- ChimeraX-users - RBVI Mailing Lists

Coloring maps based on segmentation
by M. Elizabeth Stroupe 05 Feb '24

05 Feb '24

Hi, I am having some trouble coloring my map based on segmentation. It used to be straightforward from the “Regions” menu of the segmentation tool, but now I am getting an error "TypeError: unsupported operand type(s) for *: 'float' and 'NoneType' File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/segger/regions.py", line 1884, in color_surface_pieces xyz = v - offset*n” I also tried to do it by line command but I confess I am not sure what to put for “seg-map”. Thank you for your help, Beth

2 4

Information storage
by Cygler, Miroslaw 05 Feb '24

05 Feb '24

Hi, When ChimeraX opens, it restores list of commands used in previous session(s) and the files/sessions there were accessed previously (history). Where is this data stored on the computer? How can I preload specific settings to take effect on ChimeraX opening? Thanks, Mirek

3 5

ChimeraX on new Apple cpus
by Enrico Martinez 05 Feb '24

05 Feb '24

Dear ChimeraX users! I am considering purchasing one of the recent macbook pro equipped with the modern M2 or M3 apple chips. Assuming that presently I am using the 2015 model equipped with the i7 4 core cpu and discrete radeon gpu, what should be expected increase of the performance in the case of recording of MD movies with ChimeraX using the performance of a new mac ?? Many thanks in advance Enrico

3 4

Save PDB relative to map - does not store relative postion
by Dennis Dannecker 03 Feb '24

03 Feb '24

Hello, I am running into an issue with saving pdb coordinates and their relative postioning. I am fitting an atomic model into a map model, explicitly the atomic model is rotated and translated into the map using fitmap (local optimization, rigid body fitting). Once the fit is complete, the atomic model is saved as a PDB file with the checkmark set on "Save relative to model...", here I have chosen the map the atomic model has just been fit to. This is, I think, in accordance with what is adviced in the doc of the "Fit in Map" Tool. However, when I reopen said atomic model and map in a new chimerax session (loading the map and loading the pdb file just saved relative to this map), none of the rotational and translational information is kept and the map and atomic model are in no meaning full spatial relationship. I wanted to use this procedure to prepare for cryofit and/or real space refinement in phenix, so I would like to use map and pdb for another software. As is mentioned in the doc of the "Fit in Map" Tool, volume files generally do not store rotation, thus the pdb file should be chosen to capture the rotational and translation information. Am I understanding something wrongly here or how come that the postioning is completely off when I reload map and model? Thank you for your help. Best regards, Dennis --------------------------------------------- Dennis Dannecker Master Student of Biochemistry Department of Chemistry Faculty of Mathematics and Natural Sciences University of Cologne Albertus-Magnus-Platz 50923 Cologne, Germany

2 2

Display volume default threshold level
by Chenwei Zhang 02 Feb '24

02 Feb '24

Dear UCSF ChimeraX developers, I am Chenwei Zhang, a PhD student from UBC, Canada. I am currently using ChimeraX for cryoEM density map visualization, which did a really nice job. There's one question I would like to seek answers from you. When I show a density map in ChimeraX GUI, it show automatically show a threshold level. Here's a quick example when I open emd_6272.map file: _Opened emd_6272.map as #1, grid size 108,108,108, pixel 1.02, shown at level 0.0555, step 1, values float32_ May I ask how does ChimeraX get this threshold? Or more generally, how does ChimeraX calculate the density values to get this final threshold value? Is there any command I could use in ChimeraX to extract this value? I tried to find answers in your documentation but failed so I am writing this email for help. Thank you in advance and look forward to your reply. Best, Chenwei

2 2

Using GPU in chimerax
by Sharif, Omar 01 Feb '24

01 Feb '24

Hello, I am using Chimerax with a tool called DeepSSETracer, a model that performs segmentation on the secondary structure of 3d cryo density maps. I need GPUs and CUDA enabled to test the tool. When I run the model, I have a message in the log that says Cuda is not available although I am running on a machine where relevant Nvidia GPU drivers and Cuda are already installed and working properly. I am attaching the screenshot [cid:d821ceae-9b2c-4a88-a7ba-c45b2935bee2] Is there any way to enable GPU usage within the ChimeraX? Is there any way to check if ChimeraX is using GPU and CUDA? I will be waiting for your reply. Thanks in advance, Omar Omar Sharif Ph.D. student Department of Computer Science Old Dominion University Email: osharif(a)cs.odu.edu https://odu.zoom.us/my/omarsharif786

2 2

Center atom
by Cygler, Miroslaw 01 Feb '24

01 Feb '24

Hi, I just started using ChimeraX and am confronted with how to do a simple task, namely, to placer a specific atom at the centre of the screen. What is the replacement for the command “centre” in Chimera? Thanks, Mirek

2 4

opening the session made with the new ChimeraX version using old ChimeraX
by Dmitry Semchonok 31 Jan '24

31 Jan '24

Dear colleagues, I made a session (cxs) in the newest ChimeraX. It contains the models only. How can I open it in the older ChimeraX version? Maybe I can save the session in a different format to be able to open with the older version? Unfortunately, I cannot update the older version on one PC. Thank you. Kind regards, Dmitry

3 2

transparency around the model only
by Dmitry Semchonok 31 Jan '24

31 Jan '24

Dear colleagues, I have a cryo-EM 3D map and model. A model is fitted for only part of my cryo-EM map. Is there a command to make the map transparent only where the model is fitted in? Thank you. Kind regards, Dmitry

3 2

Antivirus software warns about "Trojan.Win32.Diple" in 1.7.1 ChimeraX executable
by thomas.coudrat＠gmail.com 31 Jan '24

31 Jan '24

Hi ChimeraX list, When trying to install ChimeraX 1.7.1 Windows (md5: c79878497cfa2c1e0944e732ea4adc21) I get a warning from my antivirus software. See the description here: https://www.virustotal.com/gui/file/cc9b4af4e1a04fc647d082e04f60c111c7aeed1… In case the link doesn't work, it says that "Ikarus" is warning about "Trojan.Win32.Diple", while passing the checks with several other antivirus software. (I've seen a similar thread in the archive but it was from last year, therefore this one might be different) Kind regards, Thomas

2 1