D coordinates file (txt or tbl)? Best wishes, Josh

3 2

Morph movie saving from a script file
by Pranav Shah 09 Jan '23

09 Jan '23

Hi Team, Would there be a way to record a morph between two structures using the command line? Currently, I am clicking the play and record buttons from the GUI in quick succession to achieve this. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

3 2

Re: [chimerax-users] [Chimera-users] Stereo glasses
by Jonathan Sheehan 06 Jan '23

06 Jan '23

I'm always on the lookout for new options for 3D stereo display hardware (Chimera or Chimerax). I just saw this Asus system with glasses-free stereo, using eye-tracking cameras and a lenticular screen. It looks to me like a premium OLED laptop targeted to gamers and CAD designers. I'm unfamiliar with Asus Spatial Vision and Acer SpatialLabs, but one reviewer said that it works with multiple people viewing it- I'm slightly sceptical. :-) https://arstechnica.com/gadgets/2023/01/asus-new-16-inch-workstation-laptop… Tom, you suggested that VR headsets were the best option a few years ago. What are your thoughts about this release? (Replies from non-Tom individuals are also welcomed.) Thanks! -Jonathan On Thu, Jun 13, 2019 at 10:32 PM Jonathan Sheehan <jonathan.sheehan(a)gmail.com> wrote: > > Thanks for the information, Tom- I was hoping somebody had better > news. It sounds like we're in a dead zone between the epochs of stereo > glasses and VR headsets. > > I suppose I'll have to start looking into VR systems. > > Thanks, > -Jonathan > > > On Mon, Jun 10, 2019 at 1:19 PM Tom Goddard <goddard(a)sonic.net> wrote: > > > > Hi Jonathan, > > > > Nvidia was the main distributor of 3D active LCD stereo glasses, and they dropped support for their Nvidia 3D Vision glasses and emitters in April 2019 as described here > > > > https://www.ghacks.net/2019/03/11/nvidia-3d-vision-end-of-support/ > > > > https://nvidia.custhelp.com/app/answers/detail/a_id/4781 > > > > Nvidia graphics driver released after April 2019 won't work with these glasses. You can continue to use Nvidia 3D Vision with old graphics drivers, maybe that is the best option. > > > > The LCD active stereo glasses technology appears to be nearly dead. If you try to use it be prepared for problems getting it to work and to pay a lot of money. We have been using active stereo LCD with a stereo projector for many decades. We use it infrequently now, instead using virtual reality headsets with our ChimeraX software. Virtual reality headsets give better immersion but don't yet easily handle having a half-dozen people viewing the same scene in the same room (would require 6 separate computers driving the 6 headsets). > > > > Here are details on the old LCD glasses projector system we are have which is working: > > > > 10 pairs of RealD CE4 and CE4s stereo glasses ($280 each) > > > > http://www.colorlinkjapan.com/brand/product/ce4s.html > > > > A Stereo Graphics EXXR extra long range emitter ($780) > > > > http://www.colorlinkjapan.com/brand/product/exxr-emitter.html > > > > A Christie Mirage S+4K projector circa 2006, (1440 x 1050 resolution), no longer in production > > > > https://www.projectorcentral.com/Christie-Mirage_S+4K.htm > > > > An Nvidia Quadro P6000 graphics card ($3700) > > > > https://www.amazon.com/PNY-Quadro-P6000-Graphic-Card-x/dp/B01M0S2FKR > > > > with a stereo emitter bracket > > > > http://www8.hp.com/h20195/v2/GetPDF.aspx/c04658472.pdf > > > > This system breaks about once a year after graphics driver updates, the fix usually being to set the projector to be either the primary display or secondary display (depends on graphics driver version). Also the glasses fail at maybe the rate of 1 out of 10 pairs per year. > > > > Tom > > > > > > On Jun 7, 2019, at 8:30 AM, Jonathan Sheehan <jonathan.sheehan(a)gmail.com> wrote: > > > > Hi all, > > > > What stereo setup are people recommending these days? It seems that > > NVIDIA has discontinued the 3D Vision 2 goggles+emitter. Is there > > something else that is available and works well? > > > > Thanks for any advice! > > -Jonathan > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

3 3

Coloring according to the secondary structure
by Enrico Martinez 06 Jan '23

06 Jan '23

Dear ChimeraX users! I need to color cartoon representation of a protein according to its secondary structure (e.g. to color helix in red, b-stands in blue and coils in violet etc). I have already seen a built-in plugin in UCSF Chimera (but not in Chimera-X) that could do this job! Could you suggest commands that would be useful in Chimera-X? Many thanks in advance Cheers Enrico

2 2

Unable to find the distance between centroid & any other atom in chimeraX
by Prathvi Singh 05 Jan '23

05 Jan '23

Hi Elaine, I declared the centroid of a tyrosine residue's ring by first selecting its ring members & then using the command: *define centroid sel radius 0.5* Next, when I try to find the distance between the centroid, I get an error whose screenshot I have attached with the email. The command that I am using to find the distance are: *dist sel* dist #1.1 #1.2 (here the distance is being calculated between two centroids) Please help - Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

Unfocus in chimeraX using command line
by Prathvi Singh 05 Jan '23

05 Jan '23

Hi Elaine, Is there any equivalent of the "~focus" command in chimeraX? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Re: [chimerax-users] Remote control / Threading in ChimeraX
by Albert Smith-Penzel 05 Jan '23

05 Jan '23

Hi Tom, Thanks for the explanation. I’ll have to think and investigate a bit to see if my thread use is causing some problems elsewhere. Most of our code has been pretty stable, but there are still a few occasional glitches that I haven’t completely understood. Anyway, session.ui.thread_safe is perfect for resolving the issues we have with adding the surface to the empty session and running commands remotely. The curl solution also works; I had something like this implemented previously for some other purposes, but my own preference is to send commands/data directly rather than writing out a file to be read on the other end. Thanks again! Cheers, Albert ––––––––––––––––––––––––––––––––––– Albert Smith-Penzel, Ph.D. DFG Project Leader Institute for Medical Physics and Biophysics Leipzig University 04107 Leipzig, Germany E-mail: albert.smith-penzel(a)uni-leipzig.de <mailto:albert.smith-penzel@medizin.uni-leipzig.de> > On 4. Jan 2023, at 21:41, Tom Goddard <goddard(a)sonic.net> wrote: > > WARNUNG: Diese E-Mail kam von außerhalb der Organisation. Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge, es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist. > > WARNUNG: Diese E-Mail kam von außerhalb der Organisation. Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge, es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist. > > Hi Albert, > > ChimeraX is not designed to run arbitrary Python code multithreaded. There are many reasons. First the Qt window toolkit is not thread safe -- all Qt GUI calls have to be done in the main thread. Violating that often results in a crash. But even without the GUI, imagine the main thread is looping over the list of open models while a second thread decides to add a model to that list -- this could break the looping thread many ways. Python has a global interpreter lock which means it only can run one thread at a time. Still if you pause one thread and then change the state of the ChimeraX session in another thread, the first thread could throw errors in countless ways when it resumes at an arbitrary point in the code with the data structures changed. In general very little software is thread safe because it is very difficult to implement. Usually that is only done by making threads not modify any data structures used by other threads. > > Here are two solutions. 1) Have your listener thread run the Python code it receives in the main thread rather than the listener thread. There is a ChimeraX function that takes a function and queues it to be run in the main thread. > > session.ui.thread_safe(func, args...) > > Here is the code if you want to see how it works > > https://github.com/RBVI/ChimeraX/blob/2e33222fabb48edec76df6e82a10efedb54a8… > > A second solution is to use the ChimeraX remotecontrol communication for everything. That mechanism just runs ChimeraX commands, but you can run Python code using it by just sending the command "open script27.py" where you put the Python you want to run in a file script27.py. > > Tom > > >> On Jan 4, 2023, at 4:40 AM, Albert Smith-Penzel via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hello, >> >> I am working on a Python project that uses ChimeraX (currently running 1.5 to interactively view dynamics data by mapping it onto a molecule. All the figures/movies in this paper, https://www.nature.com/articles/s41467-021-27417-y <https://www.nature.com/articles/s41467-021-27417-y>, were made possible by Chimera! Also thanks to Tom Goddard for explaining to me how some of those figures could be made awhile ago (https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo… <https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo…> ). >> >> So we’re controlling ChimeraX remotely; we launch a session and then can send commands from Python over to Chimera and edit images from within our python code (while still allowing us to interact via the ChimeraX interface). The basic way this works is as follows >> >> launch chimeraX from our code, including a short python script >> python script imports our libraries, launches “cmxr” (chimeraX remote) >> cmxr uses multiprocessing.connection.Listener to listen for commands/data coming from Client in our python code >> !!!The Listener runs in a thread (threading.Thread) so that we continue to be able to interact normally with ChimeraX (launching the Listener without using a thread freezes ChimeraX while waiting for commands, rendering it unusable) >> Then, we just tell it to run some function(s) that we’ve imported into ChimeraX, and provide some data, atom ids, etc. over the Client/Listener connection >> >> There are a few things that I can’t figure how to make work via this process. We’ve had a few long-standing workarounds, but I’ve always been a little disturbed that we can’t get this all to work from python alone. At the moment, when we launch ChimeraX, we also enable remote control via curl, and some commands are then sent that way (remotecontrol rest start port XXXX) >> >> In particular, if I want to send commands that would normally be executed at ChimeraX’s command line, in principle I should be able to use chimerax.core.commands.run. If I execute “run” from a simple python script, everything works, but if I run it from within a thread (as required by our Listener setup), then ChimeraX freezes. So, we send these commands via curl on the remotecontrol instead. >> >> Second, is there a right way to open models/surfaces from the ChimeraX python shell? At the moment, we also open pdbs via curl commands. For pdbs, maybe I just don’t know the right python command. However, I am re-implementing spherical harmonics referenced above. Once I have prepared the surface (“s”), if I add it to session.models, it crashes chimeraX if it is being added within the listener thread, and if there are no models already open. If another model is already open, then it works just fine, and if I load the same modules/execute the same commands from within the python shell provided in ChimeraX, it also works (regardless of other models being open). It seems like maybe ChimeraX isn’t able to fully initialize the session from within a thread. >> >> I’ve grouped these problems together because I guess mainly they have to do with being unable to do some actions from within threads, and if there’s an explanation/workaround for dealing with that. >> >> Thanks for your help! >> >> Cheers, >> Albert >> >> >> >> ––––––––––––––––––––––––––––––––––– >> Albert Smith-Penzel, Ph.D. >> DFG Project Leader >> Institute for Medical Physics and Biophysics >> Leipzig University >> 04107 Leipzig, Germany >> E-mail: albert.smith-penzel(a)uni-leipzig.de <mailto:albert.smith-penzel@medizin.uni-leipzig.de> >> >> >> >> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >

1 0

Remote control / Threading in ChimeraX
by Albert Smith-Penzel 04 Jan '23

04 Jan '23

Hello, I am working on a Python project that uses ChimeraX (currently running 1.5 to interactively view dynamics data by mapping it onto a molecule. All the figures/movies in this paper, https://www.nature.com/articles/s41467-021-27417-y <https://www.nature.com/articles/s41467-021-27417-y>, were made possible by Chimera! Also thanks to Tom Goddard for explaining to me how some of those figures could be made awhile ago (https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo… <https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo…> ). So we’re controlling ChimeraX remotely; we launch a session and then can send commands from Python over to Chimera and edit images from within our python code (while still allowing us to interact via the ChimeraX interface). The basic way this works is as follows launch chimeraX from our code, including a short python script python script imports our libraries, launches “cmxr” (chimeraX remote) cmxr uses multiprocessing.connection.Listener to listen for commands/data coming from Client in our python code !!!The Listener runs in a thread (threading.Thread) so that we continue to be able to interact normally with ChimeraX (launching the Listener without using a thread freezes ChimeraX while waiting for commands, rendering it unusable) Then, we just tell it to run some function(s) that we’ve imported into ChimeraX, and provide some data, atom ids, etc. over the Client/Listener connection There are a few things that I can’t figure how to make work via this process. We’ve had a few long-standing workarounds, but I’ve always been a little disturbed that we can’t get this all to work from python alone. At the moment, when we launch ChimeraX, we also enable remote control via curl, and some commands are then sent that way (remotecontrol rest start port XXXX) In particular, if I want to send commands that would normally be executed at ChimeraX’s command line, in principle I should be able to use chimerax.core.commands.run. If I execute “run” from a simple python script, everything works, but if I run it from within a thread (as required by our Listener setup), then ChimeraX freezes. So, we send these commands via curl on the remotecontrol instead. Second, is there a right way to open models/surfaces from the ChimeraX python shell? At the moment, we also open pdbs via curl commands. For pdbs, maybe I just don’t know the right python command. However, I am re-implementing spherical harmonics referenced above. Once I have prepared the surface (“s”), if I add it to session.models, it crashes chimeraX if it is being added within the listener thread, and if there are no models already open. If another model is already open, then it works just fine, and if I load the same modules/execute the same commands from within the python shell provided in ChimeraX, it also works (regardless of other models being open). It seems like maybe ChimeraX isn’t able to fully initialize the session from within a thread. I’ve grouped these problems together because I guess mainly they have to do with being unable to do some actions from within threads, and if there’s an explanation/workaround for dealing with that. Thanks for your help! Cheers, Albert ––––––––––––––––––––––––––––––––––– Albert Smith-Penzel, Ph.D. DFG Project Leader Institute for Medical Physics and Biophysics Leipzig University 04107 Leipzig, Germany E-mail: albert.smith-penzel(a)uni-leipzig.de <mailto:albert.smith-penzel@medizin.uni-leipzig.de>

2 1

How to get the average pTM scores from an Alphafold multimer prediction
by Chen, Henry 04 Jan '23

04 Jan '23

Dear Chimarax devs/users, I'm using ChimeraX Alphafold tool to do a multimer structure prediction. I was wondering how can I determine the average pTM score for each structure prediction? I get PAE.png and plddt.png file, but not a text file or anything that tells me the average pTM. (I was hoping the ranking file would give the average score but it does not) The models come with the pdb file as well as the scores.json files, but again I don't see anything that tells me the average pTM for the structure. Clearly the pTM per residue scores are saved in my pdb file, is there a command to average them all up? Thanks! Henry

