Opened 4 years ago

Closed 4 years ago

#6636 closed defect (not a bug)

setattr type

Reported by: Tristan Croll Owned by: pett
Priority: normal Milestone:
Component: Command Line Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
`setattr` on the command line doesn't allow setting the chain ID to a numeric character (but it can be done fine via the Python layer via `residues.chain_ids="3"`). Tried:

setattr sel residues chain_id 3
setattr sel residues chain_id "3"

Both failed.

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18-Fab19-3bound/working.cxs"

Opened cryosparc_P77_J197_007_volume_map_sharp_zflip.mrc as #1.1.1.1, grid
size 400,400,400, pixel 0.83, shown at level 0.159, step 1, values float32  
Opened cryosparc_P77_J197_007_volume_map_sharp_zflip.mrc gaussian as #1.1.1.2,
grid size 400,400,400, pixel 0.83, shown at level 0.0748, step 1, values
float32  
Log from Thu Feb 17 19:00:50 2022UCSF ChimeraX version: 1.3rc202112030319
(2021-12-03)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18-Fab19-3bound/working.cxs"

Opened cryosparc_P77_J197_007_volume_map_sharp_zflip.mrc as #1.1.1.1, grid
size 400,400,400, pixel 0.83, shown at level 0.159, step 1, values float32  
Opened cryosparc_P77_J197_007_volume_map_sharp_zflip.mrc gaussian as #1.1.1.2,
grid size 400,400,400, pixel 0.83, shown at level 0.0748, step 1, values
float32  
Restoring stepper: NA18_FNI19_4fab_245_glyc.pdb  
Log from Thu Feb 17 17:59:37 2022

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3rc202112030319 (2021-12-03)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18-Fab19-3bound"

Current working directory is: C:\Users\tristan\OneDrive - University of
Cambridge\Structures\VIR\2022_02_Flu\Flu\NA18-Fab19\NA18-Fab19-3bound  

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18-Fab19-3bound/cryosparc_P77_J197_007_volume_map_sharp_zflip.mrc"
> "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18-Fab19-3bound/NA18_FNI19_aligned_to_P77_J197-coot-1.pdb"

Opened cryosparc_P77_J197_007_volume_map_sharp_zflip.mrc as #1, grid size
400,400,400, pixel 0.83, shown at level 0.04, step 2, values float32  
Chain information for NA18_FNI19_aligned_to_P77_J197-coot-1.pdb #2  
---  
Chain | Description  
A | No description available  
E F H | No description available  
G | No description available  
L | No description available  
  

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18-Fab19-4bound/NA18_FNI19_4fab_245_glyc.pdb"

Chain information for NA18_FNI19_4fab_245_glyc.pdb #3  
---  
Chain | Description  
A B C D | No description available  
G H I J | No description available  
L M N O | No description available  
  

> matchmaker #3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 NA18_FNI19_aligned_to_P77_J197-coot-1.pdb, chain G (#2) with
NA18_FNI19_4fab_245_glyc.pdb, chain G (#3), sequence alignment score = 2030.7  
RMSD between 383 pruned atom pairs is 0.361 angstroms; (across all 388 pairs:
0.617)  
  

> select #3/D,O

3659 atoms, 3689 bonds, 256 residues, 1 model selected  

> delete sel

> matchmaker #1 to #3

No molecules/chains to match specified  

> clipper associate #1 toModel #3

Opened cryosparc_P77_J197_007_volume_map_sharp_zflip.mrc as #1.1.1.1, grid
size 400,400,400, pixel 0.83, shown at level 0.207, step 1, values float32  
Chain information for NA18_FNI19_4fab_245_glyc.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | No description available  
1.2/G 1.2/H 1.2/I 1.2/J | No description available  
1.2/L 1.2/M 1.2/N | No description available  
  

> close #2

> set bgColor white

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Done loading forcefield  

> volume gaussian #1 bfactor 80

Opened cryosparc_P77_J197_007_volume_map_sharp_zflip.mrc gaussian as #2, grid
size 400,400,400, pixel 0.83, shown at step 1, values float32  

> clipper associate #2 toModel #1

Opened cryosparc_P77_J197_007_volume_map_sharp_zflip.mrc gaussian as #1.1.1.2,
grid size 400,400,400, pixel 0.83, shown at step 1, values float32  

> cs 0.25

> delete :HOH

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1

35814 atoms, 36321 bonds, 2331 residues, 21 models selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
ISOLDE: started sim  

> select clear

> view /J:245

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 25 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

135 atoms, 134 bonds, 11 residues, 1 model selected  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select /J

6252 atoms, 6342 bonds, 405 residues, 1 model selected  
ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> st /J

Multiple residues selected! Going to the first...  

