- ChimeraX-users - RBVI Mailing Lists

no gui mode and redirecting output of some commands
by Shubham Devesh Ramgoolam 12 May '22

12 May '22

Hi, I hope you are doing well. I have a python script (myscript.py) as follows: from chimerax.core.commands import run import os os.chdir("C:\\Users\\Shubham\\Desktop") run(session, "open C:\\Users\\Shubham\\Desktop\\PDB_Script\\1ebt.pdb") # location of my pdb file run(session, "sel aromatic & protein") run(session, "log clear") run (session, "info residue sel") run(session, "log save aromatic_list.html") I am using the following prompt for calling chimerax from command prompt: Gui enabled: chimerax --script C:\\Users\\Shubham\\Desktop\\myscript.py Gui disabled: chimerax --nogui --script C:\\Users\\Shubham\\Desktop\\myscript.py With gui mode enabled, the html file, aromatic_list.html, is created. However, when disabling gui, nothing is created. I suspect this is because I am relying on the log which may not be functional when gui is disabled? Is there a way of redirecting the output of certain commands (e.g info, distance, angle) to a desired text file when disabling gui? I tried with sys.stdout but it did not work (empty text files were created.). Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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interface plot
by Pranav Shah 12 May '22

12 May '22

<3 <3 <3 <3 <3 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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Cartoon “Highlight color” and “Suppress false” Feature
by Gupta, Arun 12 May '22

12 May '22

Hello ChimeraX team, I am just wondering whether the “Pymol Cartoon highlight color” feature of helix and strand has been brought in the newer or the daily build versions of the ChimeraX. Someone has been just recently verbally referring to me that this feature has been updated in the newer versions of ChimeraX, but I couldn’t locate the mention in the ChimeraX mailing list. Also, I have noticed that “cartoon suppress false” command doesn’t work for the NMR ensemble PDBs I think it's more to do with specifying the “cartoon suppress false” command for the individual PDB model within ensemble PDBs. I did try to play around with selection notation for individual model with “cartoon suppress false” command but couldn’t get it right. Can you please specify the exact command notation to work around with NMR ensemble PDBs Thanks! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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Model number of geometric objects(axes, planes)
by Shubham Devesh Ramgoolam 11 May '22

11 May '22

Hi, I hope you are doing well. I am writing a python script to do the following: 1. Define planes and axes 2. Measure the angle between specific planes and between specific plane and axis The issue I am facing is that I need the model number of these geometric objects when using the command angle. Is there a command that will give the model number of the geometric objects? (In chimera, I would assign a number to the geometric objects when defining them and I would refer to it in the command angle. In chimeraX, I could assign a name to the geometric object but the command angle accept only model number for axes and planes.) Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Re: [chimerax-users] [Chimera-users] Get rotation between two views?
by Elaine Meng 11 May '22

11 May '22

Hi Oliver, Not exactly -- the closest thing I can think of is ChimeraX command "view matrix" but then you'd have to figure it out by comparing the camera matrices given for the two views, if that's even possible. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> When I make figures that differ by N-degree rotation I have to just save one view, then use a command to make that exact rotation, and then save another view before saving the session. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2022, at 8:50 AM, Oliver Clarke via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > In either Chimera or X, is there a way to obtain the orientational relationship between two views? > > E.g. if I have two views saved, I would like to be able to say "view 1 is related to view 2 by a 45deg rotation about X and a 25deg rotation about Y" - this would be very useful for figure making/writing purposes. Does this exist? > > Cheers > Oli

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select atoms nearest to chain
by Pranav Shah 10 May '22

10 May '22

Hi Elaine, How does one select atoms on one chain that are close to another chain based on a distance cut off? for eg: chain A and B form an interface. I now want to know which residues on chain A fall within a distance of 4Å from chain B and vice versa. 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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AlphaFold colouring of models predicted outside of ChimeraX
by James Hodgkinson-Bean 10 May '22

10 May '22

Hi Recently I’ve been performing batch AlphaFold predictions on colab. I was wondering if it’s possible to apply the confidence colour pallete to these structures in chimera if they have not been predicted in ChimeraX directly? Thanks, James.

