Opened 5 years ago

Closed 5 years ago

#3326 closed defect (fixed)

'rename' command: maximum recursion depth exceeded

Reported by: sitins07@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0rc202005220559 (2020-05-22 05:59:43 UTC)
Description
Trying to rename chain id from #8 to #4.3.1, why its not possible? That would be very convenient during 3D classifications reviewing and summarizing results. 
Also one more issue appears while renaming #3 into #3.1 

Log:
UCSF ChimeraX version: 1.0rc202005220559 (2020-05-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open X:\Work\Projects\48S\ChimeraX\Literature.cxs format session

Log from Mon May 25 18:18:18 2020UCSF ChimeraX version: 1.0rc202005220559
(2020-05-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6FEC

6fec title:  
Human cap-dependent 48S pre-initiation complex [more info...]  
  
Chain information for 6fec #1  
---  
Chain | Description  
1 | Eukaryotic translation initiation factor 3 subunit A  
2 | Eukaryotic translation initiation factor 3 subunit C  
3 | Eukaryotic translation initiation factor 3 subunit E  
4 | Eukaryotic translation initiation factor 3 subunit F  
5 | Eukaryotic translation initiation factor 3 subunit H  
6 | Eukaryotic translation initiation factor 3 subunit K  
7 | Eukaryotic translation initiation factor 3 subunit L  
8 | Eukaryotic translation initiation factor 3 subunit M  
9 | eukaryotic translation initiation factor 3 subunit D  
A | 18S ribosomal RNA  
F | Messenger RNA (26-MER)  
G | 40S ribosomal protein S11  
H | 40S ribosomal protein S16  
I | 40S ribosomal protein S4, X isoform  
J | 40S ribosomal protein S29  
K | 40S ribosomal protein S9  
L | 40S ribosomal protein S18  
N | Transfer RNA (75-MER)  
P | Eukaryotic translation initiation factor 2 subunit 1  
Q | 40S ribosomal protein S23  
R | 40S ribosomal protein S19  
S | Eukaryotic translation initiation factor 2 subunit 3  
U | 40S ribosomal protein S5  
V | 40S ribosomal protein S30  
W | 40S ribosomal protein S25  
X | 40S ribosomal protein S7  
Y | 40S ribosomal protein S27  
Z | 40S ribosomal protein S13  
a | 40S ribosomal protein S15a  
b | 40S ribosomal protein S21  
c | 40S ribosomal protein S2  
d | EUKARYOTIC TRANSLATION INITIATION FACTOR 2 β SUBUNIT (eIF2-Beta)  
e | 40S ribosomal protein S17  
f | 40S ribosomal protein SA  
g | 40S ribosomal protein S3  
h | 40S ribosomal protein S20  
i | 40S ribosomal protein S3a  
j | 40S ribosomal protein S14  
k | 40S ribosomal protein S26  
l | 40S ribosomal protein S28  
m | Receptor of activated protein C kinase 1  
n | 40S ribosomal protein S15  
o | 40S ribosomal protein S8  
p | Ubiquitin-40S ribosomal protein S27a  
q | 40S ribosomal protein S6  
r | 40S ribosomal protein S12  
s | 40S ribosomal protein S24  
t | 40S ribosomal protein S10  
u | Eukaryotic translation initiation factor 4B  
w | Eukaryotic translation initiation factor 3 subunit B  
  

> ui mousemode right select

Drag select of 117189 atoms, 1670 pseudobonds  

> hide sel atoms

> style sel stick

Changed 117189 atom styles  

> show sel cartoons

> select clear

> sequence chain #1/u

Alignment identifier is 1.u  

> select /u:1-76

608 atoms, 619 bonds, 1 model selected  

> open "X:/Work/Projects/48S/closed state 3.7A
> overall/3d360_closedagain_c3_ctf_5A.ccp4"

Opened 3d360_closedagain_c3_ctf_5A.ccp4, grid size 360,360,360, pixel 1.16,
shown at level 4.62, step 2, values float32  

> open "X:/Work/Projects/48S/open state 4.7A
> overall/3d360_openagain_c2_ctf_5A.ccp4"

