- ChimeraX-users - RBVI Mailing Lists

Isolde | ARG Sidechain Bond Angle Outliers
by Anderson, Jacob 31 May '22

31 May '22

I have been using Isolde inside Chimerax 1.3 - it works fantastic! However, when I go to validate on OneDep, invariably all the ARG have outliers, specifically the NE-CZ-NH1 bond angle. Has anyone else observed this and overcome it? Perhaps something wrong with my build?

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ChimeraX - XMAS pluggin modification questions
by Moya Clark, I.O. de (Isabel) 31 May '22

31 May '22

Good morning, I am a student intern at the Richard Scheltema Laboratory, and I am going to be continuing with the modification of the XMAS bundle submitted to ChimeraX recently. Right now, we are trying to extend the bundle to be able to extract specific distances between specific amino acids for two different proteins but for a molecular dynamics simulation. Either by loading a trajectory coordinates + topology files or by using the “morph” command and then “coordset slider”. So, the idea would be to extract the distances between the alpha carbons, of a set of pre-selected amino acids, in each frame of the simulation. Do you have any suggestions about any modules or methods that I should look into to extract this information in each frame? I saw there is a CooordSets class but I do not know if this would be the right way to go about it. Kind regards, Isabel de Moya Clark

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no text in log gui after ubuntu 22.04 upgrade
by Sean Connell 30 May '22

30 May '22

Hi, I was wondering if you have some suggestions for me to solve a problem I have after upgrading to ubuntu 22.04. I am running UCSF ChimeraX version: 1.3 (2021-12-08) and after upgrading ubuntu the log window in the GUI has no text. If I use the command "log save chimerx.html" and open chimerax.html in a browser I can see everything I expect in the log. It is just not being displayed. I installed using the Ubuntu 20.04 (Linux) 64-bit deb on the download page. many thanks for your help in advance sean -- --------------------------------- Sean Connell, PhD Ikerbasque Associate Structural Biology Unit, BioCruces Bizkaia Health Research Institute, Plaza Cruces s/n, 48903, Barakaldo, Spain Phone: +34 634 623 493 sean.connell(a)gmail.com https://www.biocrucesbizkaia.org <https://www.biocrucesbizkaia.org/areas-investigacion/bc3.19> frozenribosomes.com ---------------------------------

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Filled helix tube when clipped
by Zheng Ruan 27 May '22

27 May '22

Dear ChimeraX users, I'm curious to know if there is a way to have the helix tube filled when after using the clip command? I know that the clip plane of surface representation can achieve this as found in this example (https://www.rbvi.ucsf.edu/chimerax/feature_highlights/pmc.png) However, I'm not able to make it when I display my structure in cartoon cylinder representation. I attached an example image that I made. Thank you for your input. Best, Zheng

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Nonstandard residues
by Abhilash Padvannil 27 May '22

27 May '22

Hi, I am trying to open PDB (multi subunit complex) from phenix refinement in ChimeraX. One of the chains is A7. While the PDB’s open normally in coot, ChimeraX recognizes a couple of chains as nonstandard residues and is showing XXXX for the entire length of the amino acid sequence (ALA as ALAA 7 , MET as META 7) and so on. The residues correspond to subunit with chain ID A4. Attached is the sequence view Please suggest how to fix this. Thanks Abhilash. [cid:10AB2EAB-7B93-4DBA-8BFF-7329E82724B0@mcb.ucdavis.edu]

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lighting Flat + ambiant Occlusion ?
by Thibault TUBIANA 27 May '22

27 May '22

Dear Chimera X community and developpers :) I would like to create a flat representation for a protein but with ambiant occlusion, a little bit like on the example joined (made with [ https://3dproteinimaging.com/ | https://3dproteinimaging.com ] ). Is it something that it is possible with ChimeraX ? I've been playing with the shaddows but the "flat effect" is disappearing then :/ Thank you :) 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

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chimerax-1.4-rc2022.05.25 generic Linux 64-bit doesn't work
by Xiaoguang Xue 26 May '22