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exporting crosslinks histogram
by Pim Huis in 't Veld 10 May '22

10 May '22

Dear ChimeraX team, I am analysing multiple datasets generated using crosslinking-ms, loaded as separate pseudobond files on my model. The crosslinks histogram plots works just fine and I’d now like to put some plots neatly side-by-side. My questions: - can the histogram be saved or exported? Ideally as an svg or pdf file. But png or jpg would also already be useful. I could export the .pb files and plot them elsewhere, but that seems like a workaround. - is it possible to specify the x and the y axis of the generated histograms, as well as the bin size? This would be helpful to show them side-by-side. Many thanks in advance, Pim -running v1.2.5 on mac os catalina 10.15- --- Pim J. Huis in ’t Veld, PhD Postdoctoral researcher in the lab of Andrea Musacchio Dept. of Mechanistic Cell Biology Max Planck Institute for Molecular Physiology ---

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Align Structures at Specific Residues
by Cameron Larson 10 May '22

10 May '22

Hello, I would like to know how to align structures at specific residues. For example, how do I align an ion channel at the selectivity filter instead of aligning the entire structure? Does this ability exist with chimeraX? -Thanks CL

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exporting crosslinks histogram
by Pim J. Huis in t Veld 10 May '22

10 May '22

Dear ChimeraX team, I am analysing multiple datasets generated using crosslinking-ms, loaded as separate pseudobond files on my model. The crosslinks histogram plots works just fine and I’d now like to put some plots neatly side-by-side. My questions: - can the histogram be saved or exported? Ideally as an svg or pdf file. But png or jpg would also already be useful. I could export the .pb files and plot them elsewhere, but that seems like a workaround. - is it possible to specify the x and the y axis of the generated histograms, as well as the bin size? This would be helpful to show them side-by-side. Many thanks in advance, Pim -running v1.2.5 on mac os catalina 10.15-

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Crossfade just one element
by Rabuck-Gibbons, Jessica 09 May '22

09 May '22

Hello, Would there be a way to apply crossfade ust one part of the model while making a movie? For example, I’m trying to make a movie of several different ligands in one protein. In Chimera, I can show or hide the ligands over a certain number of frames, but this functionality doesn’t seem to exist in ChimeraX. Crossfade is the closest command, but it crossfades the rocking motion as well as the show and hide motion. Is there a way to get around this? Thanks, Jessica [cid2741084884*image001.png(a)01D84823.06CD9060]<https://www.takeda.com/> [cid2741084884*image002.jpg(a)01D84823.06CD9060]<https://www.takeda.com/> Jessica Rabuck-Gibbons Scientist I, Structural Biology Drug Discovery Sciences Takeda Development Center Americas, Inc. (TDCA) 9625 Towne Centre Drive San Diego, CA 92121 USA jessica.rabuck-gibbons(a)takeda.com<mailto:jessica.rabuck-gibbons@takeda.com> The content of this email and of any files transmitted may contain confidential, proprietary or legally privileged information and is intended solely for the use of the person/s or entity/ies to whom it is addressed. If you have received this email in error you have no permission whatsoever to use, copy, disclose or forward all or any of its contents. Please immediately notify the sender and thereafter delete this email and any attachments.

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Side by side view in ChimeraX (like pymol grid_mode)
by Thibault TUBIANA 06 May '22

06 May '22

Hello all :-) In ChimeraX, is there a way to display multiple models into the same windows like the "grid_mode" mode in Pymol ? Thank you! Best regards, Thibault Tubiana.