Opened 3d360_openagain_c2_ctf_5A.ccp4, grid size 360,360,360, pixel 1.16,
shown at level 4.37, step 2, values float32  

> hide #!1 models

> volume #3 level 3.621

> open X:/Work/Projects/48S/ChimeraX/closed/40S/40S.cif

Chain information for 40S.cif #4  
---  
Chain | Description  
S2 | 18S ribosomal RNA  
SA | 40S ribosomal protein SA  
SB | 40S ribosomal protein S3a  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15a  
SX | 40S ribosomal protein S23  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | 40S ribosomal protein S30  
  
Drag select of 2 3d360_closedagain_c3_ctf_5A.ccp4 , 73334 atoms, 1619
pseudobonds, 39 bonds  

> select clear

> select #4

73334 atoms, 78115 bonds, 1619 pseudobonds, 4 models selected  

> hide sel atoms

> show sel cartoons

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected atoms"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> fitmap sel inMap #2

Fit molecule 40S.cif (#4) to map 3d360_closedagain_c3_ctf_5A.ccp4 (#2) using
73334 atoms  
average map value = 6.866, steps = 232  
shifted from previous position = 13  
rotated from previous position = 22 degrees  
atoms outside contour = 22635, contour level = 4.6191  
  
Position of 40S.cif (#4) relative to 3d360_closedagain_c3_ctf_5A.ccp4 (#2)
coordinates:  
Matrix rotation and translation  
-0.18879488 0.02996703 0.98155924 -55.71378433  
0.57598823 0.81292505 0.08596799 -212.12304033  
-0.79535785 0.58159686 -0.17073673 487.78422784  
Axis 0.25762266 0.92362276 0.28381606  
Axis point 209.55089554 0.00000000 291.69997403  
Rotation angle (degrees) 105.86092581  
Shift along axis -71.83380263  
  

> cd X:/Work/Projects/48S/ChimeraX/closed/40S/

Current working directory is: X:\Work\Projects\48S\ChimeraX\closed\40S  

> save 40S-rigfit.cif models #4

> ui mousemode right select

> select clear

> lighting full

> hide #!4 models

> show #!4 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #!1 models

> info #1

3 models  
#1, 6fec, shown  
117189 atoms, 122900 bonds, 11850 residues, 50 chains
(1,2,3,4,5,6,7,8,9,A,F,G,H,I,J,K,L,N,P,Q,R,S,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,w)  
1668 hydrogen bonds, 2 missing structure  
#1.1, hydrogen bonds, shown, 1668 pseudobonds  
#1.2, missing structure, shown, 2 pseudobonds  

> info chains #1

chain id #1/1 chain_id 1  
chain id #1/2 chain_id 2  
chain id #1/3 chain_id 3  
chain id #1/4 chain_id 4  
chain id #1/5 chain_id 5  
chain id #1/6 chain_id 6  
chain id #1/7 chain_id 7  
chain id #1/8 chain_id 8  
chain id #1/9 chain_id 9  
chain id #1/A chain_id A  
chain id #1/F chain_id F  
chain id #1/G chain_id G  
chain id #1/H chain_id H  
chain id #1/I chain_id I  
chain id #1/J chain_id J  
chain id #1/K chain_id K  
chain id #1/L chain_id L  
chain id #1/N chain_id N  
chain id #1/P chain_id P  
chain id #1/Q chain_id Q  
chain id #1/R chain_id R  
chain id #1/S chain_id S  
chain id #1/U chain_id U  
chain id #1/V chain_id V  
chain id #1/W chain_id W  
chain id #1/X chain_id X  
chain id #1/Y chain_id Y  
chain id #1/Z chain_id Z  
chain id #1/a chain_id a  
chain id #1/b chain_id b  
chain id #1/c chain_id c  
chain id #1/d chain_id d  
chain id #1/e chain_id e  
chain id #1/f chain_id f  
chain id #1/g chain_id g  
chain id #1/h chain_id h  
chain id #1/i chain_id i  
chain id #1/j chain_id j  
chain id #1/k chain_id k  
chain id #1/l chain_id l  
chain id #1/m chain_id m  
chain id #1/n chain_id n  
chain id #1/o chain_id o  
chain id #1/p chain_id p  
chain id #1/q chain_id q  
chain id #1/r chain_id r  
chain id #1/s chain_id s  
chain id #1/t chain_id t  
chain id #1/u chain_id u  
chain id #1/w chain_id w  

