Opened 6 years ago

Closed 6 years ago

Last modified 6 years ago

#2391 closed defect (not a bug)

Surface cap not colored

Reported by: susan.lea@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Surface 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-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-07)
Description
I'm trying to have a cut through of a molecular surface where the color is applied to the capping surface - this seemed to work for a while but now the cap is always grey - assuming I've managed to turn on/off some option - but cannot identify what it is

Log:
UCSF ChimeraX version: 0.91 (2019-09-07)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/smlea/Nexus365/Pathology Dunn School - SMLLAB -
Documents/Documents/MotAB/models_and_maps/gld-on-csp-by-outer-helices.pdb"
"/Users/smlea/Nexus365/Pathology Dunn School - SMLLAB -
Documents/Documents/MotAB/models_and_maps/5sv1_on_cspor-by-helices.pdb"
"/Users/smlea/Nexus365/Pathology Dunn School - SMLLAB -
Documents/Documents/MotAB/models_and_maps/bsub-on-cspor-by-outer-helices.pdb"
"/Users/smlea/Nexus365/Pathology Dunn School - SMLLAB -
Documents/Documents/MotAB/models_and_maps/cspor_motAB_may13_2plug_relabel.pdb"

  
  
  
  
Chain information for gld-on-csp-by-outer-helices.pdb #1.1  
---  
Chain | Description  
A | No description available  
B | No description available  
C D E F G | No description available  
  
Chain information for 5sv1_on_cspor-by-helices.pdb #1.2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
  
Chain information for bsub-on-cspor-by-outer-helices.pdb #1.3  
---  
Chain | Description  
A B | No description available  
C F G | No description available  
D E | No description available  
  
Chain information for cspor_motAB_may13_2plug_relabel.pdb #1.4  
---  
Chain | Description  
A B | No description available  
C D E G | No description available  
F | No description available  
  

> hide atoms

> show cartoons

> set bgColor white

> color #1.1 silver

> camera ortho

Unknown command: GldL 6-29 & 39-57  

Unknown command: GldM 7-28  

> color #1/A grey

> color #1/B darkgrey

> color #1/C salmon

> color #1/E "dark sea green"

> color #1/D steelblue

> color #1/F teal

> color #1/G burlywood

> color #1.1 silver

> surface enclose #1.1/C-G:6-29,39-57

> color #1.1/A:7-26 grey

> color #1.1/B:7-26 darkgrey

> color #1.1/C:6-29,39-57 salmon

> color #1.1/E:6-29,39-57 "dark sea green"

> color #1.1/D:6-29,39-57 steelblue

> color #1.1/F:6-29,39-57 teal

> color #1.1/G:6-29,39-57 burlywood

> hide #!1.2 models

> hide #!1.3 models

> hide #!1.4 models

> toolshed show "Side View"




OpenGL version: 4.1 ATI-1.68.22
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (4)

comment:1 by Eric Pettersen, 6 years ago

Cc: Elaine Meng added
Component: UnassignedSurface
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionSurface cap not colored

comment:2 by Tom Goddard, 6 years ago

Resolution: not a bug
Status: assignedclosed

To color a surface cap you would have to use the color zone command. For example

open 1a0m
color :5-10 blue
surface
clip
color zone #1.1 near #1
surface cap subdivision 10

I also used the "surface cap subdivision 10" command so the cap coloring has finer edges.

in reply to:  3 ; comment:3 by susan.lea@…, 6 years ago

Thanks - about half an hour ago I realised of my PDB files were read in as model 1,2,3 rather than 1.1,1.2,1.3 then the colour was transferred - I suspect the default behaviour should always be for the clip to be the colour assigned to the surface......

Sent from my iPhone

comment:4 by Tom Goddard, 6 years ago

When you color a molecular surface to match the atom colors that works because ChimeraX associates each surface point with the nearby atom. But surface clip caps do not have an association with nearby atoms, and that is why color zone is needed. The clip caps move so the association would need to be recomputed on every move.

Other non-molecular surfaces (e.g. electron microscopy maps) are also clipped. The coloring of clip caps currently just matches the single color of the surface (every surface has a single color defined even if it is being multiply colored). Possibly an enhancement could allow surfaces to define how clip caps should be colored.

Note: See TracTickets for help on using tickets.