26 May '22

Dear developers, It seems the most recent chimerax-1.4-rc2022.05.25 generic Linux 64-bit doesn't work correctly for me. I got the following errors: NOTE: Traceback (most recent call last): File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/ChimeraX_main.py", line 1021, in <module> exit_code = init(sys.argv) File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/ChimeraX_main.py", line 573, in init from chimerax.ui import initialize_qt File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/chimerax/ui/__init__.py", line 21, in <module> from .gui import MainToolWindow, initialize_qt, menu_capitalize File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/chimerax/ui/gui.py", line 130, in <module> from Qt.QtWidgets import QApplication ModuleNotFoundError: No module named 'Qt' BUG: ModuleNotFoundError: No module named 'Qt' File "/home/test/Downloads/chimerax-1.4-rc2022.05.25/lib/python3.9/site- packages/chimerax/ui/gui.py", line 130, in from Qt.QtWidgets import QApplication _See log for complete Python traceback._ Best, XG

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Coordset command not working in nogui mode
by Shubham Devesh Ramgoolam 26 May '22

26 May '22

Hi all, I hope you are doing well. I have a python script for measuring the distance between aromatic rings of specific residues for different frames of a trajectory. To measure the distance, I am first defining centroids at the center of aromatic rings and then use the command distance. This process is repeated for each frame to be analyzed. To navigate between frames, I am using the command ‘coordset #1 {desired frame}’. When executing the script in no gui mode, the centroids are always defined with respect to the residue’s location in frame 1 even though the command coordset has changed the frame. In gui mode, the script only works if a delay is created between changing the frame and defining the new centroids. I introduced that delay by asking for a dummy user input (I ran the script from python Shell): run(session, 'coordset #1 ' + {new_frame}) y = input('dummy') run (session, 'define centroid /A:8 & aromatic-ring radius 0.3 color yellow mass false name d1’) My chimeraX version: 1.4rc202205060510 (2022-05-06) Should I be using a different command for changing frames of trajectories when in nogui mode? Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Display the boundary of a density map
by C.J. 25 May '22

25 May '22

Hi, If a similar function to chimera to show the boundary of a density map in ChimeraX? In Chimera, it is in "Volume viewer" > "Features" > "Data display options" > "Show outline box using color" option. Thanks! Jianhao

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relative position of a marker
by C.J. 25 May '22

25 May '22

Hi, I place a marker in a cryoEM map with "Volume Tracer" tool. How can I know the relative position of the marker to the origin or center of the map? Thank you! Best, Jianhao

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Surface Coloring of EM density maps by radius
by Das, Sayan 25 May '22

25 May '22

Hi, I'm trying to figure out if there is any way to color the electron density map by radius(something similar to the surface color feature on Chimera) in ChimeraX. I'm trying to color the map of a virus from the center to the outside of the capsid proteins using a series of color range based on its radius from the center. Is this feature available in ChimeraX? Any leads will be helpful. Thanks, Sayan.

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Executing a script in chimerax python shell for an interactive session
by Shubham Devesh Ramgoolam 25 May '22

25 May '22

Hi all, I hope you are doing well. I have a python script that allows the user to visualize specific residue pairs. Here is an overview of how the script functions: * Ask the user to input the path of a .cxs file (created previously) and a text file containing the pairs to be visualized * Print the names of the pairs along a uniquely assigned number * Ask the user to input a number in order to visualize the pair assigned to it To run the script currently, I have to do the following: i)Open chimerax ii)Show the shell iii) Call the script from the shell Now, is it possible to include some codes in the script that would allow me to just open chimerax, click on File -> Open -> this script, and then the shell would show up and the execution would continue there? Right now, if I ran the script using File -> Open -> this script, I would get this error: Traceback (most recent call last): File "C:/Users/Shubham/Desktop/this_script.py", line 8, in session_path = input('Enter file (.cxs) to be visualized with path: \n') RuntimeError: input(): lost sys.stdin Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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How to get all values from Fit List table
by Ioannis Skalidis 25 May '22

25 May '22

Hello all, I am doing some fit searches in Chimera X and I would like to use the values reported not only for "Correlations and times found" (which is reported in the log and can be copied) but also the "Ave" and "Inside" values reported for each fit in the Fit list. But unfortunately, I cannot copy any of the values in the Fit List. Is there any workaround available so I can get all these values? Thanks a lot, Yiannis. -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