3 3

Capping termini ends
by Pranav Shah 04 Jan '23

04 Jan '23

Hi Team, Happy New Year! I look forward to all new developments you guys have in store for ChimeraX in 2023. Speaking of, is it possible to somehow display the ends of a protein termini with a spheres or something? I have certain view of my model in which the termini get partially obscured so it would be nice to prominently have them displayed in some manner... Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 2

Extracting the color name/hex code of a colored ribbon
by Theodora Bruun 23 Dec '22

23 Dec '22

Hello, I am just curious if there is a command for listing the current color name or hex code of an atom/ribbon that is colored in ChimeraX. For example, I open a previously colored structure and like the color of chain A and now I would like to use that same color and maybe apply to other chains in the structure. Is there a way other than just eye-balling it? Best, Theo

2 2

using atomic coordinates to measure volume
by Harrison, Daniel P 23 Dec '22

23 Dec '22

Hello: I would like to calculate the maximum volume made by selection of atoms in a given structure. Can you provide guidance on how to go about this process? It seems like there should be a simple procedure in ChimeraX but I have failed to locate it. My specific problem: I would like to calculate the volume of the void created by ice under various conditions so that my physical chemistry students can quantify and visually understand partial molal volume non-ideality. I would greatly appreciate any assistance you can provide. Dan

4 9

PDB upload TER card error
by HONG ZHAN 21 Dec '22

21 Dec '22

Dear all, I saved my protein coordinates in ChimeraX as pdb (it has multiple chains), however, when I was doing upload on the PDB, it shows this error, I am using ChimeraX 1.5rc202211091945 on Linux ubuntu 22.04 LTS. Coordinates issues: ERROR: There is no TER card at the end of polymer chain 'X'. All polymer chains should have a TER card at the end of each chain. Please add TER card and restart again. Many thanks! Hong

3 4

phosphorylation
by Fabian Glaser 21 Dec '22

21 Dec '22

Dear experts, I would like to mutate a ser and a thr to phospo-serine and phospho-threonine, what is the easiest way to do it? Thanks a lot, fabian -------------------------- Fabian Glaser, PhD Structural and Computational Biology Unit The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel

2 2

ChimeraX linux binary problems
by Добромир Калчевски 19 Dec '22

19 Dec '22

Hello, I have installed Chimera linux from binary and everything was OK from the get-go. ChimeraX however, fails to start for library dependencies. As I understand the source depends on around 50 packages. I don't know (and I can find no indication on internet) how many libraries am I missing, but I'm also kind of limited in terms of disk space / linux size and my distro does not have a very nice package manager - Clear Linux (it installs entire bundles of similar packages, instead of single packages and once removed the disk size does not go down). Is it possible to make a ChimeraX linux binary which is as easy to run as the Chimera linux binary - universal for all distributions and including all necessary dependencies ? Best Regards, Dobromir

3 2

ChimeraX linux binaries too inconvenient
by Добромир Калчевски 19 Dec '22

19 Dec '22

Hello, Can you provide ChimeraX linux binary as useful as the Chimera linux binary ? - without all of the dependencies being outside of the package. Also, can the package simply install in the /home/username/.local/CHIMERAX... directory, just as Chimera or in a similar path ? (makes uninstallation easy, saves disk space). Many distros do not have package managers as convenient as those of Red Hat or Debian. For example I use Clear Linux (for the performance) and the dependencies are not even in the package manager. There is also no explicit list of dependencies and according to your web site there are about 50 of them, anyway. Basically whatever I do there is always a missing library I cannot easily find / compile / have no time for it, etc., so ChimeraX for me is out of reach. I tried Chimera from the linux binary and it ran just fine, but it lacks something in the GUI, which ChimeraX does not. The visualization settings fields can be scrolled up and down, so if I load let's say 12 molecular orbitals - I can easily hide / show the ones I need, instead of having them all on the screen and using the "Data set list" to manually show / hide each one. Best Regards, Dobromir

2 1

Re: [chimerax-users] color
by Elaine Meng 19 Dec '22

19 Dec '22

Hi Guan, To ensure you get an aswer, we recommend sending ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here). You can click the square "color well" for each model listed in the Model Panel to open your system color browser, which will show the code. See also this page for the names of the initial model colors... <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html> ...and then this page which shows the codes for the names <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#builtin> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 18, 2022, at 5:46 PM, Guan, Lan <Lan.Guan(a)ttuhsc.edu> wrote: > > Dear Elaine: > I like the color usage in chimeraX. I wonder if we could know the color code for the color auto-painted when we open it. > Thanks, > Lan

1 0

Aligning atoms
by Noriega, Heather 18 Dec '22

18 Dec '22

Hello, I have a question about the alignment. Is there a way to get the glycans to align, one has a PEG docked to it and I was hoping to place the PEG and delete the glycan #2. I am unsure if it is possible. It gives me an error because the number of atoms are not equal. I attached the session. Thanks in advance. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

2 2

ChimeraX Alphafold Multiple jobs
by Rayees Mattoo 16 Dec '22

16 Dec '22

Hi, I was wondering if I could run multiple Alphafold jobs via ChimeraX using my Colab Pro. Also, very often Alphafold job submitted gets disconnected after some time (15 min or so) without completing the job, any solution to that? Best Rayees

2 1

help please - electrostatic potential units and fit in map correlation
by Leslie Bridges 15 Dec '22

15 Dec '22

Dear All What are the units for electrostatic potential in ChimeraX? Is it possible to say whether the fit in map correlation represents a "good" fit for the atoms (e.g. if my correlations are above 0.75, can I conclude all the fits are good?) All the best, thanks Dr Leslie R Bridges Hon Snr Lecturer in Neuropathology St George's University of London

2 2

no conformation comparison category in ChimeraX1.5 and ChimeraX-daily
by Jiang Xu 14 Dec '22

14 Dec '22

Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions? Thank you, Best, Jiang Xu

3 8

Analysis of docking results
by Luigi Marongiu 14 Dec '22

14 Dec '22

Dear sir or madam, I am new to docking analysis. I obtained a model from SwissDock but there are some commands that do not work on ChimeraX. 1. I can load the molecule, which is composed by 4 homo-chains. I can select one chain (A); how can I delete or hide chains B-D. I can select chain A using select>chain`; is there a way to hide the others? 2. The model (saved in the file clusters.dock4.pdb) shows several ligands: [cid:c289e47f-ca49-4f27-9ad6-acef069f976e][cid:728d8f47-8cfb-445c-9476-ebb8a9d54ef9] Is there a way to show only the ligands with the highest docking score? 3. the tools>binding analysis>ViewDockX` says that "No suitable models found for ViewDockX". But is not this the "clusters.dock4.pdb"? How can I load the model into ChimeraX? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

2 2

Morphing structures with ligands (glycans)
by Nebojsa Bogdanovic 13 Dec '22

13 Dec '22

Hello, I am looking into morphing several protein structures that contain glycans important form the function. The structures are all the same protein, in different states so the sequence info is good. Is there any function that retains the glycans visible once the command* morph #1-5 same true* produces a new model? I can just show them from origin structures but this does not look the best. Thank you and best regards Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

2 3

Primer in chimeraX
by Luigi Marongiu 13 Dec '22

13 Dec '22

Dear sir/madam, I am new in the use of ChimeraX (for Linux). I would like to use ChimeraX for two jobs: 1. calculate the volume of a molecule (namley: maltose). I have uploaded the pdb of the molecule, selected the tools>volume>volume viewer, but I don't see any actual output. How can I get the value for the volume of this molecule? 2. show the docking of a ligand. I have obtained a docking model with swissdock, which I have loaded; how can I show the bonds between target and ligand? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

2 2

Isolde loading issue
by Dmitry Semchonok 13 Dec '22

13 Dec '22

Dear colleagues, Is there any alternative for ISOLDE installation? >From ChimeraX 1.5 it doesn't load on my Mac - it stops. Kind regards, Dmitry

2 1

using chimerx on unix
by Barak Yariv 11 Dec '22

11 Dec '22

Dear Chimera team, I'm from the ConSurf webservere https://consurf.tau.ac.il/consurf_index.php We have been working with chimera for many years and we want to update to chimerax. We have trouble installing chimerax on our unix system. We did manage to install it on our local computers in windows but when installing on unix we get an error: missing library PyQT6 Can you help us? Barak

5 5

Specify unmodelled residues
by Jaremko, Matt Joseph 09 Dec '22

09 Dec '22

Hello ChimeraX Team, What information in the PDB file specifies the unmodelled residues (in black box)?: [cid:image001.png@01D90BDD.3983D7C0] I’d like to have this information in my own PDB files. Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko(a)merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

2 3

Perframe and distance
by Simonson, Benjamin Thomas 09 Dec '22

09 Dec '22

Hello! I am trying to measure the distance between two atoms in my trajectory in every 10th frame. My approach was to use the perframe command paired with the distance command. Below was my attempt: perframe "distance /D:15@NH1 /B:42@OD1;distance save dist$1.txt;~distance /D:15@NH1 /B:42@OD1" interval 10 However, it instead simply outputs the distance of the currently displayed frame over and over again. Any help would be appreciated! Ben ......................................... Benjamin Simonson MCIBS PhD Candidate Penn State University

2 2

How do I NOT "show disjoint surfaces"?
by Sungwook Woo 06 Dec '22

06 Dec '22

Hi I've been using UCSF Chimera and recently encountered ChimeraX -- I really like the modern look and feel! One feature I cannot find in the X version, though, is editing the attributes of an MSMS surface model, where I was able to disable (make 'false') the 'show disjoint surfaces' setting, in the original version. Most of the time dealing with models I don't need it, but sometimes I like to 3D print molecular models to really get a 'grip' on the models, and that feature of not showing disjoint surfaces has been useful to remove internal 'bubbles', which I learned about through this posting: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html . If internal bubbles are not removed, they waste printing material and increase printing time. Is there any way to disable showing disjoint surfaces, or otherwise achieve a similar goal in the X version? Thanks! Best, Sungwook

2 3

swapna in ChimeraX
by Shahid, Taha (Dr.) 01 Dec '22

01 Dec '22

Hi all, Does ChimeraX have swapna functionality? I can find the swapaa command but not swapna. Is there another way to achieve its effects? If not, I think it would be useful addition. Kind regards, Taha

2 2

ChimeraX 1.5 release not visible on website
by Shahid, Taha (Dr.) 01 Dec '22

01 Dec '22

Dear ChimeraX Team, I would like to update, but can't see either the ChimeraX 1.5 release candidate or production release on the USCF ChimeraX download page (only ChimeraX 1.4 and the daily build are available). Many thanks, Taha Dr Taha Shahid Postdoctoral Research Associate Leicester Institute of Structural and Chemical Biology Henry Wellcome Building | University Road | Leicester | LE1 7RH | UK e: ts387(a)leicester.ac.uk<mailto:XXXX@leicester.ac.uk> w: https://www2.le.ac.uk/institutes/liscb Follow us on Twitter<https://twitter.com/leicstructbio> [cid:D64185E6-9A9E-47F3-98A6-A33685D0B03A]

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chimerax freezing
by HOH Francois 30 Nov '22

30 Nov '22

Hi I had to change my hard drive and reinstall everything. When launching chimerax, it starts but freeze. Have to kill it. OS ubuntu 22.04. No special message in the log when using chimerax --debug Any idea ? Thank's FH ________________________________________ Hoh François, PhD Research Engineer Team BSME: Biologie structurale multi-échelles Centre de biochimie Structurale de Montpellier CNRS UMR 5048 - UM - INSERM U 1054 29 rue de Navacelles 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr Tel: (33) 04 67 41 77 29

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ChimeraX 1.5 release
by Elaine Meng 30 Nov '22

30 Nov '22

UCSF ChimeraX version 1.5 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/ Updates since version 1.4 (Jun 2022) include: - AlphaFold search/fetch uses database v4 (fixes ~4% of v3 entries) - show AlphaFold residue-residue errors (PAE) with colored lines - Axes/Planes/Centroids tool to define objects, use in measurements - transform surface models (scale, shift, rotate) - add hydrogens GUI - calculate and assign charges, including for nonstandard residues - dock prep command - renumber residues, change chain IDs - crosseye and walleye stereo - cleaner close session (reverts more settings) - UniProt sequence fetch updated to work with UniProtKB's new API - DICOM browser shows patient-study-series hierarchy in medical image data For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

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Ribbon coloring
by F.Xavier Gomis-Rüth 30 Nov '22

30 Nov '22

Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier --

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Re: [chimerax-users] Placing a ligand in a protein structure from PDB
by Elaine Meng 30 Nov '22

30 Nov '22

> On Nov 30, 2022, at 7:41 AM, Amit Kugler <amit.kugler(a)kemi.uu.se> wrote: > > Hej Elaine, > > I found you on the ChimeraX website, and I have a question. > > I have a PDB file of my protein, but not showing a ligand. > > I am wondering if there a way I can add a ligand to the active site of the protein and write out the new PDB file on ChimeraX? > > Best regards, > Amit > Hi Amit, We recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) to make it more likely you get a response. Not sure what you mean by add a ligand. Sure you can open a file of a ligand and open a file of the protein, and then combine them into one model, and then save. But probably you want to put the ligand in some sensible position, which could be done by moving it individually by hand, or by using some docking program. ChimeraX does not do docking. You would have to use some docking program (Glide, DOCK, Gold, Autodock, Autodock Vina, etc.) and then open the output from that docking program in ChimeraX. Moving models by hand, see this previous post: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2017-November/000157.html> There is a "combine" command to combine the two separate models into a new single model, and "save" (or menu File... Save) to save the resulting combined model as a PDB file. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> Or maybe you don't have a structure of the ligand. If there is some other PDB structure that contains it you can open that structure and delete all the rest of the atoms, or if you can find it in PubChem you can try fetching by PubChem ID into ChimeraX, e.g. command open pubchem:12120 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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font size on the task bar
by Krishnan Raman 29 Nov '22

29 Nov '22

Is it possible to change the font size(larger) on the first line of the of the taskbar file…edit select etc… For viewing at from a distance on a big screen? Thanks Krish Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 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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tile and 2dlabels
by Krishnan Raman 29 Nov '22

29 Nov '22

Hi guys, Trying to show multiple binding protein sites on a large protein. Could successfully make footprints on the protein in different colors on the protein for different binding sites. Was trying to include binding constants as 2dlabels with each model protein. How to associate these labels with models to tile them along with the models? Combining the models (combine on (2dlabel model and structure models did not work.) Trying to use tile command with the 2dlabels to show IC50’s with the individual proteins. What is best way to do this… May be use the label command? Thanks Krish Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 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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chimerax hbonds batch analysis
by Visvaldas K. 28 Nov '22

