Atom specifiers not handling chain case correctly

[pascal.albanese@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.8 (2018-11-08)
Description
I'm trying to load a pseudobond set of ditances, either on a custom PDB or on the 5xnl form the PDB database. 

However i see errors as the atom don't exist, for any atom. 

I tought it was a problem of the custom PDB (built in chimera as well) ... but is not. 

The same happens when i try just to se the distance (e.g.: distance #1/P:166@CA #1/P:170@CA radius 0.5 dashes 12 color gold)

Log:
UCSF ChimeraX version: 0.8 (2018-11-08)  
How to cite UCSF ChimeraX  

> open D:\Chimera_PSIIsc\PSII06\5xnl.pdb

5xnl.pdb title:  
Structure of stacked C2S2M2-type psii-lhcii supercomplex from pisum sativum
[more info...]  
  
Chain information for 5xnl.pdb #1  
---  
Chain | Description  
1 2 5 6 G N Y g n y | lhcii TYPE I CAB-8  
3 7 | chlorophyll A-B binding protein, chloroplastic  
4 8 | light harvesting chlorophyll A/B-binding protein LHCB6, CP24  
A a | photosystem II protein D1  
B b | photosystem II CP47 reaction center protein  
C c | photosystem II CP43 reaction center protein  
D d | photosystem II D2 protein  
E e | PSII reaction center subunit V  
F f | cytochrome B559 subunit β, PSBF  
H h | photosystem II reaction center protein H  
I i | photosystem II reaction center protein I, PSBI  
J j | PSII-J  
K k | PSII-K  
L l | PSII-L  
M m | PSII-M  
O o | oxygen-evolving enhancer protein 1, chloroplastic  
P p | oxygen-evolving enhancer protein 2, chloroplastic  
Q q | oxygen-evolving enhancer protein 3  
R r | light harvesting chlorophyll A/B-binding protein LHCB4, CP29  
S s | light harvesting chlorophyll A/B-binding protein LHCB5, CP26  
T t | PSII-T  
W w | photosystem II reaction center protein W  
X x | photosystem II reaction center protein X  
Z z | PSII-Z  
  

> set bgColor white

> hide selAtoms

> show selAtoms ribbons

> open D:/UTRECHT_MS/Xlink_results/Pres_data/mAPPING/All_dsso_on5xnl.pb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 542, in _qt_safe  
run(session, "open " + quote_if_necessary(paths[0]))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
from_database=from_database, ignore_cache=ignore_cache, **kw))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 117, in open  
models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
return f(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 583, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 461, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 416, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\read_pbonds\\__init__.py", line 23, in open_file  
return readpbonds.read_pseudobond_file(session, stream, file_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 33, in read_pseudobond_file  
% (i, len(a), aspec))  
File "<string>", line None  
SyntaxError: Line 0, got 0 atoms for spec "#1/P:166@CA", require exactly 1  
  
File "", line None  
SyntaxError: Line 0, got 0 atoms for spec "#1/P:166@CA", require exactly 1  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 33, in read_pseudobond_file  
% (i, len(a), aspec))  
  
See log for complete Python traceback.  
  

> sequence chain #1/P

Chains must have same sequence  

Chains must have same sequence  




OpenGL version: 3.3.0 NVIDIA 388.75
OpenGL renderer: GeForce 940M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[pett]

"open 5xnl ; sel /P" selects nothing

[pascal.albanese@…]

However,
i noticed that the only distances he keep are when referred to the same AA
(upper and lower case either)

Il giorno gio 8 nov 2018 alle ore 19:37 ChimeraX <
ChimeraX-bugs-admin@cgl.ucsf.edu> ha scritto:

[pett]

On a probably related note "sel #1/o:15@ca #1/o:49@ca" selects 4 atoms when it should only select 2.

[Conrad Huang]

Fixed (I think) in 5ffe7f337.

Case-sensitive comparison was broken when I added wildcard support in atom specifiers. It should be fixed in tomorrow's daily build. Can you please confirm? Thanks.

Conrad

[pascal.albanese@…]

Great thanks,

I’ll let you know if it’ll work ...

Il giorno dom 11 nov 2018 alle 22:53 ChimeraX <
ChimeraX-bugs-admin@cgl.ucsf.edu> ha scritto:

[Elaine Meng]

Works for me in version: 0.8 (2018-11-14)

Tested with Pascal’s example 5xnl (photosystem) and another example 6h4n (ribosome).  In each case, selecting by an uppercase chain ID and the corresponding lowercase chain ID both work, and as expected, they select different sets of atoms.

Tested both with commands and with menu: Select… Chain […]

Elaine