> st interp 5

> st

[Repeated 161 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> delete sel

> select /J

6232 atoms, 6321 bonds, 404 residues, 1 model selected  
ISOLDE: started sim  

> st

[Repeated 28 time(s)]ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> ht NE

Set protonation of HIS #1.2/J:274 to NE  

> select /J

6249 atoms, 6338 bonds, 405 residues, 2 models selected  
ISOLDE: started sim  

> select clear

> st

[Repeated 192 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: stopped sim  

> view /I:245

> view /G:245

> isolde restrain torsions /G:243-253 templateResidues /I

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> select /G:240-260

304 atoms, 304 bonds, 21 residues, 1 model selected  
ISOLDE: started sim  

> select clear

> select /G

6252 atoms, 6342 bonds, 405 residues, 1 model selected  

> ra

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> pwd

Current working directory is: C:\Users\tristan\OneDrive - University of
Cambridge\Structures\VIR\2022_02_Flu\Flu\NA18-Fab19\NA18-Fab19-3bound  

> save working.cxs

Taking snapshot of stepper: NA18_FNI19_4fab_245_glyc.pdb  

——— End of log from Thu Feb 17 17:59:37 2022 ———

opened ChimeraX session  

> view /G:431

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> view /H:431

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> view /I:431

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> view /J:431

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> save working.cxs

Taking snapshot of stepper: NA18_FNI19_4fab_245_glyc.pdb  
Taking snapshot of stepper: NA18_FNI19_aligned_to_P77_J182-coot-1.pdb  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1338, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 199, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 329, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000025B4D317880> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000025B66794700>
'NA18_FNI19_aligned_to_P77_J182-coot-1.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000025B4D317880> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000025B66794700>
'NA18_FNI19_aligned_to_P77_J182-coot-1.pdb': Error while saving session data
for 'isolde residue stepper 1' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000025B4D317880> -> <chimerax.atomic.structure.AtomicStructure
object at 0x0000025B66794700> 'NA18_FNI19_aligned_to_P77_J182-coot-1.pdb'  
  
ValueError: error processing: 'isolde residue stepper 1' -> ->
'NA18_FNI19_aligned_to_P77_J182-coot-1.pdb': Error while saving session data
for 'isolde residue stepper 1' -> ->
'NA18_FNI19_aligned_to_P77_J182-coot-1.pdb'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1338, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 199, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 329, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000025B4D317880> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000025B66794700>
'NA18_FNI19_aligned_to_P77_J182-coot-1.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000025B4D317880> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000025B66794700>
'NA18_FNI19_aligned_to_P77_J182-coot-1.pdb': Error while saving session data
for 'isolde residue stepper 1' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000025B4D317880> -> <chimerax.atomic.structure.AtomicStructure
object at 0x0000025B66794700> 'NA18_FNI19_aligned_to_P77_J182-coot-1.pdb'  
  
ValueError: error processing: 'isolde residue stepper 1' -> ->
'NA18_FNI19_aligned_to_P77_J182-coot-1.pdb': Error while saving session data
for 'isolde residue stepper 1' -> ->
'NA18_FNI19_aligned_to_P77_J182-coot-1.pdb'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> ui tool show Shell

> save working.cxs

——— End of log from Thu Feb 17 19:00:50 2022 ———

opened ChimeraX session  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18.fasta"

Summary of feedback from opening C:/Users/tristan/OneDrive - University of
Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18.fasta  
---  
notes | Alignment identifier is NA18.fasta  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain G to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain H to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain I to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain J to NA-18 with 0
mismatches  
  
Opened 1 sequences from NA18.fasta  

> view /G:86

> al BMA

Deleted the following atoms from residue BMA G2227: HO1, O1  

> show sel

> ui mousemode right "translate selected atoms"