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Chimerax scripting error and passing user supplied arguments
by Ryan Woltz 06 May '22

06 May '22

Dear community, I'm sorry if this is a repeated question, I've seen a few posts about taking in a file for the command line and doing some things then exiting. I got most of this down and I'm sure at this point it is just a matter or correcting a few lines of code. I'm trying to automate a protein modeling protocol and I have 1000 decoys at this point. Now I need to insert the 5 metals into 5 different pockets into all my decoys for a final relax before selecting my top model. I have a template pdb with all the metals in place. For 4 of these metals I have used rosetta align mover to align a decoy onto the template around a single metal binding site, save the pdb, then add on the metal coordinates then repeat for the next binding site. So this method works because the chain is continuous around these metal binding sites. However the final metal binding site is in the center and coordinated by 4 chains coming together and the positioning needs to be very precise. Chimera or chimerax solves this very well but I don't know how to put this into a script. I have a few solutions if someone can help me edit this to work. My script (chimera-data-processing.cxc) looks like this right now. cd results/ open S_0001_X-4-all-chain-A.pdb ###X = 1-1000 open hsk2-cam-homology-from-map-refined-6cno-alignment-template-1-all-chain-A.pdb info align #1:240-244,765-769,1290-1294,1815-1819@o to_atoms #2:240-244,765-769,1290-1294,1815-1819@o matchAtomNames true; wait 300 save S_0001_X-4-all-chain-A-sf-aligned.pdb #1 format pdb relModel #2; wait 30 cd ../ close quit This script is perfect if run for have a single model with the exact name written into the script after typing: chimerax-daily --nogui chimera-data-processing.cxc I have two main solutions A) run a while loop that counts down and passes a filename to chimerax: while ( X < 1000 ) chimerax-daily --nogui chimera-data-processing.cxc S_0001_X-4-all-chain-A.pdb hsk2-cam-homology-from-map-refined-6cno-alignment-template-1-all-chain-A.pdb Where in the chimerax script I take the arg1 (S_0001*.pdb) and arg2 (hsk2*.pdb)(assuming chimera-data-processing.cxc is arg0) and modify to look like this: open $arg1 open $arg2 ... save $arg1-sf-aligned.pdb #1 format pdb relModel #2; wait 30 Option B is to use the foreach command described in the open command documentation ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html) However, a copy and past of that command: *open myscript.cxc foreach ~/data/*.cif * *or* *open chimera-data-processing.cxc foreach results/S_0001_*-4-* all-chain-A.pdb results in this error: Missing filename suffix foreach I also tried this: chimerax-daily --nogui chimera-data-processing.cxc foreach results/S_0001_*-4-all-chain-A.pdb But it just runs the command. this seems to ignore everything after the first filename. I also read that if I used foreach inside the script I could use $file to replace the filename it is currently working on, would there be a way to fave $file1 and $file2? to automate this I'd also like the change the name of the template file I'm aligning to. I also attempted the python method using sys.arg = arg[1] then running things but I couldn't get it to work because I have no experience in python. What is the suggested way to complete this task? Again this is in a much larger script with user inputs so ideally it would look like this in a script (very shorthanded just for the concepts). I can also run a python command script in my bash sctipt pdb transformations if (y = 5) ###alignment metal number) while ( x < 1000) ###arg0 = command script arg1 = pdb to align arg2 = template pdb with metals chimerax-daily --nogui chimera-command-script.cxc $filenamebase$x-$alignmentnumber-*.pdb $template.pdb ###strings for variables are provided when script is initialized. ###code to extract metal coords for S_0001_$x-4-*.pdb done fi chimera-command-script.cxc: open arg1 open arg2 align model #1 to model #2 on specific atoms save arg1-new-filename.pdb close exit if someone would like a follow-up email with my attempt at chimera python sctipt using runcommand I'm very happy to supply that as a foundation to help fix, I just thought this one is easier to fix since it is really close, the script works but only for 1 pdb at a time. Apologies for bad scripting terminology and confusion with python, I've had to teach coding to myself so I might have misused terms. Thanks for any help that can be given, Ryan

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volume threshold-level
by Dmitry Semchonok 05 May '22

05 May '22

Dear colleagues, Is there a tool in chimeraX that can set the correct volume threshold level when the Molecular weight of the molecule is known? Thank you! Kind regards, Dmitry

