February 2024 - ChimeraX-users - RBVI Mailing Lists

ChimeraX AlphaFold
by Nadine Hellmold 06 Feb '24

06 Feb '24

Hi dear support team, I am so happy to use AlphaFold directly in ChimeraX and it work's so smooth! Thanks a lot for it. I was wondering what the feature "Use pdb templates when predicting structures" exactly means? I understood it like during the prediction up to 4 templates from pdb database can be used. I used the option for one prediction, for a protein complex prediction with five proteins, and found way more than four templates used for each protein. If the option is switched off, what is used as a template then? Bests Nadine -- NadineHellmold PhD student Department of Environmental Biotechnology | Helmholtz Centre for Environmental Research - UFZ 0341 235-1766 <tel:0341 235-1766> nadine.hellmold(a)ufz.de <mailto:nadine.hellmold@ufz.de> PermoserstraCe 15, 04318 Leipzig, Germany <https://www.hubspot.de/email-signature-generator?utm_source=create-signature>

3 2

ChimeraX: AlphaFold data saving help
by Anthony Newcombe 06 Feb '24

06 Feb '24

Hello ChimeraX team I am evaluating ChimeraX (non-commercial use) but have an issue you may be able to help with. When I run a structure prediction: Tools > structure prediction > AlphaFold I enter two primary sequences and hit ‘predict’ The simulation completes, but nothing opens in ChimeraX, also there is no data saved in the location below. I have tried alternative locations, but no data is saved ~/Downloads/ChimeraX/AlphaFold/prediction_[N] Do you know how I obtain saved predicted results ChimeraX? Do I need a paid service for this? Many thanks Tony Anthony Newcombe Brook Lodge Lisnacunna Ballinascarthy Clonakilty Cork

2 1

DNA/RNA style in ChimeraX
by Woo-Ri Shin 06 Feb '24

06 Feb '24

Hi I have a question about making images for protein-DNA(or RNA) complex structures. I want to make the round shape of DNA (or RNA) backbone using "nucrib" command which is provided on the web ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html) But this command doesn't work. I have the docking structure including RNA of chain A and protein of chain B. So then I modified the command like this: *alias nucrib cartoon style /A xsect oval width 1.6 thick 1.6* This command doesn't work and still initial cartoon style. Could you check this problem? [image: image.png] Thank you Best, Woo-Ri Shin -- *Woo-Ri Shin, Ph.D.* Department of Bioengineering University of Pennsylvania E-mail: wr1203(a)seas.upenn.edu Phone: +1 (267)213-2572 ᐧ

2 1

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 02 Feb '24

02 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 31 Jan '24

31 Jan '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