> delete sel

> al NAG

Deleted the following atoms from residue NAG G2228: HO1, O1  

> show sel

> delete sel

> al MAN

Deleted the following atoms from residue MAN G2229: HO1, O1  

> show sel

> delete sel

> al MAN

Deleted the following atoms from residue MAN G2230: O1, HO1  

> show sel

> delete sel

> al NAG

Deleted the following atoms from residue NAG G2231: O1, HO1  

> show sel

> delete sel

> al NAG

Deleted the following atoms from residue NAG G2232: HO1, O1  

> show sel

> delete sel

> select up

73 atoms, 75 bonds, 3 residues, 1 model selected  

> select up

122 atoms, 126 bonds, 5 residues, 1 model selected  

> select up

150 atoms, 155 bonds, 6 residues, 1 model selected  

> select up

199 atoms, 206 bonds, 8 residues, 1 model selected  

> ui tool show Shell

> setattr sel residues chain_id a

Assigning chain_id attribute to 8 items  

> cbc

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> al GAL

Deleted the following atoms from residue GAL a2233: O1, HO1  

> show sel

> delete sel

> al NGB

Fetching CCD NGB from http://ligand-expo.rcsb.org/reports/N/NGB/NGB.cif  

place_ligand() was called with use_md_template=True, but no suitable template
was found. This command has been ignored.  

> select up

57 atoms, 59 bonds, 1 residue, 1 model selected  

> delete sel

> al GAL

Deleted the following atoms from residue GAL a2233: HO1, O1  

> show sel

> ui mousemode right "translate selected atoms"

> delete sel

> al SIA

Deleted the following atoms from residue SIA a2234: HO2, O2, HO1B  

> show sel

> delete sel

> select /a

256 atoms, 265 bonds, 10 residues, 1 model selected  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select /a

256 atoms, 265 bonds, 10 residues, 1 model selected  

> save A2G1S1B.pdb #1 selectedOnly true

> select clear

> view /G:146

> pwd

Current working directory is: C:\Users\tristan\OneDrive - University of
Cambridge\Structures\VIR\2022_02_Flu\Flu\NA18-Fab19\NA18-Fab19-3bound  

> cd "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_04_Flu/Glycosylation"

Current working directory is: C:\Users\tristan\OneDrive - University of
Cambridge\Structures\VIR\2022_04_Flu\Glycosylation  

> cd "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_04_Flu/Glycosylation/NA18-Fab19-3bound"

Current working directory is: C:\Users\tristan\OneDrive - University of
Cambridge\Structures\VIR\2022_04_Flu\Glycosylation\NA18-Fab19-3bound  

> open ../A2G1S1B.pdb

Summary of feedback from opening ../A2G1S1B.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 SER G 105
ARG G 107 1 3  
Start residue of secondary structure not found: HELIX 2 2 LEU G 108 GLY G 111
1 4  
Start residue of secondary structure not found: HELIX 3 3 VAL G 143 SER G 145
1 3  
Start residue of secondary structure not found: HELIX 4 4 THR A 28 ASN A 30 1
3  
Start residue of secondary structure not found: HELIX 5 5 SER A 88 ASP A 90 1
3  
173 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (92 )  
Cannot find LINK/SSBOND residue CYS (124 )  
Cannot find LINK/SSBOND residue CYS (175 )  
Cannot find LINK/SSBOND residue CYS (183 )  
Cannot find LINK/SSBOND residue CYS (232 )  
99 messages similar to the above omitted  
  

> select #2

256 atoms, 265 bonds, 10 residues, 1 model selected  

> select #1/a

256 atoms, 265 bonds, 10 residues, 1 model selected  

> select #2/a:1

27 atoms, 27 bonds, 1 residue, 1 model selected  

> align #2/a:1 toAtoms #1/G:1101

Unequal number of atoms to pair, 27 and 28  

> align #2/a:1&~H toAtoms #1/G:1101&~H

RMSD between 14 atom pairs is 3.526 angstroms  

> select #2

256 atoms, 265 bonds, 10 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> select up

28 atoms, 28 bonds, 1 residue, 1 model selected  

> delete sel

> select #2

256 atoms, 265 bonds, 10 residues, 1 model selected  

> hide #2 models

> select up

37 atoms, 37 bonds, 1 residue, 1 model selected  

> delete sel

Must have exactly two atoms selected!  