28 Nov '22

Dear ChimeraX wizards, I was trying to generate hbond analysis via nogui, by issuing "chimerax --nogui --script "myscript.cxc", where in the script I put the following commands: open /Users/visvaldas/temp0000.pdbselect /B hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true quit However, something is wrong with hbonds line since I am getting this error:Executing: runscript myscript.cxc Traceback (most recent call last): File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/scripting.py", line 83, in open_python_script code = compile(data, stream.name, 'exec') File "myscript.cxc", line 4 hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true ^ SyntaxError: invalid syntax What I am doing wrong? (Also, when using GUI, the hbonds line was much longer, so I deleted those reveal, color, etc entities to make it more relevant to batch. (The "long" line hbonds sel saveFile /Users/visvaldas/temp00.hbonds color #fffb00 dashes 5 restrict cross reveal true retainCurrent truefrom the GUI does not work either) Best wishes, Visvaldas

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Cα distance per residue in alignment
by Michael Habeck 28 Nov '22

28 Nov '22

Dear ChimeraX forum, I'm interested in getting the distance between Cα for all residues in an alignment. I've noticed that the Cα RMSD values in the txt file obtained from the header of the sequence alignment created by matchmaker via sequence header rmsd save are different from the distances measured using the rmsd or distance command. The Cα distance measured is approx. 41% higher across the entire alignment than in the saved output. When selecting a pair of aligned residues from the alignment viewer, the distance shown does not match the one in the output file but the distance measurement. I've attached a file with the respective distances for the alignment of chains A in 3c4f and 3gqi as an example. Not sure if this is a misunderstanding from my side or a bug, yet I'd greatly appreciate a clarification of the differences. With thanks in advance and best regards, Michael

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Align with specific atoms (but against all other molecules)
by Kim, Doo Nam 28 Nov '22

28 Nov '22

Hi, I’ve used align #2/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N align #3/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N align #4/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N … to align #2 molecule against #1 molecule with backbone atoms #3 molecule against #1 molecule with backbone atoms #4 molecule against #1 molecule with backbone atoms etc… However, how can I align all rest molecules (e.g. #2~#100) against #1 molecule with backbone atoms at once in chimeraX? I’ve used align all toAtoms #1 matchAtomNames true align all toAtoms #1 matchNumbering true to align all molecules to #1 molecule at once. However, with this command, I cannot specify to use backbone atoms (e.g. CA,O,C,N) only when aligning. I think that there should a 1 line command that aligns all molecules with specific atoms only or there is chimeraX equivalent python script as from chimera import runCommand as rc # use 'rc' as shorthand for runCommand from chimera import replyobj # for emitting status messages Best, Doo Nam

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input delay on one computer and only for ChimeraX
by Barbara S Holme 28 Nov '22

28 Nov '22

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Re: [chimerax-users] [Chimera-users] Writesel command in chimeraX
by Elaine Meng 27 Nov '22

27 Nov '22

Hi Prathvi, Please use the chimerax-users(a)cgl.ucsf.edu address to ask ChimeraX questions (instead of chimera-users(a)cgl.ucsf.edu) so that users will not be confused about which program we are discussing. In ChimeraX you can use the "info" command to report the selection to the Log, as detailed in this previous post. <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-July/003963.html> "info" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html> It does not have an option to save a file. Instead you have to save the ChimeraX Log in another step. You can use "log clear" before you use "info" and then "log save" to save to HTML file. "log" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 26, 2022, at 5:04 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > Is the writesel command available in chimeraX because I could not find it in the Actions menu? > If not, then is any equivalent available apart from the command which saves selection as a new PDB file? > > Thanks once again in advance

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how to remove axes?
by Francisco Murphy Pérez 26 Nov '22

26 Nov '22

After loading a mtz file, 3 axes appear in the middle of the screen. How do I remove them? Thanks

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Display sequence alignment from structure alignment
by James H Naismith 25 Nov '22

25 Nov '22

In Chimera I can sort of print out a sequence alignment based on structural superposition. (Match-align) I can make a very nice structural superposition of very unrelated proteins with matchmaker, all I want to do is print out the resulting sequence alignment (where residues are with y A of each other) Any help gratefully received. With best wishes Jim Division of Structural Biology, Roosevelt Drive, Oxford, OX3 7BN james.naismith(a)strubi.ox.ac.uk Pronouns: he, him, his

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Opening .xyz file in ChimeraX
by Carina Luo 23 Nov '22

23 Nov '22

Hello, I am trying to open an .xyz file in ChimeraX. I installed SEQCROW (1.5.9) as prompted, but ChimeraX still says "Opener for format 'XYZ file' is not installed; see log for more info." Here is the output I got when I installed SEQCROW (1.5.9): Downloading bundle SEQCROW-1.5.9-py3-none-any.whl Errors may have occurred when running pip: pip standard error: --- [notice] A new release of pip available: 22.2.2 -> 22.3.1 [notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip --- pip standard output: --- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\user\downloads\seqcrow-1.5.9-py3-none-any.whl Requirement already satisfied: jinja2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (3.1.2) Collecting Send2Trash Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB) Requirement already satisfied: ChimeraX-Core<=1.5,>=1.2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.5rc202210312311) Requirement already satisfied: scipy in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.9.0) Requirement already satisfied: psutil in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (5.9.1) Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax\bin\lib\site-packages (from jinja2->SEQCROW==1.5.9) (2.1.1) Requirement already satisfied: numpy<1.25.0,>=1.18.5 in c:\program files\chimerax\bin\lib\site-packages (from scipy->SEQCROW==1.5.9) (1.23.1) Installing collected packages: Send2Trash, SEQCROW Successfully installed SEQCROW-1.5.9 Send2Trash-1.8.0 Could you please help me figure out what I still need to do in order to successfully open .xyz files in ChimeraX? Sincerely, Carina

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How do you submit a sequence text file to BLAST/Modeller in ChimeraX?
by Ralph Loring 23 Nov '22

23 Nov '22

Hi, When I was using Chimera and wanted to use Modeller, I would go to sequence/Blast, paste in my sequence text file, Blast and then pick homologous structures and then connect to Modeller. Both Blast and Modeller appear to be present in ChimeraX, but I can't see how to enter my text file. Is everything supposed to go to AlphaFold now? Are there any tutorials on how to use Modeller in ChimeraX? Thanks! P.S. Hope you have a Happy Thanksgiving! I'm not planning on doing anything with this until after the holidays, so don't rush in answering. Ralph Lorini Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

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Developing a ChimeraX bundle - accessing programmatically ChimeraX(GUI open) session
by Stylianos Iliadis 23 Nov '22

23 Nov '22

Hello, I would like to develop a small bundle-plugin for automatically annotating residue labels in protein structures. I tried to access ChimeraX via command line when ChimeraX was running (GUI open) with an opened protein structure in order to study the structure objects hierarchy( chain ->residue ->atoms). This would help me understand it better and code accordingly. Unfortunately, I didn’t manage to do so. Could you please suggest me a way, a page or terminal where I could read more about the internal structure of ChimeraX and if possible to programmatically access a session when it’s running in ChimeraX. Kind regards, Stel Iliadis

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suggestion
by Hassan, Sergio (NIH/NIAID) [E] 22 Nov '22

22 Nov '22

Hello, I recently requested via Phil Cruz the 'tile' command, which I learned it was recently introduced. I have been using it successfully. However, there are two points I would like to bring to your attention (I asked Phil to ask you, but not sure he reached out) 1) when a session is saved as .cxs and I quit the program, after opening it again, the most important feature of the 'tile' command (rotations around each own axis) is lost. The tile distribution is still there, but now the entire thing rotates around a common axis. I need to apply 'tile' again to make it work, but this resets all the modifications I made in the saved session (these modifications include those in point 2 below). 2) any chance to add an argument to the 'tile' command so that the default spatial distribution, which assigns a 'distance' between near neighbors, can be adjusted with, say, 'zoom in" or "zoom out" or crowd in/out? I noticed the default puts each panel too far away from its neighbors for my taste, so I need to "move" them to make them look closer to one another. thanks s _____________________________________ Sergio A. Hassan https://bioinformatics.niaid.nih.gov/cmm/ BCBB/NIAID/NIH/DHHS 301 761 7221 (office) 301 741 5579 (mobile)

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Re: [chimerax-users] Export pLDDT scores
by Tom Goddard 22 Nov '22

22 Nov '22

Hi Asmahan, The pLDDT scores for an AlphaFold prediction are in the bfactor column of the PDB atomic model file. Here is an example of lines from such a file where the value 85.53 is the pLDDT for residue 1. ATOM 1 N ASP B 1 -0.818 -36.026 -12.912 1.00 85.53 N ATOM 2 CA ASP B 1 0.545 -35.783 -13.373 1.00 85.53 C ATOM 3 C ASP B 1 0.706 -34.352 -13.882 1.00 85.53 C The bfactor is assigned to every atom. But pLDDT is only assigned for each residue and measures CA position so you might want to look at only the CA lines. $ grep CA ~/Downloads/ChimeraX/AlphaFold/prediction_14/af252_unrelaxed_rank_1_model_2.pdb ATOM 2 CA ASP B 1 0.545 -35.783 -13.373 1.00 85.53 C ATOM 10 CA CYS B 2 1.983 -32.130 -13.721 1.00 95.45 C ATOM 16 CA PRO B 3 3.029 -30.770 -17.151 1.00 93.20 C ATOM 23 CA SER B 4 6.629 -31.094 -18.066 1.00 93.36 C You can also write the values into a ChimeraX attribute file using ChimeraX commands select #1@CA save ~/Desktop/plddt.defattr attrName bfactor models #1 selectedOnly true and that file looks like the following attribute: bfactor recipient: atoms match mode: 1-to-1 /A:1@CA 56.150001525878906 /A:2@CA 53.33000183105469 /A:3@CA 53.59000015258789 /A:4@CA 59.380001068115234 documentation here https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#attributes Tom > On Nov 22, 2022, at 7:08 AM, Asmahan Alghamdi <Asmahan.Alghamdi(a)nottingham.ac.uk> wrote: > > Dear Tom, > I hope you are well. I was wondering if there is away to export pLDDT scores of the best predicted model of a protein using ChimeraX e.g. 1.5 (which I am using in my investigations)? > > Thank you very much. > Asmahan

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Zoom over frames
by Krishnan Raman 21 Nov '22

21 Nov '22

Hi , Can I have the zoom command execute over several frames? Thanks Krish

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Re: [chimerax-users] [Chimera-users] Coloring the unit cell box
by Elaine Meng 21 Nov '22

21 Nov '22

(switching to chimerax-users address since this is all about ChimeraX, not Chimera) Sorry no, there is no linewidth setting on the unit cell outline box. However, you can "fake it" by selecting that model so that there are green outlines to show the selection, and then changing the selection-outline color and width: (1) select the outline box model, e.g. as described in the previous message by checking the selection box in the Model Panel (2) use "graphics selection" command to change the selection-outline color and thickness <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 18, 2022, at 9:12 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks a lot, Elaine, this worked indeed! > Just one final point: how can I make the linewidth larger? When I make a picture, the thin lines of the box disappear. > I understand ChimeraX interpretes these lines as a surface, I can change the colour when choosing surface in the colour blow up. > > On 18/11/22 17:49, Elaine Meng wrote: >> Hi Xavier, >> As far as I can tell, it is exactly the same in ChimeraX as in Chimera. First, make sure you aren't using a very old version of ChimeraX. I tried it in ChimeraX 1.5 release candidate (2022-11-08) just now: >> >> - open your structure that has unit cell information, e.g. 1fav >> >> - in Unit Cell tool (menu: Tools... Higher-Order Structure... Unit Cell) click Outline to show unit cell box >> >> - if you want to change box outline color, can use the same method as described below for Chimera. I wasn't able to select it by Ctrl-click, however, so instead use the selection (hand with green dot) checkbox in the Model Panel to select it, then use Actions... Color... [...]. Or, you can just click the color square in the Model Panel and use the system color chooser to change the color interactively. Screenshot: >> >> <Screen Shot 2022-11-18 at 8.48.02 AM.png> >> >> >> 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. for ChimeraX questions specifically, you may want to use the other mailing list, chimerax-users(a)cgl.ucsf.edu >> >>> On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>> >>> Dear Elaine, >>> I am now trying to get this done in ChimeraX where there is indeed a similar option. Unfortunately, if I proceed as in the instructions >>> I do not get the cell box, in contrast with old Chimera. I also tried through the command line but unsuccessfully. >>> Am I missing something? >>> Thanks a lot in advance, >>> Xavier >>> >>> On 26/10/22 17:45, Elaine Meng wrote: >>>> Hi Xavier, >>>> You can select the box (Ctrl-click on it) and then use menu: Actions... Color... [choose color], then clear selection by Ctrl-click on blank area of window or menu Select... Clear Selection. >>>> I hope this helps, >>>> Elaine >>>> ----- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Chimera(X) team >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>> >>>>> On Oct 26, 2022, at 1:56 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> >>>>> wrote: >>>>> >>>>> Dear all, >>>>> is there a way in Chimera or ChimeraX to get the unit-cell box being drawn in another colour than white? >>>>> This forces the background to be dark.... >>>>> Thanks a lot in advance, >>>>> Xavier >>>>> >>> >> > > -- > <fxgr_signanew.jpg> > _______________________________________________ > 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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Re: [chimerax-users] [Chimera-users] Alphafold
by Tom Goddard 20 Nov '22

20 Nov '22

AlphaFold prediction is running fine in ChimeraX, just tested a monomer and heterodimer prediction in the ChimeraX release candidate. AlphaFold prediction is not available in the old Chimera software. You would have to give details such as the exact pasted error, the input you were running on, the ChimeraX version, and best to do that with ChimeraX menu Help / Report a Bug.... Tom > On Nov 19, 2022, at 11:38 PM, Kornelius Zeth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear all – > > I’m using Alphafold in Chimera and I have a problem to run this properly on Colab. The people from Colab say that the error messages I get since recently are related to Alphafold developers having installed a new version. Could you please let me know what I could do to get the program running again? > > Thanks and have a nice day > > Kornelius > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Chimerax Error
by Natalie Loui 20 Nov '22

20 Nov '22

Hi all, I’m trying to visualize a capsid by using the sym command but I keep getting this error ”Assembly "1" not found, have" If you have any advice, please let me know. Natalie Loui PhD Student | Skaggs Graduate School of Chemical and Biological Sciences Email: nloui(a)scripps.edu | Phone #: (808)221-8270 Scripps Research Institute | 130 Scripps Way, Jupiter, FL 33458 | https://education.scripps.edu

