zoom on the selection after orientation of the selected object
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
Please send ChimeraX questions to Chimerax-users@cgl.ucsf.edu instead of chimera-users@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@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
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 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@cgl.ucsf.edu>:
Please send ChimeraX questions to Chimerax-users@cgl.ucsf.edu instead of chimera-users@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@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
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@cgl.ucsf.edu>:
Please send ChimeraX questions to Chimerax-users@cgl.ucsf.edu instead of chimera-users@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@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
participants (2)
-
Elaine Meng -
Enrico Martinez