- ChimeraX-users - RBVI Mailing Lists

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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