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Multi color information export for 3D printing in ChimeraX
by M. Elizabeth Stroupe 24 May '22

24 May '22

Hi- Is there a way to export the multi-color information in ChimeraX for 3D printing? I have figured out how to combine the .mtl and .x3d information in Chimera, but would like to use rendering in ChimeraX that is not available in Chimera. Thank you (and sorry if you have answered this a million times - I couldn't find it in the archive despite my best efforts!). Beth --- Dr. M. Elizabeth (Beth) Stroupe Professor, Department of Biological Science Director, Graduate Program in Molecular Biophysics Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306

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Assembling 2 proteins
by SANTOSH RAMA BHADRA RAO TATA 24 May '22

24 May '22

Hi, I would like to create a pentamer, how can I assemble 5 different proteins subunits into a pentamer. I was trying to use matchmaker but I couldn't. can you please help me with some video how to get in use it or if there is any other way to use the software and create pentamer please let me know. Thanking you, With best wishes, Tata Santosh Rama Bhadra Rao, PhD Scholar, C/O Prof Helen Irving, La Trobe university, Bendigo, Vic-3550, Australia. Email: 19807877(a)students.latrobe.edu.au; S.Tata(a)latrobe.edu.au Phone: 0499263974

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(no subject)
by Andrea Dallapè 24 May '22

24 May '22

Dear ChimeraX Team, I would like to ask you if there's a simple and easy method (without using external software) to label the steric clashes, as in the attached image (the red line between the ball densities). Thank you for your help and attention! Andrea

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Colouring submodels using a palette
by Lorena Zuzic 24 May '22

24 May '22

Hi all, I have a model that contains 256 submodels of a ligand across trajectory frames. I would like to colour the individual models using a palette (e.g., blue:orange) so that the time progression across frames is depicted in colour. Is there a way to assign palette range to submodels? Best wishes, Lorena

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Asking copyright for one of your picture
by Catherine Duverger 23 May '22

23 May '22

Hello, I'm a French artist and I want to ask you for using one of your picture in a project. How it's possible to use it for a double exposure photography in order to prepare an exhibition in Rennes France. I probably made a book in 200 ex. Thanks a lot to answer if it's possible. Catherine

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Selecting atoms outside (or inside) a density map's contour
by Mateusz Dobrychłop 23 May '22

23 May '22

Dear ChimeraX Team, I'm a structural bioinformatician working on my PhD thesis. I've been a long time user of Chimera, and I'm now using ChimeraX to create figures for my dissertation. I genuinely love both programs. Thank you for creating them. I found myself stuck trying to perform one operation in ChimeraX that is very easy to perform in Chimera. What I'm trying to do is select (and color) all atoms of an atomic model, that are located outside of a density map's contour. In Chimera, I was able to just select the model and use the shortcut "ac oa" and that was it. Unfortunately I am not able to find a way to do that in ChimeraX. I even tried to select the atoms in Chimera, then save the selected atoms as a PDB file, and then the inverted selection as a separate PDB file, and then open the two files in ChimeraX and color them separately. This could even work for a full atom representation, but does not work well for ribbon representation. That said, if the solution to my problem could be to somehow transfer the list of atoms that are outside the map from Chimera to ChimeraX, that would work for me as well. I will appreciate any tips and suggestions! Kind regards, Mateusz

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OpenGL woes on Windows
by Pranav Shah 21 May '22

21 May '22

Hi Team, I have installed the latest RC of chimerax on a windows box running v10 Pro. The box has an Nvidia RTX6000 GPU card as well. I have updated the Nvidia drivers to the latest version yet when I start ChimeraX, i see the following error message - ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 3.0 Try updating your graphics driver. Nvidia driver version - Version: R510 U6 (512.78) WHQL; Release Date: 2022.5.16; Operating System: Windows 10 64-bit, Windows 11 Do you guys have any suggestions for trouble shooting? 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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Problems with the first installation
by mykalxxxxx 20 May '22

