Context Navigation

← Previous Ticket
Next Ticket →

#16536 closed defect (fixed)

Render By Attribute: switching attributes does not preserve marker radius

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Structure Analysis	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/ava-b/OneDrive - Bar Ilan
> University/aResearch/CE/6o2p/6o2p_modified_beta.pdb"

6o2p_modified_beta.pdb title:  
Complex of ivacaftor with cystic fibrosis transmembrane conductance regulator
(CFTR) [more info...]  
  
Chain information for 6o2p_modified_beta.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6o2p_modified_beta.pdb #1  
---  
ACE — (ACE)  
ATP — adenosine-5&#x27;-triphosphate  
HSD — (HSD)  
HSE — (HSE)  
HSP — (HSP)  
MG — magnesium ion  
NME — (NME)  
VX7 — N-(2,4-di-tert-butyl-5-hydroxyphenyl)-4-oxo-1,4-
dihydroquinoline-3-carboxamide  
  
Computing secondary structure  

> open "C:/Users/ava-b/OneDrive - Bar Ilan
> University/aResearch/CE/6o2p/6o2p_beta_times4.pdb"

6o2p_beta_times4.pdb title:  
Complex of ivacaftor with cystic fibrosis transmembrane conductance regulator
(CFTR) [more info...]  
  
Chain information for 6o2p_beta_times4.pdb #2  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6o2p_beta_times4.pdb #2  
---  
ACE — (ACE)  
ATP — adenosine-5&#x27;-triphosphate  
HSD — (HSD)  
HSE — (HSE)  
HSP — (HSP)  
MG — magnesium ion  
NME — (NME)  
VX7 — N-(2,4-di-tert-butyl-5-hydroxyphenyl)-4-oxo-1,4-
dihydroquinoline-3-carboxamide  
  
Computing secondary structure  

> select add #1

19401 atoms, 19606 bonds, 13 pseudobonds, 1194 residues, 3 models selected  

> delete sel

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor #!2 target csab palette
> 0,#0fc7cf:0.435,#b2b2b2:0.87,#9e205e

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> color gray @/bfactor=0

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color grey @/bfactor=0

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color gray @/bfactor=0

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> select add #2

19401 atoms, 19606 bonds, 13 pseudobonds, 1194 residues, 3 models selected  

> color gray @/bfactor=0

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color gray atoms @/bfactor=0

Expected ',' or a keyword  

> color bfactor /all 0

> color byattribute bfactor /all 0

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color byattribute a:bfactor #!2 target csab palette
> 0,blue:0.435,white:0.87,red

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> color byattribute a:bfactor #!2 target csab palette
> 0,#b4b4b4:0.435,white:0.87,red

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> color byattribute a:bfactor #!2 target csab palette
> 0,#ffaa00:0.435,white:0.87,red

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> undo

> color byattribute a:bfactor #!2 target csab palette
> 0.0978484,#ffaa00:0.475416,white:0.87,red

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> undo

> select #!2@@bfactor>=0.013350383704885498 & @@bfactor<=0.0996761898046261

275 atoms, 262 bonds, 16 residues, 1 model selected  

> color byattribute a:bfactor #!2 target csab palette
> 0.0978484,#ffaa00:0.475416,white:0.87,red

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> undo

> color byattribute a:bfactor #!2 target csab palette
> 0.00212714,#ffaa00:0.475416,white:0.87,red

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> undo

> key #ffaa00:0.03 white:0.30 red:0.87 showTool true

> ui mousemode right "color key"

> key #ffaa00:0.03 lime:0.30 red:0.87

> ui mousemode right translate

> key #ffaa00:0.03 white:0.30 red:0.87 showTool true

> ui mousemode right "color key"

