May 2023 - ChimeraX-users - RBVI Mailing Lists

'Tunnel' hydrophobic colouring
by Kelly May Frain 16 May '23

16 May '23

Hello, Previously you were super quick and helping when answering my ‘tunnel’ question, so I thought I could try another question for chimeraX. I have a protein which via Caver I have found a tunnel which runs through. This tunnel has been exported as a pdb and using your help and python, the tunnel now changes diameter perfectly as it weaves through the structure. I had this idea to colour the tunnel according its surrounding residues and their hydrophobicity. So in chimeraX I can colour my model ‘hydrophobically’ from cyan to gold. Then I wanted to 'zone’ these colours into my tunnel pdb. But when I use color zone #2 near #1 distance 20 for example, the tunnel is coloured in red and blue patches? Even though the model is cyan and gold. Is there a way to achieve my goal please? Best wishes, Kelly

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Duplicate the model
by tim smith 15 May '23

15 May '23

Hello everybody, I would like to create copy of the model in the same session but with a different model number. Please, could you suggest how to do that. Thank you. Best Tim

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rendering of bond making/breaking along a trajectory
by Hassan, Sergio (NIH/NIAID) [E] 15 May '23

15 May '23

Hi, I am not sure whether this is a bug or something not yet implemented or else. I performed QM/MM simulations of a proton translocating along a water chain. This involves the breaking of a bond and the making of a new bond. The visualization of the trajectory does not show this process; instead, the original definition of bond is retained, without being updated at each timeframe. Is there a way to tell ChimeraX to automatically check covalent bonds at each snapshot and update the bond accordingly? A simple distance criterion will do. This is only for rendering purpose. In case further clarifications are needed: D—H.......A (with -- indicating the covalent bond between proton and domor and .... indicating the proximal acceptor) must be transformed to D.......H—A. Instead, it is rendered as D-------H..A (with an artificially elongated DH bond and no new HA bond) thanks s _____________________________________ Sergio A. Hassan https://bioinformatics.niaid.nih.gov/cmm/ BCBB/NIAID/NIH/DHHS 301 761 7221 (office) 301 741 5579 (mobile)

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Trajectory smoothing
by Shubham Devesh Ramgoolam 15 May '23

15 May '23

Hi all, Does chimeraX has a command for trajectory smoothing? Based on previous similar questions, I know a script was written for trajectory smoothing in chimera/chimeraX. However, I cannot not access this script because it is not found on the server anymore. Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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REMINDER: ChimeraX website downtime
by Elaine Meng 15 May '23

15 May '23

REMINDER: Due to a scheduled power outage at UCSF followed by server upgrades, the ChimeraX website and web services will be unavailable -- the estimated downtime is from Tuesday May 16 8pm PDT through Wednesday May 17 8pm PDT. Please pardon any inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [chimerax-users] Measuring distance between two atoms in a single protein
by Cheng, Jiaxuan (NIH/VRC) [F] 14 May '23

14 May '23

Hi Elaine, I met a problem when measuring the distance between two atoms. I entered “distance #1.16/B:94 at CA #1.35/B:94 at CA” , but the ChimeraX reports “expected a keyword”. Could you let me know how to solve it? Thanks! Jiaxuan [cid:image001.png@01D98530.82126BB0]

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Scrolling wheel feature request
by vincent Chaptal 12 May '23

12 May '23

Dear ChimeraX team, a very useful feature in Pymol is the use of the scrolling wheel on the mouse to clip the view plane and add depthcue. After centering on one element, it is very convenient to focus on some areas and remove things from the view, for both viewing and article figures. I haven't find a similar feature in ChimeraX, would it be possible to implement it? I've tried to play with the depthcue command, but it I find it much harder to get to what I would like. lighting depthcue true depthCueStart 0.3 depthCueEnd 0.5 If the view with the clipping can be saved with the "view matrix" command, it would be extremely useful. Thank you. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Re: [chimerax-users] unifold
by Tom Goddard 11 May '23

11 May '23

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coloring a clipped surface cap by property
by Elaine Meng 10 May '23

10 May '23

Hi Noam, Glad you like ChimeraX! (A) The way to color a clipped surface cap by the molecular liphilicity potential (MLP) or Coulombic electrostatic potential (ESP) is covered in this tutorial section: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#c…> (B) The way to color a clipped surface cap by an atomic or residue attribute is to: 1) color the underlying atoms by the atom or residue attribute (with command "color byattribute" or the Render by Attribute tool) 2) use command "color zone" on the surface cap model to make it match the atoms. You may need to use the disclosure triangles in the Models panel to figure out the model number of the surface cap model. Example: color zone #1.1.1 near #1 distance 3 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> Since "N" heads are better than one, we generally recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) unless you are including data or figures that should remain private. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2023, at 7:40 AM, Noam Prywes <noam.prywes(a)gmail.com> wrote: > > Dr. Meng, > > I'm a postdoc at berkeley and I'm trying to make a figure where I slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity. > > Do I need to make a .defattr file that colors by atom instead? > > Thanks for your help and the amazing service that is chimeraX. > > Best wishes, > Noam

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Hiding distance labels during trajectory playback
by Lewandowski, Jozef 10 May '23

10 May '23

Hi, Is there an easy way to hide distance labels during the playback of an MD trajectory? Even if I delete or hide the labels in one frame they get generated when next frame is loaded. I tried to include hiding/deleting the labels command in perframe but they flash on before they are removed. Ultimately, I would like to record a movie where only the pseudobonds are shown but not the labels. Thank you, Józef

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