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ChimeraX Render by Attribute tool
by Elaine Meng 18 Nov '22

18 Nov '22

Hi Prathvi, There is a different address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu CC'd here. You can see the currently available tools listed in the ChimeraX User Guide, and links to their pages: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/render.html> ... and the dates that they were added in the ChimeraX Change Log <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> ... so yes, we just started adding Render by Attribute to ChimeraX, but you have to get a recent daily build of version 1.6, and it does not have many options yet. Only ChimeraX (not Chimera) has a command to save attributes to a file. In Chimera you have to use the GUI. In ChimeraX we are specifically trying to make commands for all or nearly all actions you can perform with the GUI. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 18, 2022, at 4:23 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks once again Eric. > I have two more questions. > Is the "Render by Attribute" tool available in chimeraX because I get nothing when I run the command: ui tool show "Render by Attribute". If it isn't available, can I expect it to be added to chimeraX in the future? > Is there a command to save attributes of a residue in chimera (not chimeraX; that you covered in the previous reply) >

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cif writer broken in ChimeraX
by Pranav Shah 18 Nov '22

18 Nov '22

Hi Team, I am trying to save my coords in mmcif format to keep up with the times and I am running into the following error - ///////////////////////////////////////////////////////////////////////////////////////////////////////// AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets' File "/Users/ps/software/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/gui.py", line 130, in options_string if self.compute_sheets.isChecked(): See log for complete Python traceback ////////////////////////////////////////////////////////////////////////////////////////////////////////// Admittedly I am on a nightly build of the program details of which are - version 1.6.dev202211090831 (2022-11-09) Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Distance between two atoms
by McClean, Phillip 17 Nov '22

17 Nov '22

Hi Everyone, I have a two chain model. I would like to determine the distance between the CD1 atom of residue 77 in chain B and the CD1 atom of residue Leu 150 in chain C. What would be the proper distance command. Thanks for the help again. Phil McClean

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Re: [chimerax-users] [Chimera-users] Finding SASA for individual residues
by Elaine Meng 17 Nov '22

17 Nov '22

On Nov 17, 2022, at 8:01 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > The methods you suggested for calculating SASA for residues saved me so much time. Thank you once again for it. > But I have noticed an ambiguity. > When I calculate the SASA for the same residue using chimera and chimeraX, I am getting different values. > For ex: in the PDB file 1TY4, the SASA value for residue 174.a is 2.55 when calculated using chimera and it is 292.44 when calculated using chimeraX. The same is true for other amino acids in other PDB files as well. > Why is there such a difference? > On which of the two software should I rely on? > Also, what is the unit of SASA calculated by these two softwares? > > On Mon, Nov 14, 2022 at 9:42 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > [...] > In Chimera, they are automatically calculated when you show a molecular surface. It creates an attribute named areaSAS, as explained here: > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfa…> > > See also this previous chimera-user post on using Chimera to get a list of residue SASA values > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2018-June/014729.html> > > (If you use this page <https://www.rbvi.ucsf.edu/chimera/docs/feedback.html> to search chimera-users by "sasa", that was the top hit) > > In ChimeraX, you would use the command "measure sasa" > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> > ... then save attribute "area" to file > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> > Hi Prathvi, The atomic coordinates are in angstroms so the surface areas are in angstroms squared. Since this answer is mostly about ChimeraX, I'm also CCing the chimerax-users list. Regarding the differences in value: The programs are both right but based on different surfaces. By default, Chimera encloses all of the protein chains together into one surface (and chain A residue 174 is buried by some interactions with chain C, which you can probably see if you look at the structure). In ChimeraX, the default for display is to make each chain a separate surface, but for SASA calculation, it only depends on what you wrote in the "measure sasa" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> As mentioned in my earlier answer, the important part of what you get from "measure sasa" is not (in your case) the total reported in the Log, but instead the "area" attribute value that you will get for each residue. If you just use this ChimeraX command: measure sasa /A:174 ... then it will make a surface that only encloses that one residue, with area 292 as you said. I'm pretty sure that is NOT what you want. Instead you want tthe surface of the whole protein (or maybe one chain) and then the area of the residue given that larger surface. If you wanted to enclose all the protein chains of a model in a single surface (like Chimera default), then measure sasa protein If you wanted to make a separate surface for chain A only, then something like measure sasa /A & protein (the & protein part is still needed so that it won't enclose ligands, water, etc. that also happen to have chain ID A) Using "measure sasa" gives the residue "area" attribute that you could save to file, show in labels, etc. as explained in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> For your example structure 1TY4, using these ChimeraX commands: measure sasa protein info residues attribute area ...gives 2.55 for residue 174 in chain A, the same as in Chimera. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Multiplying the model around the helical cryo-EM map
by Dmitry Semchonok 16 Nov '22

16 Nov '22

Dear colleagues, I am trying to multiply the model subunit into the helical density. I found some command for Chimera sym #1 group c2*h,4.328,23.27,120,1 center 191.99,191.99,191.99 coord #0. Probably I have to somehow find the centre - perhaps with this command, right? Measure center #1 But not for ChimeraX. So my question is, how to do that in ChimeraX? Could you please provide the usage - it would be most helpful. Thanks in advance! Kind regards, Dmitry

2 1

Bond Rotation Questions
by FUNG Chun Po 15 Nov '22

15 Nov '22

Hello I have recently tried to use the bond rotation feature of Chimera X (Windows 10), and I have not been able to get it to work. I have tried the Bond rotation button on the toolbar, and the torsion command to no avail. The bond rotation button does not seem to do anything even when I click and drag with right click. The Torsion command states that my bond “is part of a ring/cycle and cannot be rotated” or “To set torsion, middle two atoms (/A ARG 543 N C) must be bonded;they aren't” I want to ask how do I use this function to rotate upon a simple amide bond. I am not sure am I just selecting the wrong atoms/bonds or is the function just locked for this PDB. The PDB file I am using is 7Y4P and I am trying to rotate about residues 543-544. I have also tried to do it in normal Chimera’s rotation command with no results. Thank you any advice would be welcome. Regards, Chun Po Fung

2 1

create chain as a new model from exiting PDB model
by tim smith 15 Nov '22

15 Nov '22

Hi All, I would like to create chain A as a separate model from the existing model. Could you please help me. Thank you. Best regards Tim

2 1

Question about pad parameter
by Thu Nguyen 14 Nov '22

14 Nov '22

Hello, I am using the volume cover command to crop the chain from the protein map. Here is what I did: > open 12554 from emdb > open 7ns0 > volume cover #1 atomBox #2/A1 pad 1.0 Suppose I want to add extra 17 voxels on each size of the chain, what value of pad should I add? Also, could you tell me the unit of pad in this command? Thank you very much. Best regards, Thu

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Re: [chimerax-users] Google colab sign in inquiry
by Tom Goddard 14 Nov '22

14 Nov '22

Hi Alejandro, On Windows the QtWebEngine Google Colab authentication info is in C:\Users\<username>\AppData\Roaming\ChimeraX\QtWebEngine\AlphaFold You can delete that directory and try using ChimeraX AlphaFold prediction again. Tom > On Nov 14, 2022, at 5:38 PM, Abraham, Alejandro <alejandro.abraham(a)icahn.mssm.edu> wrote: > > Hi Tom, > > Thank you for your email. I cannot see the login page anymore, and uninstalling ChimeraX to later reinstall it does not work. > Is there a folder where sign in is saved like in Macs ? I am using a Windows 10 PC. > Thanks again. > > Best, > > Alejandro > > > On Mon, Nov 14, 2022 at 12:59 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Alejandro, > > ChimeraX remembers your Google Colab sign-in. I don't understand why it would not let you sign in. A screenshot showing what you see would help understand the problem. > > If you signed in and ran AlphaFold previously but you want to change the account you sign in with, that should also be possible by clicking the image in the upper right corner of the AlphaFold Run panel which is just a web browser -- that button which shows the icon for your Google account will pull down a menu and let you sign out. And then you can also use it to sign in to another account. > > If somehow the ChimeraX remembered Google sign-in is causing problems you can delete that remembered sign-in info. On Mac you would delete the directory > > ~/Library/Caches?/UCSF ChimeraX/QtWebEngine/AlphaFold > > This is described further in this ChimeraX bug report > > https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7654#comment:2 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7654#comment:2> > > Tom > > >> On Nov 14, 2022, at 7:36 AM, Abraham, Alejandro via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Dear ChimeraX Support Team, >> >> Before all, congratulations on such awesome software. >> On another note I wanted to contact you because I am not able to connect to Google sign in when trying to predict with alpha fold. Is there a way to reset login ? >> >> Thanks again. >> >> Best, >> >> Alejandro >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

1 0

stretching protein?
by Noriega, Heather 14 Nov '22

14 Nov '22

Hello, I hope this email finds everyone well. I was wondering if ChimeraX had a function specific to "stretching" the protein. I am going to attach a picture, for reference. Is it possible to stretch the monomer to build a larger capsid? Thanks in advance. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883 [image: image.png]

3 5

Export PAE plot
by Clara Jegousse (TSL) 14 Nov '22

14 Nov '22

Dear ChimeraX team, After watching the YouTube tutorial on “how to show AlphaFold error estimates with ChimeraX”, I was wondering how to export the plot as an image (pdf, png?). Kind regards, Clara

3 2

Google colab sign in inquiry
by Abraham, Alejandro 14 Nov '22

14 Nov '22

Dear ChimeraX Support Team, Before all, congratulations on such awesome software. On another note I wanted to contact you because I am not able to connect to Google sign in when trying to predict with alpha fold. Is there a way to reset login ? Thanks again. Best, Alejandro

2 1

ChimeraX 1.5rc running on Nvidia RTX Titan [ubuntu 22.04]
by HONG ZHAN 11 Nov '22

11 Nov '22

Dear, I recently installed a Nvidia RTX Titan GPU card, and ChimeraX 1.5rc, it is a bit wired. I can open the window using intergrated GPU but if I just clicked on Chimerax or try to open it in terminal, it failed to open the program... Is ChimeraX only working on integrated GPU? Also, I cannot install the chimerax using apt install as in the website description, but dpkg -i works... is this the right way to install? many thanks! Hong

2 2

.pdb from Protein Data Bank has more chains than expected
by McClean, Phillip 10 Nov '22

10 Nov '22

Hi Everyone, I downloaded the 7FDL .pdb from the Protein Data Bank. I was expecting just two chains (it is a heteromeric complex), but I found 12 chains in the file (A-L). I was expecting two chains because the manuscript suggested they were just modeling protein fragments of the two protein. It appears that chains that A,C,E,G,I,K are multiple models of one fragment, while chains B,D,F,H,J,L are multiple models of the second fragment. Two questions. Why are multiple structures reported, and how to I visualize just two fragments at the same time, for example A and B. I have attached the .pdb file. Thanks for any advise. Phil McClean

3 5

Density extraction
by Dmitry Semchonok 09 Nov '22

09 Nov '22

Dear colleagues, I have a 3D map of the helix. 1. Do you know how can I extract 1 subunit? 2. Also, if there is no x-ray structure available. Thanks in advance. Kind regards, Dmitry

3 2

Fast Archive Search
by Kazan Ramy 09 Nov '22

09 Nov '22

Greetings to all, How can one search the archive with given keywords? Like for example, Ctrl + F search. I can only find the manual search by subject, thread ... and limited by month. Cheers, Ramy

3 2

Problem with the addcharge command
by svle＠tiscali.it 09 Nov '22

09 Nov '22

Hi all, for Chimerax version 1.4 (2022-06-03) when in the command line I use addcharge or addcharge #1 I receive in the Log panel the following: Unknown command: addcharge or Unknown command: addcharge #1. Where I'm wrong? Thanks. Saverio VOUCHER CONNETTIVITÀ per P.IVA e PMI: internet a canone 0 per 48 mesi. ATTIVA ORA https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busi…..

2 1

Re: [chimerax-users] [Chimera-users] MD simulation movie in chimeraX
by Elaine Meng 09 Nov '22

09 Nov '22

Hello! For ChimeraX questions you may want to use the other address, chimerax-users(a)cgl.ucsf.edu CC'd here. You can see what formats ChimeraX reads by using command "open formats," or view this User Guide page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory> ChimeraX can read .trr trajectory coordinates, but it cannot read .tpr trajectory topology. If your MD program can output a single PDB snapshot you can use that for the topology. First you would open the PDB file. Then to open the .trr file you would need to use the "open" command and also specify the already-open PDB file with the "structureModel" option. For example, if you open the PDB file as model #1, then something like: open myfile.trr structureModel #1 See details and more examples: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#structureModel> When you open the trajectory in ChimeraX, I believe that a playback slider will automatically appear. However, if it does not you can use "coordset slider" to show it. The "coordset" command can also be used to play the trajectory frames directly (not using the interactive slider): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 8, 2022, at 6:17 PM, Shivam Gupta via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Support Team, > > I am a commercial license user of chimeraX. I have .trr and .tpr files from the Gromacs MD simulation. I am not getting any option to create an MD movie. I know how to do it in chimera but couldn't find a similar GUI/option in chimeraX. Literature/tutorial of chimeraX didn't help me much. > > Please help me out by guiding me to generate MD movies. > Please reply to this email inline. > > I am Looking forward to hearing from you. > Thanks > > -- > With Regards > Gupta　Shivam グプタ　シヴァム > E-mail: shivam-gupta(a)pharmafoods.co.jp > Biomedical Department > Pharma Foods International, Kyoto Japan > 株式会社ファーマフーズ > 〒615-8245　京都市西京区御陵大原1-49 > TEL:075-748-9811 > FAX:075-948-9818 > URL: http://www.pharmafoods.co.jp/

1 0

side view window : lines are too thin
by Valerie Biou 08 Nov '22

08 Nov '22

Hello, I am a Chimera user slowly adapting to ChimeraX. I find that the moving lines in the Side view window are very thin, almost invisible when a cryoem map is displayed. is there a way to make them thicker ? thanks, kind regards, Valérie

2 1

RMSD Problem
by Timothy JM Clayson 08 Nov '22

08 Nov '22

Hiya, I am currently having a problem when trying to use RMSD on 2 sequences. *I am using the command: * *rmsd #1:149,264 to #2:469,553* (where a.a. on chain 1 are 149-264 and on chain 2 they're 469-553) *It is coming up with the error:* *'Number of atoms from first atom spec (21) differs from number in second (10)'* I was wondering if there is a fix to this problem? Thanks, Tim