> key #ffaa00:0.03 lime:0.30 red:0.87

> key colorTreatment distinct

> key labelColor #bfbfbf

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key fontSize 15

> key fontSize 14

> key fontSize 13

> key fontSize 12

> key fontSize 11

> key fontSize 10

> key fontSize 9

> key fontSize 8

> key fontSize 7

> key fontSize 6

> key fontSize 7

> key fontSize 6

> key fontSize 5

> key fontSize 6

> key bold true

> key numericLabelSpacing equal

> ui mousemode right translate

> color byattribute a:bfactor #!2 target csab palette
> 0.03,#ffaa00:0.3,lime:0.87,red

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> color byattribute a:bfactor #!2 target csab palette
> 0,white:0.3,lime:0.87,red

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> color byattribute a:bfactor #!2 target csab palette
> 0,white:0.3,#ffaa00:0.87,red

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> help help:user/tools/render.html

> color bfactor /all 0

> color byattribute bfactor /all 0

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color bfactor /all gray

> color byattribute bfactor /all gray

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color bfactor /A gray

> color byattribute bfactor /A gray

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color bfactor /all atoms gray

> color byattribute bfactor /all atoms gray

Expected ',' or a keyword  

> rangecol bfactor,a key min gray 0.01 blue 0.05 orange 0.3 green 0.5 red

Unknown command: rangecol bfactor,a key min gray 0.01 blue 0.05 orange 0.3
green 0.5 red  

> rangecolor bfactor,a key min gray 0.01 blue 0.05 orange 0.3 green 0.5 red

Unknown command: rangecolor bfactor,a key min gray 0.01 blue 0.05 orange 0.3
green 0.5 red  

> rangecolor bfactor min gray 0.01 blue 0.05 orange 0.3 green 0.5 red

Unknown command: rangecolor bfactor min gray 0.01 blue 0.05 orange 0.3 green
0.5 red  

> rangecolor bfactor 0 gray 0.01 blue 0.05 orange 0.3 green 0.5 red

Unknown command: rangecolor bfactor 0 gray 0.01 blue 0.05 orange 0.3 green 0.5
red  

> range kdHydrophobicity min lime green max orange novalue magenta

Unknown command: range kdHydrophobicity min lime green max orange novalue
magenta  

> range bfactor min lime green max orange novalue magenta

Unknown command: range bfactor min lime green max orange novalue magenta  

> rangecolor bfactor key 0.2 blue 0.30 red 0.50 yellow

Unknown command: rangecolor bfactor key 0.2 blue 0.30 red 0.50 yellow  

> rangecolor bfactor key 0.2 blue 0.30 red 0.50 yellow

Unknown command: rangecolor bfactor key 0.2 blue 0.30 red 0.50 yellow  

> help rangecolor

No help found for 'rangecolor'  

