CCD templates should us different XYZ fields

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-09-18)
Description
When a template is fetched from the CCD using mmcif.find_template_residue, the coordinates are currently taken from _chem_comp_atom.model_Cartn_{x,y,z}. Looks to me like these should instead be taken from _chem_comp_atom.pdbx_model_Cartn_{x,y,z}_ideal, since it turns out the former can have some coordinates undefined (3PE, for instance). This caused rather a lot of head-scratching this afternoon!

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-09-18)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed
'ChimeraX_ISOLDE-1.0b3.dev5-cp37-cp37m-linux_x86_64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/home/tic20/.cache/ChimeraX/0.91/installers/ChimeraX_ISOLDE-1.0b3.dev5-cp37-cp37m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in
/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages (from ChimeraX-
ISOLDE==1.0b3.dev5) (0.91)  
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper>=0.9.9 in
/home/tic20/.local/share/ChimeraX/0.91/site-packages (from ChimeraX-
ISOLDE==1.0b3.dev5) (0.9.9)  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in
/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages (from ChimeraX-
ISOLDE==1.0b3.dev5) (1.0)  
Installing collected packages: ChimeraX-ISOLDE  
Found existing installation: ChimeraX-ISOLDE 1.0b3.dev5  
Uninstalling ChimeraX-ISOLDE-1.0b3.dev5:  
Successfully uninstalled ChimeraX-ISOLDE-1.0b3.dev5  
Successfully installed ChimeraX-ISOLDE-1.0b3.dev5  
Lock 140711558216400 acquired on
/home/tic20/.cache/ChimeraX/0.91/toolshed/bundle_info.cache.lock  
Lock 140711558216400 released on
/home/tic20/.cache/ChimeraX/0.91/toolshed/bundle_info.cache.lock  
  

> open Mouse-d-coot-9_real_space_refined.pdb

Chain information for Mouse-d-coot-9_real_space_refined.pdb #1  
---  
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  
  

> select /H:3PE

266 atoms, 264 bonds, 1 model selected  

> hide ~sel

> toolshed show Shell

/opt/UCSF/ChimeraX-daily/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 clear

> cofr centerOfView

> cofr centerOfView showPivot true

> select up

Nothing selected  

> color sel bychain

> color sel byhetero

> color sel bychain

> color sel byhetero




OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

If that's not enough, it turns out the experimental coordinates for some more common residues are really bad. Leucine is provided as one of the least common rotamers (0.45% prevalence), the hexose ring of BMA is horribly strained, etc..

[Greg Couch]

Done.

[Tristan Croll]

Because the universe is a dark and terrible place sometimes... the 
template for HEC only provides *experimental* coordinates. Go figure.

On 2019-10-16 22:13, ChimeraX wrote:

[Greg Couch]

The code is designed to fallback to the experimental coordinates if the ideal PDB ones are missing. But it's not working.

[Greg Couch]

Didn't read the ideal PDB coordinates into the separate variables that were created for them.