[chimerax-users] Some beginner's questions

Tue Mar 7 11:19:48 PST 2023

Hi Boaz,
As to your q.2, yes, I believe that is the Side View tool:

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sideview.html>

There are also related commands "clip" "view" etc. but the Side View is interactive and probably the easier way to get what you want.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html>

For q.5, either of those that you mention will work.  For the protein-surface approach, sometimes it is tricky to just get the surface  that is in the vicinity of the ligand without too many other shreds in the way, but see "surface zone" and its "maxComponents" option:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#zone>

I hope this helps,
Elaine

> On Mar 7, 2023, at 10:14 AM, Boaz Shaanan via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> Long time no talk. It's good to be in touch again. 
> Thanks for the prompt reply. 
> The Chimerax feature I find most relevant for the question I'm dealing with now is the possibility of getting electrostatic values in internal surfaces (e.g. surface surrounding ligands). See below.
> 
> q.2 : I meant the Chimera feature that opens up the view to a larger portion of the model after you've focused on an atom. When I touch the chimera icon it says: 'manipulating clipping planes and scaling'.
> 
> q. 5: I'm using an APBS .dx file. I see two interesting options of describing the electrostatic potential seen by the ligand. One is to generate the ligand's surface and get the electrostatic potential onto it (that works for me). The other is to cover the ligands surroundings by surface followed by covering it with the potential, which I haven't tried it.
> I'll also look at the videos you mentioned.
> 
> Thanks a lot for your help.
> 
>  Boaz
>  
>  
> Boaz Shaanan, Ph.D.                                       
> Dept. of Life Sciences                                      
> Ben-Gurion University of the Negev                          
> Beer-Sheva 84105                                            
> Israel                                                      
>                                                             
> E-mail: bshaanan at bgu.ac.il
> Phone: 972-8-647-2220                    
> Fax:   972-8-647-2992 or 972-8-646-1710     
>          
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Tuesday, March 7, 2023 7:49 PM
> To: בעז שאנן <bshaanan at bgu.ac.il>
> Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Some beginner's questions
>  
> Hi Boaz,
> Glad you're getting acquainted with ChimeraX!  Now I find it easier to use than Chimera.
> 
> (1) no, it is not necessary to name the selection.  The "save" command for PDB has an option to include selected atoms only, see:
> <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2frbvi.ucsf.edu%2fchimerax%2fdocs%2fuser%2fcommands%2fsave.html%23pdb&umid=39928137-F653-0705-9032-FBDEA261C206&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-d44228aa3eaa0ac417ca7dc37d5d89e3d2ff17ea>
> 
> (2) do you mean the Side View tool?  (ChimeraX does not have a per-model clipping gui currently).  There is an icon in the Graphics tab of the toolbar across the top to show the Side View, or you can open it from the menu: Tools... General... Side View
> 
> (3) if the surfaces are different, yes, that would be the reason for different min/max values found at surface vertices
> 
> (4) Chimera's ~longbond command just hides the "missing segments" pseudobond group.  In ChimeraX, you can look in the Model Panel (may need to use disclosure triangle on the model that contains it) to find the "missing structure" model.  In that tool, you can just un-check the display box in the column under the eye icon to hide the whole model, or see what the model number is to use in a hide command, e.g.
> 
> open 1www
> hide #1.1
> 
> (5) I would need more information: 
> Are you trying to show isopotential surfaces, or to color the molecular surface by the potential value?  
> If the latter, are you coloring the molecular surface of the protein or of the ligand?
> Do you have your own dx file already or do you just want to calculate Coulombic ESP and color by that?
> 
> Coloring the protein surface by Coulombic ESP is as simple as clicking the icon in the Molecule Display tab of the toolbar.  It is also covered in several tutorials, e.g.
> <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2fchimerax%2fdocs%2fuser%2ftutorials%2fbinding%2dsites.html%23esp&umid=39928137-F653-0705-9032-FBDEA261C206&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-7a01d4ac21e1a2517ba404f2658df21d74a3fe24>
> <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2fchimerax%2fdata%2fmole%2dchannel%2fmole%2dchannel.html%23esp&umid=39928137-F653-0705-9032-FBDEA261C206&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-58f57db9ad01d3ade9cf8cbe543cb3b496ee1796>
> <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.youtube.com%2fwatch%3fv%3dFEIJ0lmybXo&umid=39928137-F653-0705-9032-FBDEA261C206&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-aa80d30e0ccf412bbb18d1ba36bd72326ea1e6ec>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> > On Mar 7, 2023, at 9:12 AM, Boaz Shaanan via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > 
> > Hi,
> > 
> > I checked the commands-user guide but couldn't find  answers:
> >        • To write out a selection of atoms to a PDB, do I need to name the selection first?
> >        • I couldn't find the clipping tool (after setting a pivot I see only small part of the model).
> >        • The min/max values of a potential from APBS (.dx) seem to be different in Chimerax than they are in Chimera. I'm working on a tetramer and while in Chimera the whole tetramer surface is covered by the potential, in Chimerax it' shown for each monomer. Is that the source of the difference?
> >        • What's the Chimerax equivalent of ~longbonds of Chimera?
> >        • Just wondering, is there a demo for  electrostatic potential surface around a ligand? I seem to be making progress on that but a demo would be most helpful.
> > Thanks,
> > 
> >            Boaz
> 