> attribute bfactor @atoms

Unknown command: attribute bfactor @atoms  

> about

Unknown command: about  

> setattr list atoms

Missing or invalid "attrValue" argument: Expected a text string  

> list atoms

Unknown command: list atoms  

> info selection

atom id /A:102@N idatm_type Npl  
atom id /A:102@CA idatm_type C3  
atom id /A:102@C idatm_type C2  
atom id /A:102@O idatm_type O2  
atom id /A:102@CB idatm_type C3  
atom id /A:102@CG idatm_type C3  
atom id /A:102@CD1 idatm_type C3  
atom id /A:102@CD2 idatm_type C3  
atom id /A:102@H idatm_type H  
atom id /A:102@HA idatm_type HC  
atom id /A:102@HB3 idatm_type HC  
atom id /A:102@HB2 idatm_type HC  
atom id /A:102@HG idatm_type HC  
atom id /A:102@HD11 idatm_type HC  
atom id /A:102@HD12 idatm_type HC  
atom id /A:102@HD13 idatm_type HC  
atom id /A:102@HD21 idatm_type HC  
atom id /A:102@HD22 idatm_type HC  
atom id /A:102@HD23 idatm_type HC  
atom id /A:106@N idatm_type Npl  
atom id /A:106@CA idatm_type C3  
atom id /A:106@C idatm_type C2  
atom id /A:106@O idatm_type O2  
atom id /A:106@CB idatm_type C3  
atom id /A:106@CG1 idatm_type C3  
atom id /A:106@CG2 idatm_type C3  
atom id /A:106@CD1 idatm_type C3  
atom id /A:106@H idatm_type H  
atom id /A:106@HA idatm_type HC  
atom id /A:106@HB idatm_type HC  
atom id /A:106@HG13 idatm_type HC  
atom id /A:106@HG12 idatm_type HC  
atom id /A:106@HG21 idatm_type HC  
atom id /A:106@HG22 idatm_type HC  
atom id /A:106@HG23 idatm_type HC  
atom id /A:106@HD11 idatm_type HC  
atom id /A:106@HD12 idatm_type HC  
atom id /A:106@HD13 idatm_type HC  
atom id /A:179@N idatm_type Npl  
atom id /A:179@CA idatm_type C3  
atom id /A:179@C idatm_type C2  
atom id /A:179@O idatm_type O2  
atom id /A:179@CB idatm_type C3  
atom id /A:179@CG idatm_type C3  
atom id /A:179@CD idatm_type C2  
atom id /A:179@OE1 idatm_type O2  
atom id /A:179@NE2 idatm_type Npl  
atom id /A:179@H idatm_type H  
atom id /A:179@HA idatm_type HC  
atom id /A:179@HB3 idatm_type HC  
atom id /A:179@HB2 idatm_type HC  
atom id /A:179@HG3 idatm_type HC  
atom id /A:179@HG2 idatm_type HC  
atom id /A:179@HE22 idatm_type H  
atom id /A:179@HE21 idatm_type H  
atom id /A:182@N idatm_type Npl  
atom id /A:182@CA idatm_type C3  
atom id /A:182@C idatm_type C2  
atom id /A:182@O idatm_type O2  
atom id /A:182@CB idatm_type C3  
atom id /A:182@OG idatm_type O3  
atom id /A:182@H idatm_type H  
atom id /A:182@HA idatm_type HC  
atom id /A:182@HB3 idatm_type HC  
atom id /A:182@HB2 idatm_type HC  
atom id /A:182@HG idatm_type H  
atom id /A:186@N idatm_type Npl  
atom id /A:186@CA idatm_type C3  
atom id /A:186@C idatm_type C2  
atom id /A:186@O idatm_type O2  
atom id /A:186@CB idatm_type C3  
atom id /A:186@CG idatm_type C2  
atom id /A:186@OD1 idatm_type O2  
atom id /A:186@ND2 idatm_type Npl  
atom id /A:186@H idatm_type H  
atom id /A:186@HA idatm_type HC  
atom id /A:186@HB3 idatm_type HC  
atom id /A:186@HB2 idatm_type HC  
atom id /A:186@HD22 idatm_type H  
atom id /A:186@HD21 idatm_type H  
atom id /A:255@N idatm_type Npl  
atom id /A:255@CA idatm_type C3  
atom id /A:255@C idatm_type C2  
atom id /A:255@O idatm_type O2  
atom id /A:255@CB idatm_type C3  
atom id /A:255@CG1 idatm_type C3  
atom id /A:255@CG2 idatm_type C3  