> mmaker #1/A to #4/S2 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 40S.cif, chain S2 (#4) with 6fec, chain A (#1), sequence alignment
score = 6806.4  
RMSD between 1227 pruned atom pairs is 1.215 angstroms; (across all 1724
pairs: 3.451)  
  

> show #!2 models

> volume #2 level 4.8

> volume #2 step 1

> volume #2 level 2.877

> volume #2 color #b2b2b201

> volume #2 color #b2b2b20f

> volume #2 color #b2b2b296

> volume #2 color #b2b2b232

> volume #2 color #b2b2b201

> volume #2 color #b2b2b20a

> volume #2 color #b2b2b264

> select /u:1-76

608 atoms, 619 bonds, 1 model selected  

> open "X:/Work/Projects/48S/closed state 3.7A
> overall/closedState_initialmodels/_48S_singleFile_closed.pdb"

Chain information for _48S_singleFile_closed.pdb #5  
---  
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  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
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  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
  

> select #5

132454 atoms, 138184 bonds, 21 pseudobonds, 2 models selected  

> style sel stick

Changed 132454 atom styles  

> hide sel atoms

> hide sel cartoons

> hide #!1 models

> show sel cartoons

> select clear

> select #5/N:231-320

717 atoms, 731 bonds, 1 model selected  

> show #!3 models

> hide #!2 models

> hide #!3 models

> select clear

> hide #!5 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> sequence chain #1/F

Alignment identifier is 1.F  

> select clear

> select #5/I:267-515

3937 atoms, 3977 bonds, 2 pseudobonds, 2 models selected  

> select #5/l:2-314

2436 atoms, 2493 bonds, 1 model selected  

> select /I:1-263

2083 atoms, 2125 bonds, 1 model selected  

> select /l:5-68

1019 atoms, 1033 bonds, 2 models selected  

> select /1:7-606

4935 atoms, 5021 bonds, 1 model selected  

> select /w:208-610

3308 atoms, 3407 bonds, 1 model selected  

> show #!2 models

> select /9:172-536

2867 atoms, 2921 bonds, 2 pseudobonds, 2 models selected  

> hide #!2 models

> select /u:1-76

1214 atoms, 1237 bonds, 2 models selected  

> show #!2 models

> show #!5 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!5 models

> show #!1 models

> select clear

> hide #!2 models

> select /w:208-610

3308 atoms, 3407 bonds, 1 model selected  

> select /w:208-610

3308 atoms, 3407 bonds, 1 model selected  

> select /u:1-76

1214 atoms, 1237 bonds, 2 models selected  

> select /u:1-76

1214 atoms, 1237 bonds, 2 models selected  

> show #!2 models

> volume #2 level 1.621

> volume #2 level 3.869

> select /w:208-610

3308 atoms, 3407 bonds, 1 model selected  

> volume #2 level 2.481

> volume #2 level 3.935

> volume #2 level 5.522

> select clear

> select #1/1-9

28676 atoms, 28836 bonds, 2 pseudobonds, 2 models selected  

> volume #2 level 1.027

> volume #2 level 2.811

> select clear

> volume #2 level 5.323

> volume #2 level 2.613

> select /G:1-158

2376 atoms, 2407 bonds, 2 models selected  

> select /l:5-68

1019 atoms, 1033 bonds, 2 models selected  

> select /F:3-28

976 atoms, 1044 bonds, 2 models selected  

> volume #2 level 4.2

> volume #2 level 3.737

> volume #2 color #b2b2b201

> volume #2 color #b2b2b20f

> volume #2 color #b2b2b296

> select /u:1-76

1214 atoms, 1237 bonds, 2 models selected  

> volume #2 level 3.076

> select /F:3-28

976 atoms, 1044 bonds, 2 models selected  

> volume #2 level 2.216

> save X:/Work/Projects/48S/ChimeraX/Literature.cxs includeMaps true

opened ChimeraX session  

> hide #!1 models

> open
> X:/Work/Projects/48S/eIF1A/48S_closed_eIF1A_substates/48S_closed_eIF1A_3Dclasses.txt