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transparency vs. opacity
by Pranav Shah 04 May '22

04 May '22

Hi Elaine, I am trying to control the opacity/transparency of maps..however it seems to me that these two different concepts within the framework although they are used to achieve the same effect... My understanding is that transparency controls the surface being displayed whereas opacity controls the opacity of the color assigned to the surface. Is there room to unify these two concepts in ChimeraX? On an operational level, how do I control the opacity of a color in chimeraX commandline? Currently I am assigning colors based on hexcodes for specific shades... but there isnt a way to take into account the opacity of that shade with hexcodes only... 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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fitmap
by Dmitry A. Semchonok 04 May '22

04 May '22

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Color by RMSD for nucleic acid
by Rundlet, Emily 03 May '22

03 May '22

Hi ChimeraX developers, Is there a way to color nucleic acids by seq_rmsd? When I use the following, no atoms are colored. mm #1 to #2 matrix Nucleic showAlignment true color byattribute seq_rmsd #2 Thank you in advance for your help! -Emily ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

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security bug in ChimeraX 1.1 and earlier on WIndows
by Greg Couch 03 May '22

03 May '22

FYI, ChimeraX uses the Qt user interface toolkit, and recently a security bug was found in it on Windows. It affects ChimeraX 1.1 and earlier. See https://kb.cert.org/vuls/id/411271 for details. Our recommended fix is to update to the current version of ChimeraX. -- Greg

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Help pages tool hyperlink from Tool index
by William Hofsøy 02 May '22

02 May '22

Hi, I am currently writing some help pages for my tools and noticed that on the Tool index page in the chimerax help pages my tools get listed but not hyperlinked to the pages I write. Is there a way I can fix this? I also noticed that my commands are not listed here. --William

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Dali server alignment
by HONG ZHAN 02 May '22

02 May '22

Dear all, I am trying to align molecules based on Dali server output. However, I can’t download the superposition results from the Dali server webpage (or anyone know?), but I can generate an alignment file with 2D structural alignment from the Dali server. Is there a way to use matchmaker to superpose molecules based on output alignment from Dali server? How to run structure conservation calculation to color the molecule? If I just give Dali’s alignment file, it still calculate conservation based on sequence not structure. Best, Hong

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Re: [chimerax-users] ChimeraX question
by Tom Goddard 29 Apr '22

29 Apr '22

Hi Ryan, ChimeraX has a "morph" command. Here's an example using it open 2vaa open 2vab matchmaker #2 to #1 morph #1,2 save morph.pdb model #3 allCoordsets true Morphing of course only contains the atoms that are in both structures. So if you have an unbound and a bound state, and the bound tapasin is only in one structure then it will not be included in the morph since there is nothing to morph it to in the unbound state. You can delete chains that the two structures do not have in common before morphing, or you can use the same true option to the morph command "morph #1,2 same true" which will ignore chains which do not appear in both structures. Tom > On Apr 29, 2022, at 9:28 AM, Kissinger, Ryan (NIH/NIAID) [C] <ryan.kissinger(a)nih.gov> wrote: > > Hi Tom, > > I’m trying to create a morph animation in ChimeraX and I am having a lot of trouble finding decent tutorials online. I have pdb entries for unbound MHC1 and Tapasin and bound MHC1 and Tapasin. If possible I would like to morph between the bound and unbound forms. I would like to do this with ribbon and the atomic models. Any advice? > > Best Regards, > > Ryan

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Re: [chimerax-users] ChimeraX crossfade
by Elaine Meng 28 Apr '22