atom id /A:255@CD1 idatm_type C3  
atom id /A:255@H idatm_type H  
atom id /A:255@HA idatm_type HC  
atom id /A:255@HB idatm_type HC  
atom id /A:255@HG13 idatm_type HC  
atom id /A:255@HG12 idatm_type HC  
atom id /A:255@HG21 idatm_type HC  
atom id /A:255@HG22 idatm_type HC  
atom id /A:255@HG23 idatm_type HC  
atom id /A:255@HD11 idatm_type HC  
atom id /A:255@HD12 idatm_type HC  
atom id /A:255@HD13 idatm_type HC  
atom id /A:256@N idatm_type Npl  
atom id /A:256@CA idatm_type C3  
atom id /A:256@C idatm_type C2  
atom id /A:256@O idatm_type O2  
atom id /A:256@CB idatm_type C3  
atom id /A:256@OG idatm_type O3  
atom id /A:256@H idatm_type H  
atom id /A:256@HA idatm_type HC  
atom id /A:256@HB3 idatm_type HC  
atom id /A:256@HB2 idatm_type HC  
atom id /A:256@HG idatm_type H  
atom id /A:307@N idatm_type Npl  
atom id /A:307@CA idatm_type C3  
atom id /A:307@C idatm_type C2  
atom id /A:307@O idatm_type O2  
atom id /A:307@CB idatm_type C3  
atom id /A:307@OG idatm_type O3  
atom id /A:307@H idatm_type H  
atom id /A:307@HA idatm_type HC  
atom id /A:307@HB3 idatm_type HC  
atom id /A:307@HB2 idatm_type HC  
atom id /A:307@HG idatm_type H  
atom id /A:337@N idatm_type Npl  
atom id /A:337@CA idatm_type C3  
atom id /A:337@C idatm_type C2  
atom id /A:337@O idatm_type O2  
atom id /A:337@CB idatm_type C3  
atom id /A:337@CG idatm_type Car  
atom id /A:337@CD1 idatm_type Car  
atom id /A:337@CD2 idatm_type Car  
atom id /A:337@CE1 idatm_type Car  
atom id /A:337@CE2 idatm_type Car  
atom id /A:337@CZ idatm_type Car  
atom id /A:337@H idatm_type H  
atom id /A:337@HA idatm_type HC  
atom id /A:337@HB3 idatm_type HC  
atom id /A:337@HB2 idatm_type HC  
atom id /A:337@HD1 idatm_type HC  
atom id /A:337@HD2 idatm_type HC  
atom id /A:337@HE1 idatm_type HC  
atom id /A:337@HE2 idatm_type HC  
atom id /A:337@HZ idatm_type HC  
atom id /A:359@N idatm_type Npl  
atom id /A:359@CA idatm_type C3  
atom id /A:359@C idatm_type C2  
atom id /A:359@O idatm_type O2  
atom id /A:359@CB idatm_type C3  
atom id /A:359@CG idatm_type C3  
atom id /A:359@CD idatm_type C2  
atom id /A:359@OE1 idatm_type O2  
atom id /A:359@NE2 idatm_type Npl  
atom id /A:359@H idatm_type H  
atom id /A:359@HA idatm_type HC  
atom id /A:359@HB3 idatm_type HC  
atom id /A:359@HB2 idatm_type HC  
atom id /A:359@HG3 idatm_type HC  
atom id /A:359@HG2 idatm_type HC  
atom id /A:359@HE22 idatm_type H  
atom id /A:359@HE21 idatm_type H  
atom id /A:370@N idatm_type Npl  
atom id /A:370@CA idatm_type C3  
atom id /A:370@C idatm_type C2  
atom id /A:370@O idatm_type O2  
atom id /A:370@CB idatm_type C3  
atom id /A:370@CG idatm_type C3  
atom id /A:370@CD idatm_type C3  
atom id /A:370@CE idatm_type C3  
atom id /A:370@NZ idatm_type N3+  
atom id /A:370@H idatm_type H  
atom id /A:370@HA idatm_type HC  
atom id /A:370@HB3 idatm_type HC  
atom id /A:370@HB2 idatm_type HC  
atom id /A:370@HG3 idatm_type HC  
atom id /A:370@HG2 idatm_type HC  
atom id /A:370@HD3 idatm_type HC  
atom id /A:370@HD2 idatm_type HC  
atom id /A:370@HE3 idatm_type HC  
atom id /A:370@HE2 idatm_type HC  
atom id /A:370@HZ1 idatm_type H  
atom id /A:370@HZ2 idatm_type H  
atom id /A:370@HZ3 idatm_type H  
atom id /A:913@N idatm_type Npl  
atom id /A:913@CA idatm_type C3  