Unrecognized file suffix '.txt'  

> open
> X:/Work/Projects/48S/eIF1A/48S_closed_eIF1A_substates/c1_cA_subCTF_eIF1A_5cl_10A_T40_c1.mrc

Opened c1_cA_subCTF_eIF1A_5cl_10A_T40_c1.mrc, grid size 360,360,360, pixel
1.16, shown at level 0.0219, step 2, values float32  

> open
> X:/Work/Projects/48S/eIF1A/48S_closed_eIF1A_substates/c1_cA_subCTF_eIF1A_5cl_10A_T40_c2.mrc

Opened c1_cA_subCTF_eIF1A_5cl_10A_T40_c2.mrc, grid size 360,360,360, pixel
1.16, shown at level 0.0223, step 2, values float32  

> open
> X:/Work/Projects/48S/eIF1A/48S_closed_eIF1A_substates/c1_cA_subCTF_eIF1A_5cl_10A_T40_c3.mrc

Opened c1_cA_subCTF_eIF1A_5cl_10A_T40_c3.mrc, grid size 360,360,360, pixel
1.16, shown at level 0.0219, step 2, values float32  

> open
> X:/Work/Projects/48S/eIF1A/48S_closed_eIF1A_substates/c1_cA_subCTF_eIF1A_5cl_10A_T40_c4.mrc

Opened c1_cA_subCTF_eIF1A_5cl_10A_T40_c4.mrc, grid size 360,360,360, pixel
1.16, shown at level 0.0212, step 2, values float32  

> open
> X:/Work/Projects/48S/eIF1A/48S_closed_eIF1A_substates/c1_cA_subCTF_eIF1A_5cl_10A_T40_c5.mrc

Opened c1_cA_subCTF_eIF1A_5cl_10A_T40_c5.mrc, grid size 360,360,360, pixel
1.16, shown at level 0.0223, step 2, values float32  

> close #6-10

> open
> X:/Work/Projects/48S/eIF1A/48S_closed_eIF1A_substates/c1_cA_subCTF_eIF1A_5cl_10A_T40_c1.mrc
> X:/Work/Projects/48S/eIF1A/48S_closed_eIF1A_substates/c1_cA_subCTF_eIF1A_5cl_10A_T40_c2.mrc
> X:/Work/Projects/48S/eIF1A/48S_closed_eIF1A_substates/c1_cA_subCTF_eIF1A_5cl_10A_T40_c3.mrc
> X:/Work/Projects/48S/eIF1A/48S_closed_eIF1A_substates/c1_cA_subCTF_eIF1A_5cl_10A_T40_c4.mrc
> X:/Work/Projects/48S/eIF1A/48S_closed_eIF1A_substates/c1_cA_subCTF_eIF1A_5cl_10A_T40_c5.mrc

Opened c1_cA_subCTF_eIF1A_5cl_10A_T40_c1.mrc, grid size 360,360,360, pixel
1.16, shown at level 0.0219, step 2, values float32  
Opened c1_cA_subCTF_eIF1A_5cl_10A_T40_c2.mrc, grid size 360,360,360, pixel
1.16, shown at level 0.0223, step 2, values float32  
Opened c1_cA_subCTF_eIF1A_5cl_10A_T40_c3.mrc, grid size 360,360,360, pixel
1.16, shown at level 0.0219, step 2, values float32  
Opened c1_cA_subCTF_eIF1A_5cl_10A_T40_c4.mrc, grid size 360,360,360, pixel
1.16, shown at level 0.0212, step 2, values float32  
Opened c1_cA_subCTF_eIF1A_5cl_10A_T40_c5.mrc, grid size 360,360,360, pixel
1.16, shown at level 0.0223, step 2, values float32  