> al GAL

Deleted the following atoms from residue GAL b10: O1, HO1  

> show sel

> ui mousemode right "translate selected atoms"

> delete sel

> select #1/b

241 atoms, 250 bonds, 10 residues, 1 model selected  
ISOLDE: started sim  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select /b

241 atoms, 250 bonds, 10 residues, 1 model selected  

> save ../A2G2B.pdb #1 selectedOnly true

> select clear

> view #1/G:200

> select up

54 atoms, 55 bonds, 2 residues, 1 model selected  

> select up

74 atoms, 76 bonds, 3 residues, 1 model selected  

> select up

117 atoms, 121 bonds, 5 residues, 1 model selected  

> select up

159 atoms, 165 bonds, 7 residues, 1 model selected  

> select up

181 atoms, 188 bonds, 8 residues, 1 model selected  

> setattr sel residues chain_id c

Assigning chain_id attribute to 8 items  

> select clear

> save working.cxs

Taking snapshot of stepper: NA18_FNI19_4fab_245_glyc.pdb  

> view /G:234

> select up

27 atoms, 27 bonds, 1 residue, 1 model selected  

> align #2:1@C1,C2,O5 toAtoms #1/G:1400@C1,C2,O5

RMSD between 3 atom pairs is 0.002 angstroms  

> show #2 models

> select up

55 atoms, 56 bonds, 2 residues, 1 model selected  

> delete sel

> hide #2 models

> al FUC

Deleted the following atoms from residue FUC d11: HO1, O1  

> show sel

> ui mousemode right "translate selected atoms"

> delete sel

> select up

37 atoms, 37 bonds, 1 residue, 1 model selected  

> delete sel

> select up

28 atoms, 28 bonds, 1 residue, 1 model selected  

> delete sel

> select /d

213 atoms, 221 bonds, 9 residues, 1 model selected  
ISOLDE: started sim  

> cs 0.25

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select /d

213 atoms, 221 bonds, 9 residues, 1 model selected  

> save ../A2G1F.pdb #1 selectedOnly true

> view /G:245

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_04_Flu/Glycosylation/A2G1F.pdb"

Summary of feedback from opening C:/Users/tristan/OneDrive - University of
Cambridge/Structures/VIR/2022_04_Flu/Glycosylation/A2G1F.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 SER G 105
ARG G 107 1 3  
Start residue of secondary structure not found: HELIX 2 2 LEU G 108 GLY G 111
1 4  
Start residue of secondary structure not found: HELIX 3 3 VAL G 143 SER G 145
1 3  
Start residue of secondary structure not found: HELIX 4 4 THR A 28 ASN A 30 1
3  
Start residue of secondary structure not found: HELIX 5 5 SER A 88 ASP A 90 1
3  
173 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (92 )  
Cannot find LINK/SSBOND residue CYS (124 )  
Cannot find LINK/SSBOND residue CYS (175 )  
Cannot find LINK/SSBOND residue CYS (183 )  
Cannot find LINK/SSBOND residue CYS (232 )  
116 messages similar to the above omitted  
  

> align #3:1@C1,C2,O5 toAtoms #1/G:2225@C1,C2,O5

RMSD between 3 atom pairs is 0.023 angstroms  

> select up

27 atoms, 27 bonds, 1 residue, 1 model selected  

> delete sel

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> delete sel

> select /d

426 atoms, 442 bonds, 18 residues, 2 models selected  

> select #2/d

Nothing selected  

> select #3/d

213 atoms, 221 bonds, 9 residues, 1 model selected  

> hide #3 models

> select /e

213 atoms, 221 bonds, 9 residues, 1 model selected  
ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> al GAL

Deleted the following atoms from residue GAL e12: HO1, O1  

> show sel

> ui mousemode right "translate selected atoms"

> delete sel

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select /e

234 atoms, 243 bonds, 10 residues, 1 model selected  

> save ../A2G2F.pdb #1 selectedOnly true

> select clear

> view /G:329

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18.fasta"

Summary of feedback from opening C:/Users/tristan/OneDrive - University of
Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18.fasta  
---  
notes | Alignment identifier is NA18.fasta  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain G to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain H to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain I to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain J to NA-18 with 0
mismatches  
  
