[chimerax-users] Fwd: [Chimera-users] zoom on the selection after orientation of the selected object

[Enrico Martinez]

Thank you very much, Elaine!
1) Sorry for the mismatch between two different lists: actually I'va
already done subscription on the chimera-X mailing list but each time
when I try to post the message, I receive an automatic response that
my message was blocked by the moderator ..

2) It works fine now, thank you!!
The only thing that, running the sequence of the batch commands in
terminal I see the following (althouh it produces the png image
correctly!!):

normalization error 162 HIS :163

prev: 0.201448 -0.871822 1.04787

this: 0 0 0

guide: -0 0 0

normalization error 164 MET :165

prev: 0 0 0

this: 0 0 0

guide: 0 0 0

normalization error 162 HIS :163

prev: 0.201448 -0.871822 1.04787

this: 0 0 0

guide: -0 0 0

normalization error 164 MET :165

prev: 0 0 0

this: 0 0 0

guide: 0 0 0

normalization error 162 HIS :163

prev: 0.201448 -0.871822 1.04787

this: 0 0 0

guide: -0 0 0

normalization error 164 MET :165

prev: 0 0 0

this: 0 0 0

guide: 0 0 0

normalization error 162 HIS :163

prev: 0.201448 -0.871822 1.04787

this: 0 0 0

guide: -0 0 0

normalization error 164 MET :165

prev: 0 0 0

this: 0 0 0

guide: 0 0 0

normalization error 162 HIS :163

prev: 0.201448 -0.871822 1.04787

this: 0 0 0

guide: -0 0 0

normalization error 164 MET :165

prev: 0 0 0

this: 0 0 0

guide: 0 0 0

normalization error 162 HIS :163

prev: 0.201448 -0.871822 1.04787

this: 0 0 0

guide: -0 0 0

normalization error 164 MET :165

prev: 0 0 0

this: 0 0 0

guide: 0 0 0

normalization error 162 HIS :163

prev: 0.201448 -0.871822 1.04787

this: 0 0 0

guide: -0 0 0

normalization error 164 MET :165

prev: 0 0 0

this: 0 0 0

guide: 0 0 0

normalization error 162 HIS :163

prev: 0.201448 -0.871822 1.04787

this: 0 0 0

guide: -0 0 0


вс, 16 янв. 2022 г. в 19:32, Elaine Meng <meng at cgl.ucsf.edu>:
>
> Please send ChimeraX questions to Chimerax-users at cgl.ucsf.edu instead of chimera-users at cgl.ucsf.edu to avoid confusing people between the two programs.
>
> The view command sets clipping planes, and my guess is that when you zoom, the clipping planes don't adjust accordingly (actually I think that may be a bug, will check with the other developers).
>
> At least in my test case, the way to avoid this is to put "clip false" in your view command, e.g.
>
> view #1.1 orient clip false; turn z 90
>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Jan 16, 2022, at 5:24 AM, Enrico Martinez via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear Chimera users!
> > I am using ChimeraX for the visualization of protein-ligand
> > interactions comparing two different pdb structures A - ensemble for
> > doclong; B- X-ray pose:
> >
> > open A.pdb
> > open B.pdb'
> > match #2 to #1.1
> > # close all docking poses with the exemption of the first pose:
> > close #1.2-end
> > view
> > wait
> > # hide the protein from X-ray pose keeping only ligand for visualisation:
> > hide #2 & protein cartoon
> > hide #2 & protein surface
> > hide #2 & protein
> > #orient view on the model 1.1 and zoom closer
> > view #1.1 orient; turn z 90
> > zoom 1.5
> > wait
> >
> > The problem is that when I use zoom 1.5 after view #1.1 it hides
> > completely the representation for the molecule on the current GUI.
> > Otherwise, it works fine if I center view on the both A and B:
> > view orient; turn z 90
> > zoom 1.5
> >
> > How could I zoom the screen properly after orientation of the view on
> > the first molecule?
> >
> > Many thanks in advance!
> > Enrico
>