28 Apr '22

> On Apr 27, 2022, at 9:43 AM, Daisy Sassoon <DES867(a)student.bham.ac.uk> wrote: > > Hi Elaine, > I hope you are well. > I am currently making an animation using chimeraX and am having some issues using the crossfade command. Crossfade will successfully fade colour changes until I try and record the animation. When using movie record/encode, the crossfade function blacks out the entire screen. I have tried extending the wait times after but this does not change anything. > Do you have any advice? > > My code is shown below: > [... edited out by Elaine ...] > > Many thanks, > Daisy > > Sent from Mail for Windows Hi Daisy, I don't know why it doesn't work for you. I tried your script and for me, the recorded movie looks the same as what is shown interactively. Unless you are including data that needs to remain private, it is best to send questions to chimerax-users(a)cgl.ucsf.edu so that any other experts can respond, or if it is a bug, use Help... Report a Bug instead of sending e-mail. (Report a Bug will still send notifications to the team, including any information you type into the dialog plus other information like what ChimeraX version you are using and on what type of computer. It may be an issue with the graphics on your specific system.) I'm CC-ing chimerax-users(a)cgl.ucsf.edu on this reply but omitting your script in case it needs to remain private. However, here are some specific notes on the script: (1) the "view 3" command causes an error so I had to comment it out of your script to try it (2) there is no reason to "select all" unless you really want a green outline around everything, including the 2D label text (3) although your "crossfade 100" command works fine for me both with and without recording, you could also try using "movie crossfade frames 100" ... however, the results are slightly different. The crossfade command shows movement at the same time as the fade, whereas the movie crossfade command does not show any movement during the color fade. They are both valid commands, just different ones. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#crossfade> 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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Apple silicon (M1 chip) native version?
by Jeffrey D. Hartgerink 28 Apr '22

28 Apr '22

Are there any plans for an Apple Silicon (M1 chip) native version of ChimeraX? While things work ok via the Rosetta emulator, it would be great to have the performance from a native app. -------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University, MS 602 6100 Main Street Houston, TX 77005 jdh(a)rice.edu / 713-348-4142 hartgerink.rice.edu

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Can not save image as tiff format
by 张宁 27 Apr '22

27 Apr '22

Hello ChimeraX group, I want to save the image as tiff format, but it gives me the error "No map chosen to save", could you please help me address this issue? here are two screenshots. Thanks, Ning

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Re: [chimerax-users] [Chimera-users] Questions in ChimeraX comparing with Chimera
by Elaine Meng 27 Apr '22

27 Apr '22

Dear Long Gui, (1) There is no way to open more than one session file in the same instance of ChimeraX, sorry. You can open multiple data files, of course, and have multiple maps, structures, etc. all at the same time, just not from multiple session files. (2) I'm told that the current way to show solid style (also called image style in ChimeraX) planes with zero transparency is to use command volume #2 colormode l8 (the last thing is the letter L except lowercase l and the number 8). See image display options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid> Theoretically the following command should also work but currently does not: volume #2 transparency 0 ...although a low almost-zero number should work: volume #2 transparency 0.01 See general display options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 27, 2022, at 11:25 AM, Long Gui via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera users, > > I have been recently transferring to ChimeraX from the conventional Chimera and I am currently struggling with two features existing in Chimera but not in ChimeraX. > > • How could I combine two or several different ChimeraX files? I have been doing in Chimera as I was opening new chimera files by "Files...Open...", this is a window pop-up as the following and if I click "No", the new Chimera will be added to the cold Chimera as the old one was not closed. However, when I performed the similar operation in ChimeraX, there is no such window and the new ChimeraX would REPLACE the old one. I wonder if there is a way (probably using command to open? but I did not find the correct open options.) to open the new ChimeraX without closing the old one? > <save.png> > • I am also working with tomogram slices and cellular segmentation. Previously, in Chimera I can set this Transparency value to 0 and the Plane of the tomogram will be totally opaque. Now in ChimeraX I have used the command "transparency #2 0" (#2 is the tomogram files) but it still look quite different from my previous images in Chimera. Is there a way to set it up in ChimeraX so it could look similar as before? > <Transparency.png> > > Thanks again and I am very grateful if any advice or help could be provided. > > Long Gui, Ph.D. > Postdoc Researcher, Nicastro Lab > University of Texas Southwestern Medical Center

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