atom id /A:913@C idatm_type C2  
atom id /A:913@O idatm_type O2  
atom id /A:913@CB idatm_type C3  
atom id /A:913@CG idatm_type Car  
atom id /A:913@CD1 idatm_type Car  
atom id /A:913@CD2 idatm_type Car  
atom id /A:913@CE1 idatm_type Car  
atom id /A:913@CE2 idatm_type Car  
atom id /A:913@CZ idatm_type Car  
atom id /A:913@OH idatm_type O3  
atom id /A:913@H idatm_type H  
atom id /A:913@HA idatm_type HC  
atom id /A:913@HB3 idatm_type HC  
atom id /A:913@HB2 idatm_type HC  
atom id /A:913@HD1 idatm_type HC  
atom id /A:913@HD2 idatm_type HC  
atom id /A:913@HE1 idatm_type HC  
atom id /A:913@HE2 idatm_type HC  
atom id /A:913@HH idatm_type H  
atom id /A:986@N idatm_type Npl  
atom id /A:986@CA idatm_type C3  
atom id /A:986@C idatm_type C2  
atom id /A:986@O idatm_type O2  
atom id /A:986@CB idatm_type C3  
atom id /A:986@CG idatm_type C3  
atom id /A:986@CD1 idatm_type C3  
atom id /A:986@CD2 idatm_type C3  
atom id /A:986@H idatm_type H  
atom id /A:986@HA idatm_type HC  
atom id /A:986@HB3 idatm_type HC  
atom id /A:986@HB2 idatm_type HC  
atom id /A:986@HG idatm_type HC  
atom id /A:986@HD11 idatm_type HC  
atom id /A:986@HD12 idatm_type HC  
atom id /A:986@HD13 idatm_type HC  
atom id /A:986@HD21 idatm_type HC  
atom id /A:986@HD22 idatm_type HC  
atom id /A:986@HD23 idatm_type HC  
atom id /A:1038@N idatm_type Npl  
atom id /A:1038@CA idatm_type C3  
atom id /A:1038@C idatm_type C2  
atom id /A:1038@O idatm_type O2  
atom id /A:1038@CB idatm_type C3  
atom id /A:1038@CG idatm_type C3  
atom id /A:1038@CD idatm_type C2  
atom id /A:1038@OE1 idatm_type O2  
atom id /A:1038@NE2 idatm_type Npl  
atom id /A:1038@H idatm_type H  
atom id /A:1038@HA idatm_type HC  
atom id /A:1038@HB3 idatm_type HC  
atom id /A:1038@HB2 idatm_type HC  
atom id /A:1038@HG3 idatm_type HC  
atom id /A:1038@HG2 idatm_type HC  
atom id /A:1038@HE22 idatm_type H  
atom id /A:1038@HE21 idatm_type H  
atom id /A:1131@N idatm_type Npl  
atom id /A:1131@CA idatm_type C3  
atom id /A:1131@C idatm_type C2  
atom id /A:1131@O idatm_type O2  
atom id /A:1131@CB idatm_type C3  
atom id /A:1131@CG1 idatm_type C3  
atom id /A:1131@CG2 idatm_type C3  
atom id /A:1131@CD1 idatm_type C3  
atom id /A:1131@H idatm_type H  
atom id /A:1131@HA idatm_type HC  
atom id /A:1131@HB idatm_type HC  
atom id /A:1131@HG13 idatm_type HC  
atom id /A:1131@HG12 idatm_type HC  
atom id /A:1131@HG21 idatm_type HC  
atom id /A:1131@HG22 idatm_type HC  
atom id /A:1131@HG23 idatm_type HC  
atom id /A:1131@HD11 idatm_type HC  
atom id /A:1131@HD12 idatm_type HC  
atom id /A:1131@HD13 idatm_type HC  
atom id /A:1135@N idatm_type Npl  
atom id /A:1135@CA idatm_type C3  
atom id /A:1135@C idatm_type C2  
atom id /A:1135@O idatm_type O2  
atom id /A:1135@CB idatm_type C3  
atom id /A:1135@CG idatm_type C3  
atom id /A:1135@CD1 idatm_type C3  
atom id /A:1135@CD2 idatm_type C3  
atom id /A:1135@H idatm_type H  
atom id /A:1135@HA idatm_type HC  
atom id /A:1135@HB3 idatm_type HC  
atom id /A:1135@HB2 idatm_type HC  
atom id /A:1135@HG idatm_type HC  
atom id /A:1135@HD11 idatm_type HC  
atom id /A:1135@HD12 idatm_type HC  
atom id /A:1135@HD13 idatm_type HC  
atom id /A:1135@HD21 idatm_type HC  
atom id /A:1135@HD22 idatm_type HC  
atom id /A:1135@HD23 idatm_type HC  

