- ChimeraX-users - RBVI Mailing Lists

Doubt
by GOTZONE BARANDIKA 19 May '24

19 May '24

Dear developers, I am a new user of ChimeraX. I need to create dimers in order to analyse adsorbate-adsorbant interactions for DFT calculation. I am able to create the image on the screen, but I don´t know how to save the atomic coordinates of the dimer in a single file. If I save a .pdb file in order to produce a .xyz file, just the information of one of the entities is kept. Can you please help me? [cid:image003.jpg@01DAA921.4F8EE270] Best regards, [Diapositiva1]

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How to copy fitted monomer in a symmetric map?
by Noha Elhosseiny 18 May '24

18 May '24

Hi, I have a map with C15 symmetry in which I already refined the fitting of a single monomer (asymmetric unit) in the map using coot. I now want to generate the complete 15-mer atomic model. I watched your tutorial : ( https://youtu.be/v3jI43YJQMg?si=WeQg2ef2MPOw2J7H) and I tried to use the command "sym #2 (my model) C15 to do that, but instead of getting the monomers fitted around the axis of symmetry, I could see that 15 versions were visible but in a circular circumference around my map, away from the center, and the monomers are widely spaced from one another. I kind of expected this because I did not specify any coordinates to do this copying, so how can I fix this? Another question: when I use the command "measure symmetry" I get "C3, center 270 270 244". So I do not understand why it's detecting a C3 when it's clearly a C15. I think the above coordinates of the center can be used to solve my fitting problem but I am not exactly sure how. Finally I understood that even if the monomers appear properly fitted, given I manage to do it, that these are just graphical copies. So how can I then make real copies of the graphical representation of the 15-mer? Thanks Noha -- *Noha M. Elhosseiny, PhD* Department of Microbiology & Immunology Faculty of Pharmacy, Cairo University. Kasr El-Ainy St, Cairo, Egypt, 11562- Lab C-407 Website: https://eg.linkedin.com/in/nohaelhosseiny <https://eg.linkedin.com/in/nohaelhosseiny>

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Re: Displaying surface model of blob clostest to a centroid
by Tom Goddard 18 May '24

18 May '24

Hi Yoseph, So you have a volume and you have markers shown in ChimeraX and you wanted to show only the connected surface piece from the volume contour surface that is closest to a specific marker? Do I have that right? You show in your image a lot of markers, but you only want to find the surface piece close to one of them? And you just want to show it and hide all the other parts of the surface? What if the closest surface piece is far away? Or what if a tiny spec of surface is close, but a bigger surface piece is nearby? I think that would require writing some Python code. There is nothing in ChimeraX that I can think of that computes connected surface pieces that are close to a marker. Did you consider just showing a zone of the surface around the marker out to a certain specified distance? The ChimeraX surface zone command does that, described here https://www.cgl.ucsf.edu/chimerax/docs/user/commands/surface.html#zone Tom > On May 17, 2024, at 4:05 PM, Yoseph Loyd <yoseph.loyd(a)mines.sdsmt.edu> wrote: > > Hi Tom, > > Sorry I was having a difficult time uploading an example image to the form. I'll attach it below, I'm displaying tracked centroids as small spheres. I was hoping that there existed a way to display the nearest yellow blob to the tracks I care about. The yellow blobs signal wise are full binary objects. Thank you for helping me with this. > > Best, > Yoseph > > On Fri, May 17, 2024 at 4:43 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Yoseph, >> >> I don't know what you mean "objects that fit to a centroid that I've tracked". What kind of object? The centroid of what? And why isn't it displayed currently? You'll have to explain better. >> >> Tom >> >> > On May 17, 2024, at 2:07 PM, Yoseph Loyd via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Hi, >> > >> > My name is Yoseph, I was wondering if there is a way to display objects that fit to a centroid that I've tracked and imported into chimera. Thank you for taking the time to read this and have a nice day. >> > >> > >> > Best, >> > Yoseph >> > _______________________________________________ >> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> > >>

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Displaying surface model of blob clostest to a centroid
by yoseph.loyd＠mines.sdsmt.edu 17 May '24

17 May '24

Hi, My name is Yoseph, I was wondering if there is a way to display objects that fit to a centroid that I've tracked and imported into chimera. Thank you for taking the time to read this and have a nice day. Best, Yoseph

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Re: [Chimera-users] Saving symmetry model in pdb format
by Elaine Meng 17 May '24

17 May '24

Hi Kailash Singh Bisht, You sent the message to chimera-users which is for Chimera questions. However, you said "ChimeraX team" so I am guessing that you are actually using ChimeraX, and I CC'd the chimerax-users address above -- please use that one for ChimeraX questions. You didn't say how you created the symmetry structure. I am guessing that when you create the symmetry structure with the "sym" command, you need to include the option "copies true" so that you get real atomic copies instead of just graphical clones. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies> 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 > On May 17, 2024, at 12:27 AM, Kailash Singh Bisht via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello ChimeraX team > > I am trying to export the symmetry structure of the protomer virus protein as a pdb file but whenever I am saving that model it only saves the same protomer instead of the whole symmetry structure. Can you please help? How to export those symmetry models as PDB files > > -- > With Regards > Thanking You > > Kailash Singh Bisht > Ph.D. Student

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prediction of 5mC modification and transcription factor interaction through AlphaFold 3
by Kaan Okay - HI 17 May '24

17 May '24

Hi, I use Alphafold through UCSF ChimeraX. It is a very nice tool, I believe its developers have done a good job. As you know, AlphaFold 3 is a new model that allows us to predict DNA modification and protein interactions (https://www.nature.com/articles/s41586-024-07487-w) What I wonder is when this model will be transferred to UCSF ChimeraX and whether we can predict protein interactions and DNA modifications (e.g., 5mC modification on cytosine bases in DNA). I'm looking forward to hearing from you. All the best.

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Cinematographic effects in MD movie recording
by Enrico Martinez 17 May '24

17 May '24

Dear Chimera-X users ! I would like to add some cinematographic effects such as changing the camera angle back and forth during a short recording time of MD movies. Could you suggest some scripting tricks that I could add to the following coordset routine: # start recording movie record size 3840,2160 supersample 1 ## play movie from beginning to the end coordset #1 1,1000,1 wait 1000 etc Would it be possible to bend the camera automatically e.g. during the first 250 steps of recording ? Any other possibilities ? Yours with thanks Enrico

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Displaying angles in chimera
by Prathvi Singh 16 May '24

16 May '24

Hi Elaine, Is it possible in chimera/chimeraX to display angles between two covalent bonds like in pymol? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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"H-Bonds" Tool Displays Non-H Bond Bonds?
by Melisa Kalaba 15 May '24

15 May '24

Hello. I wanted to display the hydrogen bonds between my ligand and protein, however when I hovered over the displayed bonds with my cursor I noticed one of the bonds being between two nitrogen atoms and I was confused. Is this a bug within the software? I'll attach a screenhot so you can take a look at it yourself: https://drive.google.com/file/d/1N5YRncOrrJnEVRpM8XD7O1tPG02ZTu8G/view?usp=…

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Missing-structure labels
by Eric Pettersen 15 May '24

15 May '24

Hi all, In the 1.9 daily build only (not the 1.8 release candidate), missing-structure pseudobonds are now labeled with the number of residues the pseudobond represents. If you do not like this new behavior, you can turn it off in the 'Labels' preference category (make sure to 'Save' your changed setting). --Eric Eric Pettersen UCSF Computer Graphics Lab

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