20 May '22

Deer developer, This is my first time install ChimeraX. What should I do if I get this prompt after installation .Thanks. (QT 5.12.12 was already installed,windows 11,ChimeraX 1.4rc202205060510). | | mykalxxxxx | | 邮箱：mykalxxxxx(a)163.com |

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Map "Blobs" tool - Generate objects?
by Ricardo Righetto 20 May '22

20 May '22

Hi again, Pardon for resurrecting another old thread: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001139.html I have needed to extract selected blobs as separate surfaces (and also separate volumes) recently and found a way to do it within ChimeraX version 1.3 (2021-12-08), here's how: 1. Right mouse → Blob → right click desired blob to color it (any color different from the rest of the volume) 2. Split the surface based on colors: sop splitbycolor #1.2 3. Use the desired split surface to mask the original volume data: vol mask #1 surf #2.2 fullMap true 4. Save as a new volume: save my_segmented_piece.mrc #3 Hope this helps :-) Best wishes, -- Ricardo Diogo Righetto

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feature request : yellow/ochre clipping planes
by Pranav Shah 18 May '22

18 May '22

Hi Guys, Would it be possible to reinstate the same color scheme used to delineate the clipping planes in Chimera into ChimeraX. The current lines are too thin and have the same color as the default map color value. This makes the manipulation of the planes harder especially when working on a smaller screen. 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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Re: [chimerax-users] [Chimera-users] interface plot
by Elaine Meng 18 May '22

18 May '22

Oops, I meant to send this to chimerax-users(a)cgl.ucsf.edu , not chimera-users(a)cgl.ucsf.edu (apologies to the latter folks)! Elaine > On May 12, 2022, at 12:27 PM, Elaine Meng via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Pranav, > If you mean that you wanted a list of the interface residues, you can use the "interfaces" network diagram edge context menu to select the residues, then list them in the Log with "info residues sel" ... and either cut-n-paste from the Log to text file or use "log save" to save it as an HTML file. The "info" command should really allow saving a text file directly, but it doesn't do that yet. I believe we have an open ticket to fix that omission. > > In the chain-chain network diagram, e.g. when the mouse cursor is over the edge representing the chain B-C interface, context-menu choices include > > Select Contact Residues of B and C > Select Contact Residues of B with C > Select Contact Residues of C with B > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#diagram> > > Or if you get a new daily build, another way to select the residues is to use menu: Select... Contacts, the Chains section of the resulting dialog: > <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> > > Then use "info residues sel" and possibly "log save" as mentioned above. > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save> > > Alternatively, you could use "measure buriedarea" specifying the two chains and "list true", which also reports each residue's buried area. (thus avoiding having to select and use "info") > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> > > Example: > measure buriedarea (/A&protein) with (/B&protein) list true > > 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 12, 2022, at 9:06 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: >> >> Indeed! Although, as a suggestion, would it be possible to highlight >> in the description that in order for the plot to inherit residue >> colors, one needs to invoke the plot _after_ the residues have been >> identified and colored? Also, could I save the output of the analysis >> to a text 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 >> >> On Thu, May 12, 2022 at 4:53 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>> haha, glad you like it!! >>> >>> Best, >>> Elaine >>> >>>> On May 12, 2022, at 8:27 AM, Pranav Shah via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>> >>>> <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 >>>> <image.png>_______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users(a)cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> > > > _______________________________________________ > 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] exporting crosslinks histogram
by Tom Goddard 17 May '22

17 May '22

Hi Pim, I added a Save Plot As... menu entry to the crosslinks histogram, can save as svg or pdf or png. I also added bins, maxLength, minLength and height options to the command to control how many bins, the x scale and height of y scale (in counts per bin). These changes will be in tomorrow's ChimeraX daily build which will become ChimeraX 1.5 eventually. Too late to make it into ChimeraX 1.4. Tom > 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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Re: [chimerax-users] [Chimera-users] Set scale factors from displayed contours?
by Tom Goddard 17 May '22