Opened 1 sequences from NA18.fasta  

> view /G:367

> select /c

181 atoms, 188 bonds, 8 residues, 1 model selected  

> save M6.pdb #1 selectedOnly true

> save ../M6.pdb #1 selectedOnly true

> open ../M6.pdb

Summary of feedback from opening ../M6.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 SER G 105
ARG G 107 1 3  
Start residue of secondary structure not found: HELIX 2 2 LEU G 108 GLY G 111
1 4  
Start residue of secondary structure not found: HELIX 3 3 VAL G 143 SER G 145
1 3  
Start residue of secondary structure not found: HELIX 4 4 THR A 28 ASN A 30 1
3  
Start residue of secondary structure not found: HELIX 5 5 SER A 88 ASP A 90 1
3  
173 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (92 )  
Cannot find LINK/SSBOND residue CYS (124 )  
Cannot find LINK/SSBOND residue CYS (175 )  
Cannot find LINK/SSBOND residue CYS (183 )  
Cannot find LINK/SSBOND residue CYS (232 )  
125 messages similar to the above omitted  
  

> align #4:1@C1,C2,O5 toAtoms #1/G:1301@C1,C2,O5

RMSD between 3 atom pairs is 0.011 angstroms  

> select up

28 atoms, 28 bonds, 1 residue, 1 model selected  

> delete sel

> select #4

181 atoms, 188 bonds, 8 residues, 1 model selected  

> hide #4 models

> select /g

181 atoms, 188 bonds, 8 residues, 1 model selected  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> view #1/G:402

> select #1&~prot

Expected an objects specifier or a keyword  

> select #1&~protein

2475 atoms, 2573 bonds, 106 residues, 21 models selected  

> select /G

5857 atoms, 5931 bonds, 389 residues, 1 model selected  

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> clipper spotlight radius 16.00

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18.fasta"

Summary of feedback from opening C:/Users/tristan/OneDrive - University of
Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18.fasta  
---  
notes | Alignment identifier is NA18.fasta  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain G to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain H to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain I to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain J to NA-18 with 0
mismatches  
  
Opened 1 sequences from NA18.fasta  

> select /G:402

12 atoms, 11 bonds, 1 residue, 1 model selected  

> view /G:402

> save woring.cxs

Taking snapshot of stepper: NA18_FNI19_4fab_245_glyc.pdb  

> select #1/G,a-g

7163 atoms, 7292 bonds, 444 residues, 1 model selected  

> save monomer.pdb #1 selectedOnly true

> close #2-4

> open monomer.pdb

Summary of feedback from opening monomer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 4 4 THR A 28
ASN A 30 1 3  
Start residue of secondary structure not found: HELIX 5 5 SER A 88 ASP A 90 1
3  
Start residue of secondary structure not found: HELIX 6 6 SER L 80 ASP L 82 1
3  
Start residue of secondary structure not found: HELIX 7 7 SER H 105 ARG H 107
1 3  
Start residue of secondary structure not found: HELIX 8 8 LEU H 108 GLY H 111
1 4  
146 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (22 )  
Cannot find LINK/SSBOND residue CYS (23 )  
Cannot find LINK/SSBOND residue CYS (92 )  
Cannot find LINK/SSBOND residue CYS (124 )  
Cannot find LINK/SSBOND residue CYS (175 )  
75 messages similar to the above omitted  
  
Chain information for monomer.pdb #2  
---  
Chain | Description  
G | No description available  
  
Associated monomer.pdb chain G to NA-18 with 0 mismatches  

> select clear

> matchmaker #2 to #1/G

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 NA18_FNI19_4fab_245_glyc.pdb, chain G (#1.2) with monomer.pdb,
chain G (#2), sequence alignment score = 2052.7  
RMSD between 388 pruned atom pairs is 0.000 angstroms; (across all 388 pairs:
0.000)  
  

> matchmaker #2 to #1/H

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 NA18_FNI19_4fab_245_glyc.pdb, chain H (#1.2) with monomer.pdb,
chain G (#2), sequence alignment score = 2042.2  
RMSD between 388 pruned atom pairs is 0.129 angstroms; (across all 388 pairs:
0.129)  
  

> view /H:86

> select up

55 atoms, 56 bonds, 2 residues, 1 model selected  

> delete sel

> select #2/a

256 atoms, 265 bonds, 10 residues, 1 model selected  

> hide #2 models

> select /i

256 atoms, 265 bonds, 10 residues, 1 model selected  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> view #2/b:1