2 1

Re: [chimerax-users] Applying symmetry operations to generate an oligomeric model
by Tom Goddard 07 Nov '22

07 Nov '22

Hi Rob, Hopefully you are using ChimeraX, not Chimera -- we have only done maintenance on Chimera for the past 6 years. The ChimeraX commands all work in physical coordinates (Angstroms), not grid index units (pixels), and usually they use scene coordinates, not local model coordinates which makes a difference if you have moved individual models relative to one another in the scene. Your Dn symmetry problems are because the two-fold symmetry that flips one Cn ring to the other stacked Cn ring needs to be aligned on the x-axis. In your map apparently it is not aligned with the x-axis. In general it is helpful to have your map aligned in a standard way if you will be applying symmetry. For dihedral symmetry the z-axis is the cyclic symmetry axis, the origin should be on that cyclic symmetry axis mid-way between the two rings, and the x-axis should be a two-fold symmetry axis. If you don't use standard map orientations for symmetric maps it is going to be very painful to make symmetric copies of atomic models in those maps. Tom > On Nov 6, 2022, at 12:58 PM, Robert Harkness <r.harkness(a)utoronto.ca> wrote: > > Hi Tom, > > Thank you for your detailed response! > > I think I am using an older version of chimera. When I use the center <map> command, I just get one line of output that corresponds to the center of the map in grid coordinates. I have been converting these into angstrom coordinates using the pixel size and applying those in sym. > > Sometimes when I open a model and a map, I have to rotate and translate the model into a reasonable position inside the map and then do a “fit in map” to get the initial placement for sym, so this means that the model’s coordinates will now be different relative to the scene and the map. If I save the fitted model to a new PDB and then re-open it, will it now have the same coordinates of the scene (and map if I haven’t moved the map at all)? I think that way I can use scene coordinates for all maps and models. > > I am finding for other cages I am working on that have Dn symmetry, in some cases they work beautifully if I just fit the model into the portion of the map that corresponds to one unit of the cage, then save that model as a PDB relative to the map, then open it and use sym <model> group <Dn> center <map center in angstrom units> coordinateSystem <map>. In other cases doing this same procedure, the first half of the cage units are made perfectly as sym goes from the initial model around the Cn axis placing copies in the density, but when it flips over the 2-fold axis to do the other half, the model units are out of alignment with the density. So I have been adding the axis option to get it closer but find it requires a little tweaking. I guess the axis command doesn’t always give the perfect axis of rotation because the map is not perfect. Will this also be alleviated by just using everything in scene coordinates? > > Best, > > Rob > >> On Nov 5, 2022, at 7:55 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> You don't often get email from goddard(a)sonic.net <mailto:goddard@sonic.net>. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> >> Hi Rob, >> >> It sounds like you did everything right. Using "measure center #1" where model #1 is the map should give the right center of the tetrahedron. When you use that command it reports the center in map grid index units and also in scene coordinates, for example, >> >> measure center #1 <cxcmd:measure center #1>Center of mass grid index for emdb 15560 = (279.52, 279.92, 253.25) >> Center of mass xyz coordinates for emdb 15560 = (289.20, 235.85, 185.32) >> >> >> In the sym command were you use that center to copy your atomic model with tetrahedral symmetry you should use the scene coordinates (the second line of output) not the grid index coordinates. The "sym" command expects scene coordinates for the "center" option and you should not use the "sym" command coordinateSystem option. The coordinateSystem option is used only if the center coordinates are given in the coordinate system of a specific model rather than the whole scene. The models start out with the same coordinate system as the whole scene, but if you move a model in the scene (e.g. when you fit an atomic model into the map) then that model has different local coordinates than the scene. >> >> I see another potential problem in your sym command. The "axis" option is supposed to be a 3-fold symmetry axis of the tetrahedron. You are giving it the symmetry axis of the asymmetric unit trimer which may or may not be a symmetry axis of the tetrahedron. To determine the symmetry axis of the tetrahedron open two copies of the map and rotate one copy by hand using the "Move Model" mouse mode (which moves only the selected model) to roughly align two different trimeric subunits then optimize the alignment with "fitmap #2 in #1", then use measure rotation #2 to #1 and it will report a symmetry axis of the tetrahedron. Another way to go about this is if you density map already has a standard orientation, such as tetrahedron 2-fold symmetry axes along x,y,z then you don't need to specify the axis in the sym command, just use "t,222" in the sym command. Or if it has a symmetry axis along z use "t,z3" with no axis specification. You can probably see if it has a standard symmetry using "measure symmetry #1". >> >> Sorry for the delayed answer. I was at a workshop all last week and did not have time for email. >> >> Tom >> >>> On Nov 3, 2022, at 4:35 AM, Robert Harkness via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello, >>> >>> I am trying to generate a model of an oligomeric protein cage that consists of 4 trimers and has tetrahedral symmetry. I am using the asymmetric unit model consisting of one monomer (#0) and a density map (#1) as a starting point. My strategy has been to take the asymmetric unit and fit it into a portion of the map corresponding to one of the monomers within one of the trimer faces of the tetrahedron. Then I generate a copy of that asymmetric unit (#2) and fit it into the map for an adjacent protomer within the same trimer face. This results in the two asymmetric unit models being rotated 120 degrees relative to one another and part of the same trimer. Then I use the measure rotation command to measure the rotation of the second asymmetric unit relative to the first, giving me a rotation matrix and axis parameters. I then do >>> >>> sym #0 (first asymmetric unit) group t,z3 axis <axis from measure rotation> center <axis points from measure rotation> coordinateSystem #1 (the density map) >>> >>> And this generates the right looking trimers, so the 3-fold axis appears to be correct, but the center is off such that only one of the four trimers matches the density map and is placed at the top of the tetrahedron, while the other 3 trimers are off into the void of the scene but placed at the other 3 vertices. I am not sure how to appropriately define the center. My feeling is that it should be the center of the map, taken from the measure center #1 command, but implementing those numbers in sym doesn’t work either. Any thoughts on how these center coordinates are defined/should be measured, or if there is a better approach for doing this would be awesome! >>> >>> Best, >>> >>> Rob >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >>> >> >

1 0

error saving session in v 1.5
by Yoda Muppet 07 Nov '22

07 Nov '22

Greetings. We're having an issue savings session with ChimeraX 1.5. Trying to save a session file results in the following error: [save] (help: user/commands/save.html) /data/processed/staggers/cryofib- tryps/process/YTAT9-1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs [save /data/processed/staggers/cryofib- tryps/process/YTAT9 - 1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs] (cxcmd: save /data/processed/staggers/cryofib- tryps/process/YTAT9 - 1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs) Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 285, in process data = sm. take snapshot (obj session, self.-state flags) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/log/tool.py", line 542, in take snapshot "contents': self.page source, AttributeError: *Log' object has no attribute 'page source' The above exception was the direct cause of the following exception: Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 262, in discovery self.processed[key] = self.process (obj, parents) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 290, in process raise RuntimeError (msg) from e RuntimeError: Error while saving session data for "tools' -> ‹chimerax.core. tools. Tools object at 0x7f90efeb0310> => <chimerax.log. tool. Log object at 0x7f90ee2b3c10> During handling of the above exception, another exception occurred: Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 896, in save session. save (output, version=version, include maps=include maps) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py" line 625, in save mgr.discovery(self. state containers) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError ("error processing: %S: %S" % ( obj stack(parents, obj), e)) ValueError: error processing: "tools' <chimerax.core. tools. Tools object at 0x7 f90efeb0310> <chimerax.log. tool.Log object at 0x7f90ee2b3c10>: Error while saving session data for 'tools' -> <chimerax.core. tools. Tools object at 0x7f90efeb0310> <chimerax.log. tool. Log object at 0x7f90ee2b3c10> BUG: ValueError: error processing: 'tools' for "tools => -> ->: Error while saving session data File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py" line 266, in discovery raise ValueError ("error processing: %S: %5" % (obj stack(parents, obj), e)) See log for complete Python traceback.

3 2

Change luminance in color palette
by Scott, Brandon L. 07 Nov '22

07 Nov '22

I am coloring surfaces using palettes (purples or a custom green-white-magenta). These both have a single luminance value, is it possible to generate a color palette that also has changing luminance. The ideal palette would be green -> white -> magenta along the color axis, and 0 - > 255 scaling the luminance of the rgb. We would effectively have a color bar matrix that goes from dark green to black to dark magenta if the values are low and bright green to white to bright magenta if the values are high. Thanks for your insights! -Brandon Brandon Scott, PhD CZI Imaging Scientist, Assistant Professor Nanoscience & Biomedical Engineering South Dakota Mines EEP 229 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/>

2 2

Create command for subunit model
by tim smith 06 Nov '22

06 Nov '22

Hi All, I would like to create a separate subunit model in chimeraX like create command in Pymol. In my PDB model, 3 subunits are present, I want to make each subunit as a model for representation. Thank you and best regards Tim

2 1

Applying symmetry operations to generate an oligomeric model
by Robert Harkness 05 Nov '22

05 Nov '22

Hello, I am trying to generate a model of an oligomeric protein cage that consists of 4 trimers and has tetrahedral symmetry. I am using the asymmetric unit model consisting of one monomer (#0) and a density map (#1) as a starting point. My strategy has been to take the asymmetric unit and fit it into a portion of the map corresponding to one of the monomers within one of the trimer faces of the tetrahedron. Then I generate a copy of that asymmetric unit (#2) and fit it into the map for an adjacent protomer within the same trimer face. This results in the two asymmetric unit models being rotated 120 degrees relative to one another and part of the same trimer. Then I use the measure rotation command to measure the rotation of the second asymmetric unit relative to the first, giving me a rotation matrix and axis parameters. I then do sym #0 (first asymmetric unit) group t,z3 axis <axis from measure rotation> center <axis points from measure rotation> coordinateSystem #1 (the density map) And this generates the right looking trimers, so the 3-fold axis appears to be correct, but the center is off such that only one of the four trimers matches the density map and is placed at the top of the tetrahedron, while the other 3 trimers are off into the void of the scene but placed at the other 3 vertices. I am not sure how to appropriately define the center. My feeling is that it should be the center of the map, taken from the measure center #1 command, but implementing those numbers in sym doesn’t work either. Any thoughts on how these center coordinates are defined/should be measured, or if there is a better approach for doing this would be awesome! Best, Rob

2 1

Create subunit model
by tim smith 05 Nov '22

05 Nov '22

Hi All, I would like to create a separate subunit model in chimeraX like create command in Pymol. In my PDB model, 3 subunits are present, I want to make each subunit as a model for representation. Thank you and best regards Tim

1 0

Re: [chimerax-users] [Chimera-users] Jagged edges in chimera X
by Elaine Meng 03 Nov '22

03 Nov '22

Hi Prathvi, For ChimeraX questions, you may want to use the other mailing list, chimerax-users(a)cgl.ucsf.edu CC'd here. As per this recent post, ChimeraX does not have multisampling, but if you are saving an image you can use supersampling: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-September/004310.ht…> ChimeraX also has a "graphics quality" command to increase the number of facets used to draw atoms, bonds, and cartoons (ribbons), although I don't know if that is going to help your issue very much: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 3, 2022, at 4:59 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Elaine, > > Is there a way to smoothen the jagged edges seen around ribbons and sheets in ChimeraX? > The jagged edges can be removed in UCSF chimera by setting the subdivision value to 20 and enabling multisampling but I do not see these features in chimeraX. > > -- > 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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How to discover hydrophobic between two chains
by McClean, Phillip 02 Nov '22

02 Nov '22

Hi Everyone, I ran AF2 multimer and have a two-chain complex. I ran the mlp command on the two chains separately and together. The two chains seem to interact via hydrophobic residues where chain B fits into a pocket on chain C. Here are the chain residues: /b:72-124 /c:1-190 Is there any way to determine which residues (hydrophobic) in each of these two regions are interacting via hydrophobic interactions. Thanks for any help you can provide. Phil McClean

2 3

Copy attribute value from one attribute to another
by Sean Connell 02 Nov '22

02 Nov '22

Hello, I have a question with a probably obvious answer but I cannot figure it out. Is there a command to copy an attribute value from one attribute to another, for example, seq_conservation to bfactor? The idea would be to save a pdb file with the conservation stored in bfactor (for sharing). In this case I guess there is the issue that one is an atom attribute and the other is residue attribute but one could assign all atoms of the residue the same value. Sorry in advance if I miss something obvious.