> attribute statistics bfactor

Unknown command: attribute statistics bfactor  

> view atoms

Expected an objects specifier or a view name or a keyword  

> set bgColor white

> set bgColor gray

> set bgColor white

> select #!2@@bfactor>=0.0022250639508142496 & @@bfactor<=0.8695483167863565

501 atoms, 480 bonds, 29 residues, 1 model selected  

> color byattribute a:bfactor #!2 target csab palette
> 0.001,lime:0.1,#ffaa00:0.4,red noValueColor grey

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> undo

> color byattribute a:bfactor #!2 target csab palette
> 0.001,lime:0.2,#ffaa00:0.4,red noValueColor grey

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> undo

> view atoms

Expected an objects specifier or a view name or a keyword  

> view atoms

Expected an objects specifier or a view name or a keyword  

> view atoms

Expected an objects specifier or a view name or a keyword  

> color byattribute a:bfactor #!2 target csab palette
> 0,white:0.2,#ffaa00:0.4,lime:0.87,red noValueColor grey

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> key white:0.00 #ffaa00:0.20 lime:0.40 red:0.87 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color byattribute a:bfactor #!2 target csab palette
> 0,white:0.2,#ffaa00:0.4,#5500ff:0.87,red noValueColor grey

19401 atoms, 1194 residues, atom bfactor range 0 to 0.87  

> undo

[Repeated 4 time(s)]

> redo

> ui tool show "Basic Actions"

> show /A target c

[Repeated 1 time(s)]

> cartoon byattribute a:bfactor #!2 0:0.25 0.2:0.25 0.4:0.25 0.87:2

1189 residues, residue bfactor range 0 to 0.87  

> cartoon byattribute a:bfactor #!2 0:0.25 0.2:0.25 0.4:0.25 0.87:2

1189 residues, residue bfactor range 0 to 0.87  

> cartoon byattribute a:bfactor #!2 0:0.25 0.2:0.25 0.4:0.25 0.87:2

1189 residues, residue bfactor range 0 to 0.87  

> cartoon byattribute a:bfactor #!2 0:0.25 0.2:0.25 0.4:0.25 0.87:2

1189 residues, residue bfactor range 0 to 0.87  

> cartoon byattribute a:bfactor #!2 0:0.25 0.2:1 0.4:1.5 0.87:2

1189 residues, residue bfactor range 0 to 0.87  

> cartoon byattribute a:bfactor #!2 0:0.25 0.2:1 0.4:2 0.87:4

1189 residues, residue bfactor range 0 to 0.87  

> cartoon byattribute a:bfactor #!2 0:0.5 0.2:1.5 0.4:3 0.87:5

1189 residues, residue bfactor range 0 to 0.87  

> cartoon byattribute a:bfactor #!2 0:0.5 0.2:2 0.4:3.5 0.87:5

1189 residues, residue bfactor range 0 to 0.87  

> label sel atoms attribute bfactor

> select #!2@@bfactor>=0.4 & @@bfactor<=0.8695483167863565

33 atoms, 31 bonds, 2 residues, 1 model selected  

> label selection attribute bfactor

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label selection residues attribute bfactor