> hide #!7 models

> show #!7 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> show #!2 models

> volume #2 level 5.389

> volume #2 color #b2b2b200

> volume #2 color #b2b2b202

> volume #2 color #b2b2b219

> volume #2 color #b2b2b2

> volume #6 color #ffb2b201

> volume #6 color #ffb2b20f

> volume #6 color #ffb2b296

> volume #6 level 0.01594

> volume #6 step 1

> volume #6 level 0.007675

> volume #6 level 0.01181

> show #!1 models

> hide #!1 models

> show #!1 models

> volume #7 color #b2ffb201

> volume #7 color #b2ffb20f

> volume #7 color #b2ffb296

> volume #7 level 0.01281

> volume #7 step 1

> volume #7 level 0.01054

> volume #7 level 0.008271

> volume #7 level 0.01124

> volume #7 level 0.01263

> volume #8 step 1

> volume #8 level 0.01295

> volume #9 level 0.01273

> volume #9 step 1

> volume #9 level 0.01057

> volume #10 level 0.01525

> close #4

> rename #6 id #4.1

> rename #7 id #4.2

> rename #4.1 id #4.1.1

Traceback (most recent call last):  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\std_commands\rename.py", line 34, in rename  
change_model_id(session, models, id, new_name = nname)  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\std_commands\rename.py", line 53, in change_model_id  
ml.add(models, parent = p)  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\models.py", line 592, in add  
self.add(children, parent=model, _notify=False,
_need_fire_id_trigger=_need_fire_id_trigger)  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\models.py", line 592, in add  
self.add(children, parent=model, _notify=False,
_need_fire_id_trigger=_need_fire_id_trigger)  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\models.py", line 592, in add  
self.add(children, parent=model, _notify=False,
_need_fire_id_trigger=_need_fire_id_trigger)  
[Previous line repeated 977 more times]  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\models.py", line 581, in add  
model.id = None  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 243, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\models.py", line 127, in _set_id  
self._id = val  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 243, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
RecursionError: maximum recursion depth exceeded while calling a Python object  
  
RecursionError: maximum recursion depth exceeded while calling a Python object  
  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 243, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
  
See log for complete Python traceback.  
  

> rename #8 id #4.3.1

Traceback (most recent call last):  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 169, in <lambda>  
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 194, in _fill_tree  
part_selected_models = self.session.selection.models()  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\selection.py", line 29, in models  
return [m for m in self._all_models if m.get_selected(include_children=True)]  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\selection.py", line 29, in <listcomp>  
return [m for m in self._all_models if m.get_selected(include_children=True)]  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\models.py", line 192, in get_selected  
if d.get_selected(include_children=True):  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\models.py", line 192, in get_selected  
if d.get_selected(include_children=True):  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\models.py", line 192, in get_selected  
if d.get_selected(include_children=True):  
[Previous line repeated 978 more times]  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\models.py", line 186, in get_selected  
if self.highlighted:  
RecursionError: maximum recursion depth exceeded  
  
Error processing trigger "new frame":  
RecursionError: maximum recursion depth exceeded  
  
File "X:\Soft\ChimeraX\ChimeraX-1.0-22-05-2020\bin\lib\site-
packages\chimerax\core\models.py", line 186, in get_selected  
if self.highlighted:  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 445.87
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GE73VR 7RF
OS: Майкрософт Windows 10 Pro (Build 18363)
Memory: 17,059,950,592
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by pett, 5 years ago

Component: UnassignedCore
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submission'rename' command: maximum recursion depth exceeded

comment:2 by Tom Goddard, 5 years ago

Resolution: fixed
Status: assignedclosed

Fixed.

The rename command didn't handle the case where a model id number was changed to a child of that same model. The case of "rename #8 id #4.3.1" should work. But if #4 is a volume I would not be surprised if bad behavior arises. Volume models manage all their child models and were not designed to handle submodels the user puts under them. It might work, but has not been tested. And it will create some bad behaviors using the volume command, like "volume #4 level 1.5" will set the level of any volumes placed under #4 which is probably not intended -- would need "volume #!4 level 1.5" to avoid touching the child volumes.

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