Opened 6 years ago

Closed 6 years ago

#2130 closed defect (fixed)

Surface caps not working consistently

Reported by: yazan.abbas@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Surface Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-51-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.9 (2019-06-06)
Description
surface cap not working

Log:
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/yazan/Dropbox/Abbas_etal_2019_brainV-
ATPase/Figures/Figure3/maps_and_models/J1509_state1_Vo.mrc

Opened J1509_state1_Vo.mrc, grid size 340,340,340, pixel 1.06, shown at level
0.16, step 2, values float32  

> open /home/yazan/Dropbox/Abbas_etal_2019_brainV-
ATPase/Maps_and_models/For_Figures/state1/State1_composite.cif

Summary of feedback from opening /home/yazan/Dropbox/Abbas_etal_2019_brainV-
ATPase/Maps_and_models/For_Figures/state1/State1_composite.cif  
---  
warnings | skipping chem_comp category: Missing column 'type' near line 297  
Unknown polymer entity '?' near line 342  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
skipping chem_comp category: Missing column 'type' near line 72840  
skipping chem_comp category: Missing column 'type' near line 72867  
  
Chain information for State1_composite.cif #2  
---  
Chain | Description  
A1 A2 A3 | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
C | No description available  
D | No description available  
E1 E2 E3 | No description available  
F | No description available  
G1 | No description available  
G2 | No description available  
G3 | No description available  
K1 | No description available  
K2 | No description available  
K3 | No description available  
a | No description available  
ac | No description available  
b | No description available  
c1 c2 c3 c4 c5 c6 c7 c8 c9 | No description available  
d | No description available  
e | No description available  
f | No description available  
pr | No description available  
  

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> surface dust #1 size 20

> surface cap true

> hide #!2 models

> surface cap true offset 0.01

> save /home/yazan/Desktop/image1.png supersample 3




OpenGL version: 3.3.0 NVIDIA 418.56
OpenGL renderer: GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
File attachment: image1.png

image1.png​

Attachments (1)

image1.png​ (824.3 KB ) - added by yazan.abbas@… 6 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by yazan.abbas@…, 6 years ago

Attachment: image1.png​ added

Added by email2trac

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Surface
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Surface caps not working consistently

comment:2 by Tom Goddard, 6 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Surface capping was not making caps if a surface had triangles hidden as was being done by the "surface dust" command. The reason was that triangles are often hidden to show a patch of a molecular surface that has boundaries. Made capping just consider the displayed triangles.

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