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Get atom from selection string in script
by Thibault TUBIANA 02 Nov '22

02 Nov '22

Hi! I would like to create a function to copy the torsion angle from a model to another one. The function would take in argument the model ID of the reference and target model (<int>) and the residue id (<int>). I looked a bit at the scripts available in [ https://rbvi.github.io/chimerax-recipes/ | https://rbvi.github.io/chimerax-recipes/ ] to have an idea of how to add function in ChimeraX, but I'm currently stuck at "how to get the list of atoms from a selection string ?". Here's my current script from chimerax.core.commands import run def copy_torsion(session, model1, model2, residue): selection = f"torsion #{model2}:{residue}@n,ca,c:{residue+1}@n" from chimerax.atomic import AtomsArg atoms = AtomsArg(selection) from chimerax.geometry import dihedral cur_torsion = dihedral([*a.scene_coord for a in atoms]) torsion=run(session, f"torsion #{model1}:{residue}@n,ca,c:{residue+1}@n {cur_torsion}") def register_command(logger): from chimerax.core.commands import CmdDesc, register, FloatArg, IntArg, BoolArg, Color8Arg, StringArg from chimerax.atomic import AtomsArg desc = CmdDesc(required = [ ('model1', IntArg), ('model2', IntArg), ('residue', IntArg), ], synopsis='Copy torsion angle') register('copyTorsion', desc, copy_torsion, logger=logger) register_command(session) Thank you for your help :) Best regards, Thibault. -- 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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Re: [chimerax-users] [Chimera-users] xyz axis indicator
by Elaine Meng 01 Nov '22

01 Nov '22

Hi Xiang, I am guessing you are using ISOLDE with ChimeraX (not Chimera) so I am cross-posting this question to the chimerax-users(a)cgl.ucsf.edu list. I am not expert with ISOLDE so I am not sure about the answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 30, 2022, at 10:58 PM, Xiang Zhang via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi all, > > I was wondering how I could hide the xyz indicator in the center of window when I was viewing the X-ray density from mtz file? It only appears in crystal unit view mode but disappears in EM projection side view. > > Best, > Xiang > <1667192316818.png>_______________________________________________ > 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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Co-centering maps and pub models
by mailman-bounces＠cgl.ucsf.edu 31 Oct '22

31 Oct '22

Dear ChimeraX users I have a density map and a pdb model opened in ChimeraX. How to move one of them to have a common axis (for both) , without disturbing the other. Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

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Re: [chimerax-users] AlphaFold Prediction
by Tom Goddard 31 Oct '22

31 Oct '22

Hi Raihan, The maximum sequence length that can be predicted by AlphaFold is limited by GPU memory. The following table says that paid Google Colab services only offer at most 16 Gbytes of GPU memory (from https://blog.paperspace.com/alternative-to-google-colab-pro/ <https://blog.paperspace.com/alternative-to-google-colab-pro/>). Not sure if it is correct since the table is from a Google competitor. You can run sequence length 1000, sometimes 1200, with 16 GB of GPU memory as shown here https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html Various cloud compute services offer modern GPUs like Nvidia A40, A100, A6000 with 48 GB, or 40 or 80 GB of GPU memory usually charging about $2-3 per hour. But ChimeraX can only currently use Google Colab for AlphaFold predictions. Tom > On Oct 31, 2022, at 2:45 PM, S.M. RAIHAN RAHMAN <smrrbtgeiu(a)gmail.com> wrote: > > Thank you. I saw the run times. Is it possible to run sequences of around 1200 in Google Colab pro plus paid service through ChimeraX? In the website link you shared, I only saw about Google Colab pro paid service. Please let me know. > > Regards, > Raihan > > On Mon, 31 Oct 2022 at 14:33, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > ChimeraX only runs AlphaFold on Google Colab. Because Google Colab provides 5 year old GPUs with little memory (16 GB) it can only run sequences of length about 1000 or less. With better equipment and your own AlphaFold installation you can run sequences up to length 3000 or 4000 although that can take 30 hours. Here are example run times > > https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> > > Tom > > >> On Oct 31, 2022, at 2:28 PM, S.M. RAIHAN RAHMAN <smrrbtgeiu(a)gmail.com <mailto:smrrbtgeiu@gmail.com>> wrote: >> >> Thank you so much. Is there any alternative to Google Colab for running AlphaFold through ChimeraX? Please let me know. >> >> Regards, >> Raihan >> >> On Mon, 31 Oct 2022 at 14:22, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Raihan, >> >> The ChimeraX AlphaFold prediction produces 5 models but it only automatically opens the best model. All 5 models are in the ~/Downloads/ChimeraX/AlphaFold/prediction directory after the job completes. There is no option to run fewer models. Running AlphaFold not through ChimeraX also produces 5 models. This is because AlphaFold works by running 5 slightly differently trained neural networks and the best is chosen. If you install your own AlphaFold (a somewhat difficult task, needs Linux and an Nvidia GPU and a few Tbytes of disk for databases) then you can modify the AlphaFold Python code to predict only one or a few models by choosing which of the 5 networks it should run. >> >> Tom >> >> > On Oct 31, 2022, at 1:39 PM, S.M. RAIHAN RAHMAN via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Hi! >> > Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence in AlphaFold prediction. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models before providing the final model in AlphaFold prediction? Please let me know. Thank you. >> > >> > Regards, >> > Raihan >> > _______________________________________________ >> > ChimeraX-users mailing list >> > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> > Manage subscription: >> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >> >

1 0

AlphaFold Prediction
by S.M. RAIHAN RAHMAN 31 Oct '22

31 Oct '22

Hi! Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence in AlphaFold prediction. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models before providing the final model in AlphaFold prediction? Please let me know. Thank you. Regards, Raihan

2 1

Copy a part of a model ?
by mailman-bounces＠cgl.ucsf.edu 31 Oct '22

31 Oct '22

Hi :) I wanted to duplicate only one part of a model and I haven't found a copy function (I found this old thread tho https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000783.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000783.html>) For now my strategy is to duplicate the model with "combine #1 close false" and then delete what I don't want on the new model like for example (to delete helices) "delete ~helix & #2" I know you are always super busy with ChimeraX dev, but I thought this could be a good "quick way" to create a "copy" function of example (if there are no alternative that I missed of course). Have a great day! Best regards, Thibault. -- Thibault Tubiana, PhD Postdoctoral Fellow @IMAPP <https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism…> Institute for integrative biology of the cell (I2BC <https://www.i2bc.paris-saclay.fr/>) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: http://www.tubiana.me/gallery <http://www.tubiana.me/>

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Re: [chimerax-users] [Chimera-users] Question regarding protein-protein interactions in ChimeraX
by Elaine Meng 31 Oct '22

31 Oct '22

Hi Camille, ChimeraX does not move the proteins to predict how they might bind each other, although you could move one relative to the other "manually" (with the mouse) yourself, or use some other program to do protein-protein docking. ChimeraX is just showing the coordinates in the Protein DataBank data files that you opened, i.e. whatever the authors deposited. If you are using ChimeraX, for future questions you may want to use ChimeraX mailing list chimerax-users(a)cgl.ucsf.edu CC'd here instead of the Chimera one. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 30, 2022, at 3:26 PM, Lake, Camille (NIH/NIAID) [C] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > > My name is Camille Lake and I have used ChimeraX to model proteins. I was wondering - if I load two completely separate proteins from PDB, what is the nature of their interaction as shown by ChimeraX? The two proteins I'm interested in, TIM-3 (5f71) and CEACAM1 (5dzl), are predicted to interact in the literature, but if I load them separately into ChimeraX, is this predicted interaction what displays automatically? It seems that they are, but I can't find anywhere on the web whether this is automatically done in ChimeraX. Other proteins I randomly add in generally keep far away from each other in space. > > Thank you, > > Camille

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can not download
by keqing yin 29 Oct '22

29 Oct '22

Hello, There is no reaction after I clicked the save as the CSV when I want to download the clipper from tools/more tools . I would be very appreciate if you could solve this problem. [cid:image003.png@01D8EAFB.ECAB74A0] 从 Windows 版邮件<https://go.microsoft.com/fwlink/?LinkId=550986>发送

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How do I visualize an amber nc file in ChimeraX?
by Yasmene Wang Elhady 28 Oct '22

28 Oct '22

Hello, I'm new to molecular modeling, and new to Chimera. I'm trying to visualize an AMBER .nc output file from an AMBER tutorial ( http://ambermd.org/tutorials/basic/tutorial0/) and I have a topology file that in VMD is the type AMBER7 Parm. How can I visualize this in ChimeraX? I saw another thread suggesting to use the MD movie tool, but I don't see that option in ChimeraX. Is this something I need to add? If so, where can I get it from, and how do I add it? Thanks in advance, Yasmene

2 1

Selection by segid
by CUNIASSE Philippe 28 Oct '22

28 Oct '22

Dear all, Is there a way in ChimeraX to make a selection by segid (column 73-76 in pdb format from CHARMM of XPLOR)? Thanks in advance. Philippe Cuniasse. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:philippe.cuniasse@cea.fr> Web: http://biodev.cea.fr/rasmot3d/ [signature_700846419][signature_2907812893][signature_966493179] -----------------------------------------------

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Re: [chimerax-users] ChimeraX sequence alignment score?
by Elaine Meng 27 Oct '22

27 Oct '22

> On Oct 27, 2022, at 4:46 PM, Budayr, Omar Mahdi <obudayr(a)vols.utk.edu> wrote: > > Dear Dr. Meng, > > I looked through the documentation for ChimeraX and I still cannot figure out what the value for sequence alignment score indicates. I aligned two b-adrenergic receptors from PDB (2RH1 and 3NH8) and it gives a value of 2423.9. What does this value actually represent? The documentation refers to it but never gives specifics besides the parameters in the table that matchmaker generates > > Sincerely, > Omar Budayr Dear Omar Budayr, The value itself is not at all important. The reason to have a score is that the alignment process tries to maximize it for the pair of sequences that it is given. By changing parameters for scoring you can change the relative importance of the different parts of the score, and thus what is most important for the alignment method to align. 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. we recommend sending questions to the chimerax-users(a)cgl.ucsf.edu address (CC'd here) so that others can benefit from the answers and/or help to answer the questions - thanks!

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Selecting residues in two chains
by McClean, Phillip 27 Oct '22

27 Oct '22

Hi Everyone, I have a .pdb file created using AF2 Multimer. It consists of two chains, B and C. Chain B is a protein with 315 residues, while Chain C is a protein with 662 residues. Each chain is modeled with structured and unstructured regions. I would like to only show residues 19-24 of Chain B and residues 1-190 of Chain C in the display window. I have tried using the information provided on the "Command-Line Target Specification" page, but I have not had any success with just displaying those ranges of residues in the display window. My goal is to highlight specific features of those ranges of residues to display their interaction. Thanks for any information you can provide. Phil McClean

2 4

segmented tomogram density in chimeraX
by Jesse HANSEN 25 Oct '22

25 Oct '22

hi all, I have segmented a tomogram in Amira and exported to chimera for visualization. I first opened the .rec file in chimera and re-saved as .mrc. Okay, the segmentation output gives a fully filled volume cube except for the regions of segmentation. Obviously things are inverted. Also, the volume viewer shows clear sharp peaks (delta functions) rather than continuous density, as volume slider moves to the right new segmentation features appear. So I used volume filter with "scale" to -1, and I turned off "displayed subregions only". This fixed the inversion problem and now as I slide toward the right I see more segmented densities. However the threshold values are all negative (-250 on the far left to -240 on the far right). This, combined with the densities being sharp peaks, makes it impossible to use this volume like a regular volume for surface coloring, filtering, segger, etc. Any suggestion on how to go from this step to a usable density would be appreciated. thanks! Jesse ================================= Dr. Jesse Hansen Schur Group Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg Austria

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Useful tools ideas/requests
by Shayne Quinn 21 Oct '22

21 Oct '22

Hello, I have been using ChimeraX for a few years now for multidimensional cell bio-imaging and cannot thank the team and developers enough for such an amazing program. I am not sure where to ask for other useful tools so I am starting here. These may already exist but I was unsuccessful in finding them in the user guide so my apologies if I missed them. 1) Is there an option to color the different axis for the 'showOutlineBox' feature for volumes? For example box lines in x-blue, y-green and z-red to help keep orientation (I have included a mock version in the attachment) 2) I work specifically with Lattice Light Sheet Data which requires our 3D cells to be placed on glass coverslip that do not show up in the captured data but are useful for referencing orientation. Is there a feature in place already that would allow me to create a mock coverslip. So far I resorted to importing a throwaway volume (Volume 4 in attachment) and made the threshold for a surface ~0, set it to grey, and made it fill the bottom 5 pixels or so, shown in the attachment. 3) Is there a time stamp feature similar to the scale bar function that has already been implemented? Thank you so much for all the time and effort that has been put in and for creating such an amazing visualization tool! Cheers, Shayne Quinn

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Installing ChimeraX on Ubuntu 16.04 or openSuse Leap 15.2
by Miguel 19 Oct '22

19 Oct '22

Hello, I am trying to install ChimeraX on Ubuntu 16.04 or openSUSE Leap 15.2 without success. Is it possible? If so, what would be the procedure? Thanks, Miguel

3 5

Center of the erase sphere
by Tianming Qu 19 Oct '22

19 Oct '22

Hi ChimeraX developers, Is there any way I can know the center of the erase sphere in CHimeraX? Best, Tianming

2 1

Generate surface from a model using user defined color
by HONG ZHAN 17 Oct '22

17 Oct '22

Dear all, I would like to generate surface using my model but I want to keep the color as I defined. My protein contains only one chain so that when I ran Surface command, it generated surface with one color... Is there a way to generate surface to keep my defined color? Super thanks! Hong

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chimeraX clipper install
by Gutierrez, Dominique 17 Oct '22

17 Oct '22

Hello, I tried to install clipper with the popup window but it takes forever. I downloaded it directly from the website. Where do I put it .whl file? Best Regards, Dominique Gutierrez

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Re: [chimerax-users] [chimera-dev] ChimeraX pyhton script
by Elaine Meng 17 Oct '22

17 Oct '22

> On Oct 17, 2022, at 7:26 AM, Jan Hofmann via Chimera-dev <chimera-dev(a)cgl.ucsf.edu> wrote: > > To whom it may concern, > I want to write a python script to open a pdb file, then load a .xplor file in as well. After one rotation which I also want to do via the script I want to export the output file as a .png file. > Could you provide any advice to me on how to write such a script? I am having troubles loading any python script into ChimeraX. Eventually I want to use this script to batch wise output structures including guest adsorption where the guest species is introduced via the .xplor from previous analysis and the structure is provided by a .pdb file. I really would need some advice/tutorial at this stage so I would be more than happy to hear back from you. > Many thanks and kind regards, > Jan Hofmann, M.Sc. > PhD Student, Department of Chemistry > Chapman Group > Stony Brook University > jan.hofmann(a)stonybrook.edu > Office: Room 563, Chemistry Hi Jan, This is the Chimera list, maybe you wanted to send to chimerax-users(a)cgl.ucsf.edu instead? (Cc'd) Maybe it can be done at least partly with ChimeraX command script instead of a python script. If you do these steps interactively in ChimeraX, it should show the corresponding commands in the Log . A ChimeraX command script is just the same commands you would enter in the Command Line, except in a plain text file named something.cxc as explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc…> There is also a "forEachFile" option of the "open" command to read a ChimeraX command file and apply it to a series of input files, e.g. all the .pdb files in some folder. If you name the .xplor files to match the corresponding .pdb files, maybe you can use the $ mechanism described for that option, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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How to hide a chain and overly the shown chain with another model
by McClean, Phillip 13 Oct '22

13 Oct '22

I have a .pdb file obtained from ColabFold. The model was developed with AlphaFold2 Multimer. It has two chains. How can I 1) hide only one chain and then 2) add a second model. The second model will be the visualized chain developed only on its own. I am looking for regions that might be different between the model with a second protein and by itself. I tried hide /c but that didn't work. Phil McClean

2 1

Loading density files
by Tianming Qu 12 Oct '22

12 Oct '22

Dear Chimerax developers: I have a lot of density files, is there anyway I can load them at the same time and view then like a protein traj? Best, Tianming