> show #2 models

> select up

28 atoms, 28 bonds, 1 residue, 1 model selected  

> delete sel

> select #2/b

241 atoms, 250 bonds, 10 residues, 1 model selected  

> hide #2 models

> select /j

241 atoms, 250 bonds, 10 residues, 1 model selected  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> show #2 models

> view #2/c

> hide #2 models

> select up

54 atoms, 55 bonds, 2 residues, 1 model selected  

> select up

74 atoms, 76 bonds, 3 residues, 1 model selected  

> select up

94 atoms, 97 bonds, 4 residues, 1 model selected  

> select up

116 atoms, 120 bonds, 5 residues, 1 model selected  

> select up

138 atoms, 143 bonds, 6 residues, 1 model selected  

> select up

159 atoms, 165 bonds, 7 residues, 1 model selected  

> select up

181 atoms, 188 bonds, 8 residues, 1 model selected  

> setattr sel residues chain_id k

Assigning chain_id attribute to 8 items  

> cbc

> show #2 models

> view #2/d:1

> select up

27 atoms, 27 bonds, 1 residue, 1 model selected  

> select up

55 atoms, 56 bonds, 2 residues, 1 model selected  

> delete sel

> select #2/d

213 atoms, 221 bonds, 9 residues, 1 model selected  

> hide #2 models

> view #2/e:1

> select up

48 atoms, 49 bonds, 2 residues, 1 model selected  

> delete sel

> select #2/e

234 atoms, 243 bonds, 10 residues, 1 model selected  

> ui mousemode right "clip rotate"

> select /m

234 atoms, 243 bonds, 10 residues, 1 model selected  
ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> view #2/f:1

No objects specified.  

> view #2/g:1

> select up

28 atoms, 28 bonds, 1 residue, 1 model selected  

> delete sel

> select #2/g

181 atoms, 188 bonds, 8 residues, 1 model selected  

> select /o

181 atoms, 188 bonds, 8 residues, 1 model selected  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18.fasta"

Summary of feedback from opening C:/Users/tristan/OneDrive - University of
Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18.fasta  
---  
notes | Destroying pre-existing alignment with identifier NA18.fasta  
Alignment identifier is NA18.fasta  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain G to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain H to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain I to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain J to NA-18 with 0
mismatches  
Associated monomer.pdb chain G to NA-18 with 0 mismatches  
  
Opened 1 sequences from NA18.fasta  

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18-Fab19-3bound/NA18_FNI19_aligned_to_P77_J197-coot-1.pdb"

Chain information for NA18_FNI19_aligned_to_P77_J197-coot-1.pdb #3  
---  
Chain | Description  
A | No description available  
E F H | No description available  
G | No description available  
L | No description available  
  

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18.fasta"

Summary of feedback from opening C:/Users/tristan/OneDrive - University of
Cambridge/Structures/VIR/2022_02_Flu/Flu/NA18-Fab19/NA18.fasta  
---  
notes | Alignment identifier is NA18.fasta  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain G to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain H to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain I to NA-18 with 0
mismatches  
Associated NA18_FNI19_4fab_245_glyc.pdb (1.2) chain J to NA-18 with 0
mismatches  
Associated monomer.pdb chain G to NA-18 with 0 mismatches  
Associated NA18_FNI19_aligned_to_P77_J197-coot-1.pdb chain E to NA-18 with 14
mismatches  
Associated NA18_FNI19_aligned_to_P77_J197-coot-1.pdb chain F to NA-18 with 14
mismatches  
Associated NA18_FNI19_aligned_to_P77_J197-coot-1.pdb chain G to NA-18 with 2
mismatches  
Associated NA18_FNI19_aligned_to_P77_J197-coot-1.pdb chain H to NA-18 with 14
mismatches  
  
Opened 1 sequences from NA18.fasta  

> select #1.2/G-J:245 #2/G:245 #3/E-H:245

91 atoms, 82 bonds, 9 residues, 3 models selected  

> select #1.2/G-J:245 #2/G:245 #3/E-H:245

91 atoms, 82 bonds, 9 residues, 3 models selected  

> view #1/G&sel

> hide #3 models

> close #3

> matchmaker #2 to #1/I

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 NA18_FNI19_4fab_245_glyc.pdb, chain I (#1.2) with monomer.pdb,
chain G (#2), sequence alignment score = 2031.4  
RMSD between 388 pruned atom pairs is 0.155 angstroms; (across all 388 pairs:
0.155)  
  