17 May '22

Hi Oliver, In tomorrow's daily ChimeraX builds you can use volume maximum #1,2 scale fromlevels and it will scale each map by 1/level where level is the displayed surface level before taking the maximum. This allows merging maps that have different intensity levels. Thanks for the suggestion. This will be in ChimeraX 1.5 but not in 1.4 and is not in Chimera. Tom > On May 6, 2022, at 2:38 PM, Elaine Meng via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Oli, > Oh, I see, you already figured out the scale factors (essentially) by adjusting thresholds interactively. So the automation would simply be doing the math of taking the ratio of the thresholds and scaling the map(s) according to that, which sounds more feasible. > > I can make a feature request ticket (probably ChimeraX), but can't make promises as I would not be the one to triage it. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On May 6, 2022, at 1:42 PM, Oliver Clarke via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >> >> Hi Elaine, >> >> I don't think I explained very well - I mean to say, calculate the scale factors from the displayed thresholds. >> >> E.g. if the user has set map1 to a threshold of 1.0, and map2 to a threshold of 2.0, in order to make them visually equivalent in a combined map, map1 needs to be scaled by a factor of 2. >> >> It would be great if this could be done automatically as a flag for the volume or vop command (as there is already a flag to provide per map scale factors). >> >> Cheers >> Oli >> >>> On May 6, 2022, at 4:39 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>> Hi Oli, >>> Our volume expert Tom is on vacation until mid-month and might not be reviewing questions for a while... so I will give my not-so-expert thoughts: >>> >>> To me, the initial identification of "overlapping bits" sounds quite subjective and thus difficult to encode. If the user could designate the boundaries of this area (by drawing a box?), perhaps automatic scaling of one map to make its values as similar as possible to the values of another map inside that box could be done. However, drawing the box would probably be just as time-consuming as the process that you are already using. >>> >>> Also, new developments/agorithms would be going only into ChimeraX, not Chimera. ChimeraX has mostly the same "vop" options as Chimera, except included in the "volume" command instead of "vop": >>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#vop> >>> >>> Best, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>>> On May 6, 2022, at 1:23 PM, Oliver Clarke via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>>> >>>> Hi, >>>> >>>> When combining maps using vop maximum (or volume maximum in chimerax), we often want to adjust the scale factors of the maps such that the overlapping bits of two aligned maps are visually on the same scale. It is possible to calculate the appropriate scale factors from the displayed thresholds, but this becomes a little time consuming when combining many maps. >>>> >>>> Would it be possible to add a flag, something like "get scalefactor from display thresholds" that would take care of this automatically? >>>> >>>> Cheers >>>> Oli >>> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > 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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Removing text labels generated with command distance
by Shubham Devesh Ramgoolam 16 May '22

16 May '22

Hi, I hope you are doing well. I have a python script, to be executed in nogui mode, which does the following: -open a pdb file -define centroids for specific residues -draw pseudobonds between specific residues -> I am using the command distance for this purpose The issue arises when I have to save the session (.cxs) when in nogui mode, I am getting this error: QGuiApplication::font(): no QGuiApplication instance and no application font set. I believe it is because of the text labels created by the command distance. So, I included the following in my code: run(session, ‘hide #2.*’) and I can now save the session. I noticed in the model panel that the pdb file is assigned to #1 and the pseudobond to #2. The text labels are created as a submodel of the pseudobond (so #2.1, 2.2,..), hence why the ‘hide #2.*’ Will this fix always work? Is the model assignment also dependent on the pdb file being opened? Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Where is the renumber sequence tool in ChimeraX?
by Phan, Isabelle 16 May '22

16 May '22

The sequence of my structure includes a tag and I want to renumber from -7 so that the first residue is the start Met. I tried the old chimera command resrenumber = FAIL. I googled and searched the docs, read the list of commands one by one, and still could not figure it out. The API has a renumber_sequence() function but I don't understand the description (what’s "the given residues”? The chain?) and was unable to find an example on how to call this from the interface. I opened the python shell and typed: from chimerax.core.commands import run run(renumber_residues('#1/A:*', -7)) # FAIL Sorry if this is trivial, I am still completely baffled by ChimeraX despite using it for years. Thanks, Isabelle CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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align 400 copies of the same density map into a circle
by SHIQING LIAO 16 May '22