2 3

Problem reading ccp4 maps
by Luca Pellegrini 11 Oct '22

11 Oct '22

When I try to read ccp4 maps from Phenix Resolve_cryoEM into ChimeraX, I’ve started getting the following message: "MRC file is truncated. Failed reading 1 values, type int32” It’s ChimeraX version 1.5.dev202210110346 (2022-10-11)/ macOS Monterey/MacBook Pro 2021, M1 Pro. Best wishes, Luca

2 1

Can you do convex hull on ChimeraX?
by Tianming Qu 10 Oct '22

10 Oct '22

Hi dear ChimeraX-Users and developers, Is ChimeraX available for drawing the convex hull of protein structures? Best, Tianming

4 4

Fit in map, save new coords of map
by Nebojsa Bogdanovic 10 Oct '22

10 Oct '22

Hello, I open two maps and I fit #2 into #1. I need to save map #2 at it's new position, but there is no option "relative to model or map". By doing "volume resample #1 onGrid #1, I match the box sizes but the new position is not maintained after saving that new map. Is there any command/function I could do that with? Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Re: [chimerax-users] alphafold contacts between 3 and more subunits
by Tom Goddard 10 Oct '22

10 Oct '22

Hi André, I added two options "replace" (default true) and "name" (default "PAE Contacts") to the alphafold contacts command. The replace option determines if existing contact pseudobonds (in the group with the specified or default name) are deleted. If replace is false the new contacts are just added to any existing ones. The name option gives the pseudobond model the specified name. So you could use alphafold contacts /A to /B alphafold contacts /B to /C replace false alphafold contacts /A to /C replace false to put all the contacts in one pseudobond submodel. If instead you wanted them in 3 different models you could use alphafold contacts /A to /B name "AB contacts" alphafold contacts /B to /C name "BC contacts" alphafold contacts /A to /C name "AC contacts" This will be in tomorrow's (Oct 11) ChimeraX daily builds. Tom > On Oct 10, 2022, at 12:38 PM, Michaelis, Andre Clemens <michaelis(a)biochem.mpg.de> wrote: > > Awesome, > Thank you so much! > > Best > André > > > —————————————————— > > >> Am 10.10.2022 um 20:50 schrieb Tom Goddard <goddard(a)sonic.net>: >> >> Hi André, >> >> The "alphafold contacts" command creates a submodel of the atomic structure containing pseudobonds with the submodel named "PAE Contacts". If you rename that submodel then it won't replace it when you do the second alphafold contacts command on the same structure. For instance, if the structure is model #1. >> >> alphafold contacts /A to /B >> rename #1.1 "AB contacts" >> alphafold contacts /B to /C >> rename #1.2 "BC contacts" >> alphafold contacts /A to /C >> >> This should be easier to do. I should add an option to the alphafold contacts command "replace false" that automatically uses new names for each group of pseudobonds. I've made a request for this. >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770> >> >> Tom >> >>> On Oct 10, 2022, at 5:47 AM, Michaelis, Andre Clemens via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hi, >>> >>> Is it possible to draw contacts (PAE, alphafold) between more than just 2 subunits? >>> e.g.: >>> alphafold contacts /A to /B >>> AND >>> alphafold contacts /B to /C >>> AND >>> alphafold contacts /A to /C >>> >>> Righ now, a new command deletes the old contacts. Not sure about a syntax that would combine/add those >>> >>> Thank you very much! >>> >>> Best André >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

1 0

alphafold contacts between 3 and more subunits
by Michaelis, Andre Clemens 10 Oct '22

10 Oct '22

Hi, Is it possible to draw contacts (PAE, alphafold) between more than just 2 subunits? e.g.: alphafold contacts /A to /B AND alphafold contacts /B to /C AND alphafold contacts /A to /C Righ now, a new command deletes the old contacts. Not sure about a syntax that would combine/add those Thank you very much! Best André

2 1

mrc to pdb
by Tianming Qu 07 Oct '22

07 Oct '22

Hi, is there any way I can convert a .mrc file to .pdb file in chimera? Best, Tianming

5 5

A question about the level option in volume viewer
by Qu Tianming 06 Oct '22

06 Oct '22

Hi ChimeraX-developers, I got a question about the level option in volume viewer. I think the level represent the isovalue for the density map. So when I set the level as 0.03, I got a density map as following : [?? ???????] When I set the level as 0.01, the density map as following: [?? ???????] So my question is that, does level 0.03 or 0.01 means, all grids with a density value lower than 0.03 or 0.01 will be present? Means when I set the level as 0.01, everything left in the density map is the density value lower than 0.01? Best, Tianming

2 1

Moving molecules in VR
by Dr. Eddie 06 Oct '22

06 Oct '22

Hello, I'm trying to move some waters away from a ligand (and eventually some lipids as well) as they overlap too much for minimization to fix it. I can't seem to figure out how to select an entire (water) molecule. The select atom lets me select one atom, but I cannot chain or add more atoms. Some atoms seem to refuse to move even when I try to move one at a time using the "Move atoms" right mouse option. Any help would be appreciated as I can't find much about translating molecules (the bond rotation works perfectly!). Thanks! Eddie

3 2

Problems with Qt6
by Hoover, David (NIH/CIT) [E] 06 Oct '22

06 Oct '22

Hi, I'm trying to create a Ubuntu 22.04 container for ChimeraX v1.4 and no matter what I do I get this error message: NOTE: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1021, in <module> exit_code = init(sys.argv) File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 573, in init from chimerax.ui import initialize_qt File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/__init__.py", line 21, in <module> from .gui import MainToolWindow, initialize_qt, menu_capitalize File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/gui.py", line 130, in <module> from Qt.QtWidgets import QApplication File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/Qt/__init__.py", line 64, in <module> from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/Qt/__init__.py", line 64, in from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION _See log for complete Python traceback._ I am attempting to install into Ubuntu 22.04 with ever Qt6 package available, but nothing seems to help. The library in question definitely exists at /usr/lib/x86_64-linux-gnu/libQt6Core.so.6, along with a multitude of other libQt6* libraries. Is there something additional that needs to be done or installed to enable ChimeraX v1.4 to run? I have tried export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH but this does not help. Any insight would be appreciated. David -- David Hoover, Ph.D. Computational Biologist High Performance Computing Services, Center for Information Technology, National Institutes of Health 12 South Dr., Rm 2N207 Bethesda, MD 20892, USA TEL: (+1) 301-435-2986 Email: hooverdm(a)hpc.nih.gov

2 1

Re: [chimerax-users] usage for multimer
by Tom Goddard 05 Oct '22

05 Oct '22

Hi Dennis, Are you asking about fetching AlphaFold database models? Those are only of monomer proteins. With AlphaFold predictions energy minimization is done using OpenMM and the Amber force field -- it has nothing to do with binding affinity. I don't know what you mean by a contact map. Maybe you are interested in the ChimeraX interfaces tool that shows contact residues at an interface. Please give enough details in your questions so they are clear, otherwise we will not be able to spend the time to answer. Tom > On Oct 5, 2022, at 7:41 PM, Dennis Poh <pohdennis90(a)gmail.com> wrote: > > Hi Tom > > Thanks, also in the chimerax GUI software, I can fetch my separated sequences delimited with a comma, but does the overall structure that appears the most energy-minimized model or just a superimposition simply based on sequence similarity? > > How is the energy-minimization done (is it based on deltaG = G(bound complex) - G(protein1) -G(protein2)) ? > Could a contact map be produced (if 2 sequences are compared pairwise) too? > > -Dennis > > On Thu, 6 Oct 2022 at 01:43, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Dennis, > > AlphaFold on Google Colab will only work for total sequence length of about 1000 because the old Google Colab GPUs only have 16 Gbytes of memory. Modern GPUs for machine learning like an Nvidia A40 (48 GB) or A100 (40 or 80GB) or A6000 (48 GB) can handle more than 3000 residues but those GPUs cost $5000-$15000. A consumer Nvidia RTX 3090 (24 GB, $1500) can manage up to 2000 residues. Setting up AlphaFold on your own machine is a bit of work. I see from your output file name "af1848" you tried to run total sequence length 1848 which certainly will fail on Google Colab. For examples of AlphaFold runs at different sequence lengths see > > https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> > > Also AlphaFold has a minimum sequence length for each individual sequence is 16 so your example ACCCC and ALLPAAAA will not work. This minimum length is because AlphaFold uses a sequence alignment made by searching a billion database sequences and searching shorter sequence produces millions of hits that are not evolutionarily related. > > The sequence length limits are described in the ChimeraX documentation > > https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#caveats <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#caveats> > > Tom > > >> On Oct 5, 2022, at 9:35 AM, Dennis Poh via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hi Eric >> >> 1. It seems that I don't have sufficient GPU memory in colab. >> >> I have the following error message: >> INFO:colabfold.batch:Running model_1 >> /usr/local/lib/python3.7/dist-packages/haiku/_src/data_structures.py:195: FutureWarning: jax.tree_flatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_flatten instead. >> leaves, structure = jax.tree_flatten(mapping) >> /usr/local/lib/python3.7/dist-packages/haiku/_src/data_structures.py:203: FutureWarning: jax.tree_unflatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_unflatten instead. >> self._mapping = jax.tree_unflatten(self._structure, self._leaves) >> /usr/local/lib/python3.7/dist-packages/haiku/_src/stateful.py:457: FutureWarning: jax.tree_leaves is deprecated, and will be removed in a future release. Use jax.tree_util.tree_leaves instead. >> length = jax.tree_leaves(xs)[0].shape[0] >> /usr/local/lib/python3.7/dist-packages/alphafold/model/geometry/struct_of_array.py:136: FutureWarning: jax.tree_flatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_flatten instead. >> flat_array_like, inner_treedef = jax.tree_flatten(array_like) >> /usr/local/lib/python3.7/dist-packages/alphafold/model/geometry/struct_of_array.py:210: FutureWarning: jax.tree_unflatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_unflatten instead. >> inner_treedef, data[array_start:array_start + num_array]) >> /usr/local/lib/python3.7/dist-packages/alphafold/model/mapping.py:50: FutureWarning: jax.tree_flatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_flatten instead. >> values_tree_def = jax.tree_flatten(values)[1] >> /usr/local/lib/python3.7/dist-packages/alphafold/model/mapping.py:54: FutureWarning: jax.tree_unflatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_unflatten instead. >> return jax.tree_unflatten(values_tree_def, flat_axes) >> /usr/local/lib/python3.7/dist-packages/alphafold/model/mapping.py:129: FutureWarning: jax.tree_flatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_flatten instead. >> flat_sizes = jax.tree_flatten(in_sizes)[0] >> ERROR:colabfold.batch:Could not predict af1819. Not Enough GPU memory? INTERNAL: cublas error >> INFO:colabfold.batch:Done >> Downloading structure predictions to directory Downloads/ChimeraX/AlphaFold >> cp: cannot stat '*_relaxed_rank_1_model_*.pdb': No such file or directory >> cp: cannot stat '*_unrelaxed_rank_1_model_*_scores.json': No such file or directory >> >> 2. Would it be possible to run this in jupyter? Or are there alternatives? >> >> 3. " Prediction may fail with total sequence length over 1000 residues due to limited GPU memory." - this total sequence length meaning all the sequences in the list to be concatenated? >> >> 4. I seem to also have some pdbxx.m8 and afxxxx.csv files - may I know what these files are for? >> >> Thanks! >> -Dennis >> >> On Thu, 6 Oct 2022 at 00:25, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> Also, if you are copying the sequence from a text editor, make sure the editor is displaying the sequence as plain text or that you are copying as plain text, otherwise invisible formatting characters may be embedded in what you paste. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> > On Oct 5, 2022, at 9:14 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Well, the message says there is an invalid character, so all I can say is to make sure that you are pasting plain text, and check to see that you have only standard amino acid codes and commas. >> > >> > WIthout seeing exactly what you pasted, we can't tell which part caused the problem. >> > >> > Elaine >> > >> > >> >> On Oct 5, 2022, at 9:09 AM, Dennis Poh <pohdennis90(a)gmail.com <mailto:pohdennis90@gmail.com>> wrote: >> >> >> >> Hi Elaine, >> >> >> >> Thanks, I was trying to predict a multimer or the overall structure of many subunit chains using individual sequences, each separated with a comma in colab. >> >> But it seems that there was some error and no pdb file was generated; the error message is as follows: >> >> >> >> ERROR:colabfold.batch:Could not generate input features af1848: Invalid character in the sequence: >> >> Traceback (most recent call last): >> >> File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 1357, in run >> >> model_type, >> >> File "<ipython-input-1-d6881d38b934>", line 122, in generate_input_feature_wrapper >> >> (input_features, domain_names) = batch.generate_input_feature_orig(*args, **kw) >> >> File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 1018, in generate_input_feature >> >> sequence, input_msa, template_features[sequence_index] >> >> File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 869, in build_monomer_feature >> >> sequence=sequence, description="none", num_res=len(sequence) >> >> File "/usr/local/lib/python3.7/dist-packages/alphafold/data/pipeline.py", line 43, in make_sequence_features >> >> map_unknown_to_x=True) >> >> File "/usr/local/lib/python3.7/dist-packages/alphafold/common/residue_constants.py", line 580, in sequence_to_onehot >> >> raise ValueError(f'Invalid character in the sequence: {aa_type}') >> >> ValueError: Invalid character in the sequence: >> >> INFO:colabfold.batch:Done >> >> Downloading structure predictions to directory Downloads/ChimeraX/AlphaFold >> >> cp: cannot stat '*_relaxed_rank_1_model_*.pdb': No such file or directory >> >> cp: cannot stat '*_unrelaxed_rank_1_model_*_scores.json': No such file or directory >> >> >> >> -Dennis >> >> >> >> On Wed, 5 Oct 2022 at 23:36, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >> >> Hi Dennis, >> >> Your sequence input is wrong - it should contain only the sequences pasted as plain text, with only a comma between them (NOT the ">description" line because it is not supposed to be in fasta format). How to input sequence(s) is explained in the AlphaFold help page. >> >> >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict>> >> >> >> >> "For predicting a complex (multimer), the sequences of all chains in the complex must be given. The same sequence must be given multiple times if it occurs in multiple copies in the complex. The sequences can be specified either collectively as a model number chosen from the menu of currently open models (e.g. when that model contains multiple chains), or individually within a comma-separated list of UniProt identifiers or pasted-in amino acid sequences." >> >> >> >> E.g. something like >> >> >> >> ACCCC,ALLPAAAA >> >> >> >> I hope this helps, >> >> Elaine >> >> ----- >> >> Elaine C. Meng, Ph.D. >> >> UCSF Chimera(X) team >> >> Department of Pharmaceutical Chemistry >> >> University of California, San Francisco >> >> >> >>> On Oct 5, 2022, at 4:12 AM, Dennis Poh via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >>> >> >>> Sorry, I couldn't generate the pdb from chimera colab - is there anything that i may have missed? >> >>> >> >>> -Dennis >> >>> >> >>> On Wed, 5 Oct 2022 at 17:11, Dennis Poh <pohdennis90(a)gmail.com <mailto:pohdennis90@gmail.com>> wrote: >> >>> Hi >> >>> >> >>> I encounter a problem in multimer prediction with the sequences I use as input. >> >>> It's always indicating: >> >>> "Missing or invalid "sequences" argument: Sequences argument" >> >>> and " is not a chain specifier, alignment id, UniProt id, or sequence characters" >> >>> >> >>> The input format is always something like a fasta format: >> >>>> seq_id >> >>> ACCCC >> >>> >> >>>> seq_id2 >> >>> ALLPAAAA >> >>> >> >>> May I know how I can rectify this? >> >>> >> >>> Thanks! >> >>> - Dennis >> >> >> > >> > >> > _______________________________________________ >> > ChimeraX-users mailing list >> > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> > Manage subscription: >> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

1 0

combining executable html commands
by Krishnan Raman 05 Oct '22

05 Oct '22

I have large presentation with several html executable commands . is there a way I can run them with one click single command for all of them? thanks Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals 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.