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label sel residues attribute bfactor

> set bgColor black

> set bgColor transparent

> set bgColor gray

> set bgColor #80808000

> set bgColor black

> set bgColor transparent

> label sel residues attribute bfactor > 0.3

Expected a keyword  

> select @/bfactor>0.3

Expected an objects specifier or a keyword  

> select #1:bfactor>0.3

Expected an objects specifier or a keyword  

> select #!1:bfactor>0.3

Expected an objects specifier or a keyword  

> ui tool show "Selection Inspector"

> style sel sphere

Changed 33 atom styles  

> select atoms #!1:bfactor>0.3

Expected an objects specifier or a keyword  

> select ::name="VAL"

1264 atoms, 1190 bonds, 79 residues, 1 model selected  

> show sel atoms

> setattr sel a bfactor 0.5

Assigning bfactor attribute to 1264 items  

> setattr sel a bfactor 1

Assigning bfactor attribute to 1264 items  

> setattr sel a bfactor 0.5

Assigning bfactor attribute to 1264 items  

> setattr sel a bfactor 0.3

Assigning bfactor attribute to 1264 items  

> setattr sel a bfactor 0.3

Assigning bfactor attribute to 1264 items  

> setattr sel a bfactor 0.3

Assigning bfactor attribute to 1264 items  

> style sel ball

Changed 1264 atom styles  

> style sel sphere

Changed 1264 atom styles  

> style sel ball

Changed 1264 atom styles  

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."  

[Repeated 13 time(s)]

> setattr sel a bfactor -0.2

Assigning bfactor attribute to 1264 items  

> setattr sel a bfactor 0.3

Assigning bfactor attribute to 1264 items  

> setattr sel a bfactor 0.8

Assigning bfactor attribute to 1264 items  

> style sel sphere

Changed 1264 atom styles  

> hide sel atoms

> show sel atoms

> style sel ball

Changed 1264 atom styles  

> show sel atoms

[Repeated 1 time(s)]

> select H

9833 atoms, 1192 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 181, in <lambda>  
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 740, in _select_marker_cb  
self._set_sel_marker(marker, drag_start=event)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 760, in _set_sel_marker  
self._select_callback(self._prev_markers, self._prev_marker,
self._active_markers, marker)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 728, in _render_sel_marker_cb  
value_entry.setText("%g" % cur_marker.radius)  
^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 728, in _render_sel_marker_cb  
value_entry.setText("%g" % cur_marker.radius)  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 181, in <lambda>  
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 740, in _select_marker_cb  
self._set_sel_marker(marker, drag_start=event)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 760, in _set_sel_marker  
self._select_callback(self._prev_markers, self._prev_marker,
self._active_markers, marker)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 728, in _render_sel_marker_cb  
value_entry.setText("%g" % cur_marker.radius)  
^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 728, in _render_sel_marker_cb  
value_entry.setText("%g" % cur_marker.radius)  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 181, in <lambda>  
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 740, in _select_marker_cb  
self._set_sel_marker(marker, drag_start=event)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 760, in _set_sel_marker  
self._select_callback(self._prev_markers, self._prev_marker,
self._active_markers, marker)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 728, in _render_sel_marker_cb  
value_entry.setText("%g" % cur_marker.radius)  
^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 728, in _render_sel_marker_cb  
value_entry.setText("%g" % cur_marker.radius)  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.2130
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: LENOVO
Model: 20KHCTO1WW
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 8,437,760,000
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 10 months ago

Component:	Unassigned → Structure Analysis
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Render By Attribute: switching attributes does not preserve marker radius

comment:2 by Eric Pettersen, 10 months ago

Check session save/restore too

comment:3 by Eric Pettersen, 10 months ago

Resolution:	→ fixed
Status:	accepted → closed

Tool is not saved in session, so that part is moot.

Note: See TracTickets for help on using tickets.

Download in other formats: