Opened 6 years ago

Closed 6 years ago

#2766 closed defect (not a bug)

"cartoon smooth" has no effect

Reported by: paulpillot@… Owned by: Conrad Huang
Priority: normal Milestone:
Component: Depiction Version:
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-01-15)
Description
Hello, it seems to me that the smooth parameter for the cartoon command has no effect:
I've tried "cartoon protein smooth 0" or "cartoon smooth 0.1" and I can't see any effect. My aim was to draw a kinked backbone between alpha C
Thanks!

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.92 (2020-01-15)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/paul0/Documents/Bordas/globin-superpose.cxs format session

opened ChimeraX session  

> cartoon protein smooth 0.1

> cartoon protein smooth 0

> cartoon protein smooth 1

Invalid "smooth" argument: Must be less than 1.0or equal to  

> cartoon protein smooth 0

> close session

> open /Users/paul0/Documents/molecules/tpevol/globines/BETA.PDB

Summary of feedback from opening
/Users/paul0/Documents/molecules/tpevol/globines/BETA.PDB  
---  
warning | Ignored bad PDB record found on line 1  
HEADER TRANSPORT DE L'OXYGENE 13-JUL-93 2HHB  
  
Chain information for BETA.PDB #1  
---  
Chain | Description  
D | No description available  
  

> cartoon protein smooth 0

> cartoon smooth 0

> ribbon smooth 0




OpenGL version: 4.1 INTEL-12.9.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Cc: Elaine Meng added
Component: Unassigned → Depiction
Owner: set to Conrad Huang
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → "cartoon smooth" has no effect

comment:2 by Elaine Meng, 6 years ago

Resolution: → not a bug
Status: assigned → closed

Hi Paul,
Smoothing is only applied to beta-strands, and 2HHB does not have beta-strands. So all over this structure, the cartoon path should already be exactly at the alpha-carbons. If that is not what you're seeing, let us know.

If you mean you just want to see straight sticks between alpha-carbons rather than a curvy cartoon, then choose menu: Actions... Atoms/Bonds... Chain Trace Only. After that, you can show additional atoms if you want.
Elaine

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