2 1

usage for multimer
by Dennis Poh 05 Oct '22

05 Oct '22

Hi I encounter a problem in multimer prediction with the sequences I use as input. It's always indicating: "Missing or invalid "sequences" argument: Sequences argument" and " is not a chain specifier, alignment id, UniProt id, or sequence characters" The input format is always something like a fasta format: >seq_id ACCCC >seq_id2 ALLPAAAA May I know how I can rectify this? Thanks! - Dennis

4 7

Using ChimeraX to predict protein-protein interaction/binding via Alphafold.
by Tan, Wei Ren 05 Oct '22

05 Oct '22

Dear Sir/Mdm, Sorry to disturb you with regards to this matter, as I am unable to find any resources online, or on your YouTube channel to solve my problem. I am William, a medical student at King's College London, UK, who have been using your software, ChimeraX, for the past few months to elucidate possible protein structure for one of the protein I am currently studying. I have faced a problem with predicting a protein interaction between a heterodimer (6z1n) and a novel protein that I am studying now. When I loaded both pdbs, I am unable to run the alphafold via the command: alphafold predict #1&#2 (where #1 is 6z1n and #2 is my protein of interest) Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead? Thank you very much and sorry to disturb you! Sincerely Yours, William Tan

3 4

ligand not showing up
by Dr. Eddie 05 Oct '22

05 Oct '22

Hi all, I've got a pdb and I can't seem to get ChimeraX to recognize the ligand (resname STR) at the end of the pdb. I've modified the ATOM to be HETATM but it still does not show up. I hide solvent and the lipids and I know where it should be (from seeing it in vmd) but only a void is there. Any ideas what is wrong with the pdb? Thanks, Eddie

3 6

alphafold contacts output file
by McClean, Phillip 04 Oct '22

04 Oct '22

Hi Everyone- I used the following command to obtain a file with the contacts between two chains: alphafold contacts /B to /C output contact_pae.txt I cannot seem to find where the output file is located. Thanks for any help. Phil McClean

3 7

ChimeraX for multimeric prediction
by Dozic,Abdul-Vehab 03 Oct '22

03 Oct '22

Greetings, Firstly, I wanted to say that ChimeraX is excellent software, and it can definitely be helpful to enhance our research experience. I wanted to ask about using ChimeraX to predict whether a protein occurs in a multimeric form. I ran Alphafold for multimeric simulations and I have analyzed the predicted aligned error qualitatively, but I was wondering if ChimeraX had some built-in package for fast error analysis such as that it can tell us automatically whether it is likely to find a protein in a particular multimeric state that was modeled by Alphafold. Thanks, Best, Abdul-Vehab

2 1

morph question
by Krishnan Raman 29 Sep '22

29 Sep '22

The morph creates a new model; when i display this new model the last(frame) with final conformation shows up on the screen. is there a way to show the first frame when i play the morph using an executable command? i do have to show the model to play the morph using coordset command. thanks Krishnan 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.

2 1

Question about resfit command
by Mary Liu 28 Sep '22

28 Sep '22

Dear Chimera X users, Is it possible to show the fit of each nucleotide (not amino acid residue) in density using the resfit command or something like that? Thanks

2 2

Re: [chimerax-users] alphafold contacts output
by Elaine Meng 28 Sep '22

28 Sep '22

> On Sep 27, 2022, at 1:59 PM, McClean, Phillip <phillip.mcclean(a)ndsu.edu> wrote: > > Hi Elaine, > > I am using output data from alphafold2 multimer as provided by Colabfold. Following the video (https://www.youtube.com/watch?v=TMcjEecFHaI&t=6s) I use the following command: > > > alphafold contacts /b to /c distance 8 > > For my complex, the links at the distance are all blue (good results). What is confusing is that the distance of some of the contacts are greater than 8 angstroms. Those distances are between backbone carbon atoms, I assume. The fact that the command asks for amino acid pairs that are less than 8 angstroms apart suggest that other atoms than those in the backbone are less than 8 angstroms. Is my conclusion correct. > > Thanks as always for the advise. > > Phil Hi Phil, Yes, your conclusion is correct - the distance cutoff applies to any atom in the residue within any atom in the other residue, whereas the pseudobond is drawn between alpha-carbons, as mentioned here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts> We generally recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) since many heads are better than my one, unless you are including some data that needs to remain private. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Fitmap on a subvolume?
by vincent Chaptal 27 Sep '22

27 Sep '22

Hi, I'd like to compare 2 maps, and would like to superposse them on specific portions of the map. Is there a way to do this? I was thinking to assign a pdb to each map, and apply a superposition of pdb1 onto pdb2 and have the maps follow the movement? Thank you 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/

3 2

transparency
by Krishnan Raman 26 Sep '22

26 Sep '22

How to set transparency on surfaces during morphing? I start out with 95% but end up with 0%. The morphing works well though. Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals 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.

3 2

mseries slider
by Krishnan Raman 26 Sep '22

26 Sep '22

The mseries slider appears inside chimerax main screen. Is there a command to make it appear outside the main screen(undock it automatically in a command line? thanks Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals 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.

3 2

Website downtime starting Tuesday, Sep 27
by Elaine Meng 26 Sep '22

26 Sep '22

Dear users, The RBVI website (Chimera, ChimeraX, etc.) and RBVI-hosted web services will be down for maintenance from Tuesday, Sep 27 9pm PDT, through Wednesday, and possibly extending to Thursday, Sep 29 5pm PDT. PDT = Pacific Daylight Time. RBVI-hosted web services called from Chimera and ChimeraX include Blast Protein, Modeller, and multiple sequence alignment with Clustal Omega or MUSCLE. Sorry for the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Combining chain #1 and residue #2: naming issue
by Dmitry Semchonok 26 Sep '22

26 Sep '22

Dear colleagues, I would like to add the residues to the secondary structure (residues come from similar structures and are aligned for the position). For that I use combine tool. When I combine the secondary structure with the residues (combine #1 #2), in the new model the residues (#2) get arbitrary names and no longer belong to each of the main chains (#1). That creates a mass. Could you please advise how to change the names of the residues so that each will belong to the corresponding main chain? (In the combined model I have chan A and residues G…ect ) I tried to use Renumber Residues tool but it did not work (renumber /A-F,I-M,X seqStart 1. 0 residues renumbered) Thanks in advance. Kind regards, Dmitry

2 1

view saves/move commands
by Krishnan Raman 26 Sep '22

26 Sep '22

I tried to play a morph including a flyin of a ligand. It worked fine exceopt for the fly-in and out part The session file did not save the views with ligand away and ligand in the active site. Is there a way around it? How do I estimate a the move coordinates for a ligand to position it where I want it using move command? Thanks again for all the quick and timely help for all my queries. Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals 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.

2 1

define contour level range when molmap
by Yanhe Zhao 25 Sep '22

25 Sep '22

Dear developer, I have docked several pdb to my reference map, there are still large area of density have not assigned any models. Right now I am doing molmap onGrid of reference map, the contour range of new generated became pretty narrow and start from 0. I was wondering which option I can use to define the contour range? Thanks and best regards, Yanhe

2 2

Orientate models
by Yanhe Zhao 23 Sep '22

23 Sep '22

Dear Developer, I have aligned all my models to one reference model, What is the right way to orient all models based on reference model's xyz axis? (They have different coordinate system) Thanks and best, Yanhe

2 2

(no subject)
by Tianming Qu 23 Sep '22

23 Sep '22

Dear ChimeraX group, My name is Tianming Qu and I am currently a phd candidate in Florida State University working on MD simulation study about enzyme proteins. I am currently trying to use chimeraX to show a water density map calculated from an MD trajectory and I got the following fig as result: [cid:image001.png@01D8CD9D.17E4A690] I wonder if the ChimeraX can grab the “red region”out of the whole map, since this the “pocket region”I want. Looking forward to your reply! And it will be my great pleasure if I can have a chance to talk (maybe zoom?) to one of the developers in ChimeraX group! Thanks a lot for the help. Best, Tianming

4 14

Website downtime starting Tuesday, Sep 27
by Elaine Meng 23 Sep '22

23 Sep '22

The RBVI website (Chimera, ChimeraX, etc.) and RBVI-hosted web services will be down for maintenance from Tue, Sep 27 9pm PDT, through Wed, possibly extending to Thu, Sep 29 5pm PDT. RBVI-hosted web services called from Chimera and ChimeraX include Blast Protein, Modeller, and multiple sequence alignment with Clustal Omega or MUSCLE. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Fixing the PDB
by Dmitry Semchonok 23 Sep '22

23 Sep '22

Dear colleagues, I tried renaming the residues. When I did so in chimeraX the file opens just fine but in pymol - it looks as a green hedgehog. I suppose that the pdb file is corrupted somehow. Is there a way to fix it? Kind regards, Dmitry

2 2

Only retrieving the first predicted model in AlphaFold?
by Yao-Chi Chen 22 Sep '22

22 Sep '22

Hi: By ChimeraX, I am using AlphaFold to predict several protein-protein complexes. These complexes totally comprised about 600-800 amino acids. To have the predicted results as soon as possible, I would like to ask: 1: Is there a way to predict only one model(the best one)? 2: what's the advantage of using the Energy-minimized structures? Could I just not use it? Thanks for your help. backy

2 1

AlphaFold July 2022 update to PAE json file - cannot open PAE file with ChimeraX.
by Brandon Payliss 21 Sep '22

21 Sep '22

Hi there, I’m having some issues loading the PAE JSON file from a recent AlphaFold multimer prediction into ChimeraX, generated using a Colab notebook. The warning message is as follows: JSON file "./predicted_aligned_error.json" is not AlphaFold predicted aligned error data, expected a dictionary with keys "residue1", "residue2" and "distance" It appears that AlphaFold reduced their JSON file size by 4X on July 28th 2022 (https://alphafold.ebi.ac.uk/faq) and it no longer uses “distances”, “residue 1” and “residue 2” keys. Just curious, will there be an update coming to ChimeraX to support the new JSON file format from AlphaFold? Thanks for your time! Best, Brandon

2 1

fitmap command in chimerax
by Yanhe Zhao 21 Sep '22

21 Sep '22

Greeting there developer, I am using fitmap command of chimerax to fit pdb to map, the command as below: fitmap #2,3 inMap #1 seq 2 res 3.7 #2 and #3 are copy of each other and I manually placed them in different positions in map, #2 and #3 come to same position after the command running, I had shift option false, but come to same result. I remember it works in chimera. Could you please point me out? Thanks and have a nice day, Yanhe

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tips for large 180kda protein for morph
by Krishnan Raman 20 Sep '22

20 Sep '22

I morphed a 180kda protein. Trying to view it in stereo with surface. Works good but slow. Any tips/ideas to make the morph faster? Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals 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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comparison of 2 similar models
by Dmitry A. Semchonok 18 Sep '22

18 Sep '22

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clickable commands
by Krishnan Raman 16 Sep '22

16 Sep '22

How do I make an html file for chimerax with clickable(executable) commands? Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals 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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Feature request: combine while keeping chain IDs
by mailman-bounces＠cgl.ucsf.edu 15 Sep '22

15 Sep '22

From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Subject: Feature request: combine while keeping chain IDs Date: September 14, 2022 at 9:10:48 AM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Dear ChimeraX team, With the addition of Isolde, ChimeraX is now such a powerful modelling tool that I would like to suggest a new option for the “combine” command. It would be great if it were possible to specify that chain IDs are kept rather than being renumbered if both input models have the same chain ID (ideally this would only work if there were no overlapping residue numbers). This is very helpful if separately refined domains of proteins are put together in one PDB. Thanks a lot in advance, Matthias

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save symmetry information to cif header
by Pranav Shah 15 Sep '22

15 Sep '22

Hi Team, Is it possible to insert BIOMT like fields into the asymmetric unit of a symmetric molecule when saving the coordinates as a cif file? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Why is this happening
by Noriega, Heather 15 Sep '22

15 Sep '22

Hello, Hi Elaine and Tom. I appreciate your help on the inner volume from before both methods with blob and shape, I think I have been able to tailor it for my usage. I also have been using the icosahedron surface in Chimera, and have not had any issues until this capsid, why is it not forming inside the capsid? Did I do something? Thanks in advance. icos_why.py <https://drive.google.com/file/d/1AozCkS-zpp1M9h3ZtXIxNZUhN420WeJB/view?usp=…> Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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cuboid eraser?
by Walton, Travis Steven 14 Sep '22

14 Sep '22

Greetings everyone, I was wondering if there is a way to change the shape of the eraser tool for manually deleting map densities. By default, it is a circle, but a flat surface could be really useful in many circumstances. Thanks, Travis

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closest to playing animation chimer to chimerax
by Krishnan Raman 14 Sep '22

14 Sep '22

What is best way to play a series of frames(images)with changing representation/colors, zooming in on regions of interest etc. in chimerax? In chimera I used to create them as individual frames and play them using the animation tool/player. I do not want to encode a movie as I want them to be in stereo3d to play them within the chimerax . All suggestions welcome... Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals 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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