16 May '22

Hi there, I am a new user and would really appreciate any input on the task I want to do using Chimerax. Currently I have a mrc map, and it is a part of a cylindrical tube-shaped structure (like the area I drew in the picture). The map looks like a curved plane from the side of the cylinder, if it helps. If I piece 400 identical copies of map with some rotation and transition, I would ideally get a cynlider shaped strutcure, without top and bottom (like the picture below). The reason why I want to piece the mrc together is that I don't have the full look of the tube, but I know the rough radius (that's how 400 was derived), and I want to make a model for the full tube, using the model of the composing protein. I managed to manually fit the models of individual protein into one map. For the other mrc copies, I tried to do the same again but it took a lot of time and not very accurate, so I'm looking for any coding solutions that might help. I'm currently thinking if it is possible for me to place a marker at the center of one mrc map. Then make 400 copies of the map with the marker. Then write a code to tell each 1/400 mrc map to rotate 0.9 degrees around the marked center and move to a coordinate. Then I can repeat the same for the protein models I mapped to one mrc map. But I have no idea how to achieve it, and any suggestions would be greatly appreciated! Thank you so much for helping me!!! Best, Shiqing [image: cf23fde5-632f-4568-9700-9307f24e0f6c.png]

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crossfade issue
by Omid Haji-Ghassemi 16 May '22

16 May '22

Dear ChimeraX community, I am having some issues with the crossfade command while making a movie. For some reason the command stretches out the image while running the transition. I am just doing a simple transition for a movie as part of a more complicated movie. To illustrate the problem I made a simple script that reproduces the issue. movie record supersample 3 size 640,480 wait 60 crossfade; cartoon hide #1/D-F; wait 60 movie encode framerate 60 output test.mov Be great if someone can let me know what I am doing wrong. Best, Omid --------------------------------------------------- --------------------------------------------------- Dr. Omid Haji-Ghassemi Assistant Professor, Biological Sciences Department University of Calgary https://hajighassemilab.org

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Re: [chimerax-users] [Chimera-users] Making a movie from map series while keeping map's colors
by Elaine Meng 16 May '22

16 May '22

Hi Michal, Since this is a ChimeraX question I'm putting it on chimerax-users(a)cgl.ucsf.edu -- otherwise the Chimera users will be confused! In the future you may want to use that address for ChimeraX questions. If I remember correctly, "vseries" re-renders the surfaces at the time of playback, unless you specify storing more of them with the "cacheFrames" option -- so try using "vseries" with "cacheFrames 20": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html> See previous answer to a similar question: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003271.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 May 16, 2022, at 12:45 AM, Michal Arie Shmuelov via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi everyone, > I have 20 maps (from 3D variability analysis) that I open as series in chimeraX. > I’m coloring the map series using the command “color zone #X near #X distance X” (coloring the map according to pdb model). > Next I’m trying to make a movie of this map series while retaining the map colors. > For some reason when the morph/ vseries starts to run the colors disappear. > Can someone help me to solve this problem? > What are the commands that I should write? > Thanks, > Michal >

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Python code for obtaining chain information
by Shubham Devesh Ramgoolam 16 May '22

16 May '22

Hi, I hope you are doing well. I have a python script in which I need generate a list of all the chains present in a structure: e.g [A,B] However, I do not know which module to import in order to write a code for this. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Showing Bond/PBond to Cartoon/Ribbons
by Anderson, Jacob 13 May '22

13 May '22

There has been a prior post on this problem, but I wanted to ask about some asymmetry I see in ChimeraX when displaying residues emanating from ribbons/cartoons. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html For example, sometimes when I select a residue on a ribbon/cartoon and write "show sel atoms,bonds", I get a floating residue. However, other times I get a nice connection between the beta carbon and the ribbon (the desired behavior). How can users get a consistent behavior where there is a connection from the beta carbon to the ribbon? Good Example - connected to ribbon [cid:6ddcc2ee-f9b2-4060-8e3f-fde8ccc74881] Two floating examples: [cid:46516984-036d-4a39-9713-9056a161548a]

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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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