[chimerax-users] [Chimera-users] ChimeraX in no-gui mode: visualisation of protein-ligand interactions

[Elaine Meng]

Hello,
If you are asking about ChimeraX, please just e-mail chimerax-users at cgl.ucsf.edu (not chimera-users at cgl.ucsf.edu so we can avoid confusing people between the two programs).

Trying to answer your ChimeraX questions interleaved below.

> On Jan 15, 2022, at 9:43 AM, Enrico Martinez <jmsstarlight at gmail.com> wrote:
> 
> Thank you Elaine!
> I played with it today and it looks great!
> Some additional questions (sorry for it at the first time the thing
> seems abit tricky):
> 1)may I automatically place the 2D label on the top left corner of the
> screen instead of manually defining its X-Y using xpos ypos?
> 2dlab create title text \"name_of_the_complex" color red font gothic
> xpos .04 ypos .99 size 40

You have to put the position in the command.  The only other way is moving it by hand, which is probably not what you want to do.

> 
> 2) assuming that I open 2 molecules in the same session
> open A.pdb
> open B.pdb
> then I remove all the models with the exemption of the first
> close #1.2-end
> How could I superimpose A to B (align the structures) and then hide
> cartoon from B.pdb (keeping only ligand) ?
> 
See "matchmaker" command for aligning structures and "show" "hide" "cartoon" "surtace" commands for hiding and showing different types of display. There are many ways  to specify certain atoms or models in a command (hide, show, cartoon, color, etc.):  you can do it by model number, residue number, residue name, chemical element, etc.  How to specify atoms in command line is explained in this page:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

For example, ChimeraX commands:

matchmaker #1 to #2
view
~cartoon #2
hide #2 & protein
hide solvent

> 3) Is there any possibility to put your signature on the screen-shot?
> like "Observed by Enrico Martinez" ? :-)
> 
Sure you can put whatever text you want on the image (titles, credits, arrows, ...)  with the 2dlabels command.

> Many thanks in advance!!
> Enrico
>