January 2024 - ChimeraX-users - RBVI Mailing Lists

Defining a variable that represents the number of models
by kkssy141＠gmail.com 20 Jan '24

20 Jan '24

Hello, Would it be possible to define a variable that represents the number of models? I want to make a chimerax script that aligns #1-#(N-1) to #N. For instance, if I have a script like this where N represents the number of models opened in ChimeraX and save it as test.cxc mm #1-#(N-1) to #N In bash, I can open my PDB files that are aligned to a crystal structure 1be9: chimerax *.pdb 1be9 test.cxc The number of models (N) will be a dynamic variable depending on how many PDB files I have. Thank you. Best, Siyoung ------------------ While writing, I figured the below would work. test.cxc: mm ~#1 to #1 In bash: chimerax 1be9 *.pdb test.cxc But I still want to ask this question to know whether it is possible to retrieve the number of models opened and set this to a variable in ChimeraX. Thanks.

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Colouring clipping plane
by GOVAERTS Cédric 20 Jan '24

20 Jan '24

Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring [Graphical user interface Description automatically generated] -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. [cid:image002.png@01D94092.6E8A2390] Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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Option to convert shape to map?
by Oliver Clarke 19 Jan '24

19 Jan '24

Hi, Would it be possible in a future release to add an option to the "shape" command to output the shape as a map (filled with 1s inside the shape, zeroes outside, maybe with an optional soft edge and an ongrid option)? This would be very convenient for making simple geometrical masks for cryoEM (e.g soft cylindrical masks for classification within a nanodisc). I currently do this using "shape cylinder", use the cylinder to mask the map, and then gaussian filter the resulting masked map to the point where I can choose a threshold that conforms to the shape, but having a way to do the same thing more directly would be very nice to have. Cheers Oli

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Sequential model display controls bound to buttonpanel button?
by Oliver Clarke 19 Jan '24

19 Jan '24

Hi all, I really like the new sequential model display controls in the daily build - thank you so much for implementing these! Would it be possible to add them as a command, e.g. nextmodel and prevmodel? This way I could add them to my box of buttons, and have them in the main GUI window, without needing to switch over to the model panel. Cheers Oli

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Re: Increase cofactor size
by Tristan Croll 19 Jan '24

19 Jan '24

(disclaimer: you should probably follow Elaine’s much more extensive advice) “atomspec” just refers to any selection string - e.g. “#1/A:50”, “:LIG”, “sel” etc. On Fri, 19 Jan 2024 at 18:52, Cameron Larson <cllarson(a)ucdavis.edu> wrote: > Thank you for your help. > A silly question, but what is might 'atomspec' be? a range of atoms? > > Thank you, Tristan > > On Fri, Jan 19, 2024 at 11:51 AM Tristan Croll <tcroll(a)altoslabs.com> > wrote: > >> Try "setattr {atomspec} bonds radius {value in Angstroms}". >> >> Best, >> Tristan >> >> On Fri, Jan 19, 2024 at 4:28 PM Cameron Larson via ChimeraX-users < >> chimerax-users(a)cgl.ucsf.edu> wrote: >> >>> Hello, >>> >>> I am using chimeraX to visualize a ligand. I am familiar with the >>> commands to increase protein thickness ('cartoon style protein thickness') >>> but how can I do this for a ligand or other molecule? >>> >>> Really appreciate the help, >>> >>> -Cameron Larson >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: >>> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>> >> >> Altos Labs UK Limited | England | Company reg 13484917 >> Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, >> United Kingdom, WA14 2DT >> <https://www.google.com/maps/search/1+Ashley+Road,+Altrincham,+Cheshire,+Uni…> >> > -- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

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Increase cofactor size
by Cameron Larson 19 Jan '24

19 Jan '24

Hello, I am using chimeraX to visualize a ligand. I am familiar with the commands to increase protein thickness ('cartoon style protein thickness') but how can I do this for a ligand or other molecule? Really appreciate the help, -Cameron Larson

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Question about Cylinder Representation
by Elaine Meng 18 Jan '24

18 Jan '24

Hi Maxine, Somehow I missed your earlier question about how to make cartoon helix tubes straight instead of curved: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu…> The short answer is that sorry, ChimeraX currently does not have an option to make them straight. This feature request is in our database as ticket #1242: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/1242> There are some possible workarounds mentioned in the comments on that ticket, namely: ---------------- (1) you could try "define axis" with "perHelix true" and some padding value to show straight cylinders for helices, and then hide the ribbon. The main problem with this workaround is that the other parts of the ribbon do not connect well to the straight cylinders in some places. Example: open 2gbp hide atoms define axis perhelix true padding 2.0 hide helix ribbon Also if you only care about one specific helix, you can hide all of the other straight cylinders and only hide the ribbon for the specific residues in that helix. (2) If you want to modify the Python code in your ChimeraX distribution you can change one line and it will always produce straight helix tubes. The line is 154 in file ChimeraX.app/Contents/lib/python3.9/site-packages/chimerax/atomic/sse.py [** NOTE this is an old comment so the python version is higher now, I believe python3.11 instead of 3.9, and the line number is also different, I believe it's line 166 instead of 154 **] ...on Mac (different location on Windows and Linux, ask if you can't find it) change MIN_CURVE_LENGTH = 13 to MIN_CURVE_LENGTH = 1300 ---------------- I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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check waters to a csv file?
by Francisco Murphy Pérez 18 Jan '24

18 Jan '24

In chimerax ... tools -> structure analysis -> check waters Can we get the information from this analysis into a csv file? Can we add also the bfactor? Thanks

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Plotting Difference Map of Electron Density
by Gourav Das 16 Jan '24

16 Jan '24

Greetings everyone! I am trying to plot difference map of electron density using ChimeraX. I have created the cube file using Multiwfn. I want to show red and blue isosurfaces (+0.0012 and -0.0012 a.u., respectively) to represent the regions in which electron density is increased and decreased respectively. Please help me regarding this issue. With regards, Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

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Different ways to crop out a map region
by Thu Nguyen 16 Jan '24

16 Jan '24

Good afternoon, I am looking for several methods to crop out a map region from a larger density map. So far I know the command "volume region" but to use the command I need to know in advance the grid indices of the region I want to crop. Are there any more convenient methods to crop out a map region (maybe using mouse to directly drag a region from the volume map)? Thank you very much. Best regards, Thu

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