Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#3543 closed defect (not a bug)

ChimeraX bug report submission

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Opening a PDB file with UNK (unknown amino acid) mid-chain yields a broken cartoon. Looks like UNK residues are only being classified as PT_AMINO if the next residue in the chain is a standard amino acid (that is, the UNK N-terminal to each stretch of standard amino acids is PT_AMINO, the remainder are PT_NONE). Attached file is the PDB output from PDB_REDO. The mmCIF from "open 6o24 from pdb" is fine.

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6o24 format mmcif fromDatabase pdb structureFactors true

Summary of feedback from opening 6o24 fetched from pdb  
---  
notes | Resolution: 1.4000158668392628  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
6o24 title:  
Crystal structure of 4498 Fab in complex with circumsporozoite protein NANP3
and anti-Kappa VHH domain [more info...]  
  
Chain information for 6o24  
---  
Chain | Description  
1.2/A | 4498 Fab heavy chain  
1.2/B | 4498 κ light chain  
1.2/I | Circumsporozoite protein  
1.2/K | Anti-kappa VHH domain  
  
Non-standard residues in 6o24 #1.2  
---  
CIT — citric acid  
EDO — 1,2-ethanediol (ethylene glycol)  
  

> set bgColor white

> save /home/tic20/Desktop/arg_tyr_arg.jpg

> view /A:3

> open /home/tic20/Downloads/6o24_final.pdb

Summary of feedback from opening /home/tic20/Downloads/6o24_final.pdb  
---  
warning | Cannot find LINK/SSBOND atom in residue TRP /B:94  
  
Chain information for 6o24_final.pdb #2  
---  
Chain | Description  
A | protein NANP3 and ANTI-κ VHH domain  
B | No description available  
I | No description available  
K | No description available  
  
Non-standard residues in 6o24_final.pdb #2  
---  
CIT — citric acid  
EDO — 1,2-ethanediol  
  

> show #2

> view /A:16

> view /A:18

> view /A:61

> view /A:57

> view /A:61

> view /A:127

> clipper isolate #1

> hide #!1.1 models

> select clear

> select :UNK

710 atoms, 614 bonds, 2 models selected  

> select #2:UNK

355 atoms, 283 bonds, 1 model selected  

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select #2/K:UNK

355 atoms, 283 bonds, 1 model selected  

> select clear

> show #!1.1 models

> clipper isolate sel

> style sphere

Changed 4883 atom styles  

> style stick

Changed 4883 atom styles  

> select clear

> open /home/tic20/Downloads/6o24_final.pdb

Summary of feedback from opening /home/tic20/Downloads/6o24_final.pdb  
---  
warning | Cannot find LINK/SSBOND atom in residue TRP /B:94  
  
Chain information for 6o24_final.pdb #2  
---  
Chain | Description  
A | protein NANP3 and ANTI-κ VHH domain  
B | No description available  
I | No description available  
K | No description available  
  
Non-standard residues in 6o24_final.pdb #2  
---  
CIT — citric acid  
EDO — 1,2-ethanediol  
  

> select #2/K:UNK

355 atoms, 283 bonds, 1 model selected  

> select clear

> style sel sphere

Changed 119 atom styles  

> style sel ball

Changed 119 atom styles  

> style sel sphere

Changed 119 atom styles  

> style sel ball

Changed 119 atom styles  

> color sel red

> hide #!1 models




OpenGL version: 3.3.0 NVIDIA 450.51.05
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        4.7G         49G        143M        8.6G         57G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: 6o24_final.pdb

6o24_final.pdb​

Attachments (1)

6o24_final.pdb​ (424.1 KB ) - added by Tristan Croll 5 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (4)

by Tristan Croll, 5 years ago

Attachment: 6o24_final.pdb​ added

Added by email2trac

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Input/Output
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted

comment:2 by Eric Pettersen, 5 years ago

Resolution: → not a bug
Status: accepted → closed

UNK residues are supposed to be in ATOM records, not HETATM records.

in reply to:  4 comment:3 by Tristan Croll, 5 years ago 

Ah - didn’t notice that. Will raise it with the PDB_REDO people.
Note: See TracTickets for help on using tickets.