> view #2/a:1

> select up

55 atoms, 56 bonds, 2 residues, 1 model selected  

> delete sel

> select #2/a

256 atoms, 265 bonds, 10 residues, 1 model selected  

> select /q

256 atoms, 265 bonds, 10 residues, 1 model selected  

> select clear

> view #2/b:1

> select up

28 atoms, 28 bonds, 1 residue, 1 model selected  

> delete sel

> select #2/b

241 atoms, 250 bonds, 10 residues, 1 model selected  

> view #2/c:1

> select up

27 atoms, 27 bonds, 1 residue, 1 model selected  

> select up

54 atoms, 55 bonds, 2 residues, 1 model selected  

> select up

74 atoms, 76 bonds, 3 residues, 1 model selected  

> select up

94 atoms, 97 bonds, 4 residues, 1 model selected  

> select up

116 atoms, 120 bonds, 5 residues, 1 model selected  

> select up

159 atoms, 165 bonds, 7 residues, 1 model selected  

> select up

181 atoms, 188 bonds, 8 residues, 1 model selected  

> setattr sel residues chain_id s

Assigning chain_id attribute to 8 items  

> cbc

> select clear

> view #2/d:1

> select up

55 atoms, 56 bonds, 2 residues, 1 model selected  

> delete sel

> select #2/d

213 atoms, 221 bonds, 9 residues, 1 model selected  

> view #2/e:1

> select up

48 atoms, 49 bonds, 2 residues, 1 model selected  

> delete sel

> select #2/e

234 atoms, 243 bonds, 10 residues, 1 model selected  

> view #2/f:1

No objects specified.  

> view #2/g:1

> select up

28 atoms, 28 bonds, 1 residue, 1 model selected  

> delete sel

> select #2/g

181 atoms, 188 bonds, 8 residues, 1 model selected  

> matchmaker #2 to #1/J

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 NA18_FNI19_4fab_245_glyc.pdb, chain J (#1.2) with monomer.pdb,
chain G (#2), sequence alignment score = 2042.2  
RMSD between 384 pruned atom pairs is 0.195 angstroms; (across all 388 pairs:
0.737)  
  

> view #2/a:1

> select up

55 atoms, 56 bonds, 2 residues, 1 model selected  

> delete sel

> select #2/a

256 atoms, 265 bonds, 10 residues, 1 model selected  

> view #2/b:1

> select up

28 atoms, 28 bonds, 1 residue, 1 model selected  

> delete sel

> select #2/b

241 atoms, 250 bonds, 10 residues, 1 model selected  

> view #2/c:1

> select up

54 atoms, 55 bonds, 2 residues, 1 model selected  

> select up

117 atoms, 121 bonds, 5 residues, 1 model selected  

> select up

181 atoms, 188 bonds, 8 residues, 1 model selected  

> setattr sel residues chain_id 3

Assigning chain_id attribute to 8 items  
Cannot set attribute 'chain_id' to '3'  

> setattr sel residues chain_id 3

Assigning chain_id attribute to 8 items  
Cannot set attribute 'chain_id' to '3'  

> cbc




OpenGL version: 3.3.0 NVIDIA 497.29
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    -: imerax-clipper
    -himerax-clipper: 0.17.0
    -himerax-isolde: 1.3.dev33
    -imerax-clipper: 0.17.0
    absl-py: 1.0.0
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    flatbuffers: 2.0
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jax: 0.2.27
    jaxlib: 0.1.75
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    opt-einsum: 3.3.0
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    python-igraph: 0.9.7
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    texttable: 1.6.4
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    typing-extensions: 4.0.1
    urllib3: 1.26.7
    versioneer: 0.21
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Command Line
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → setattr type

comment:2 by pett, 4 years ago

Resolution: → not a bug
Status: accepted → closed

Hi Tristan,

Setattr guesses the most natural looking type from the value text that your typed. So '3' is guessed to be an integer. If it should instead be a string then you have to add "type string" to the setattr command.

--Eric

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