[chimerax-users] Some beginner's questions

[Elaine Meng]

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://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>

(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://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#esp>
<https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-channel.html#esp>
<https://www.youtube.com/watch?v=FEIJ0lmybXo>

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