mmCIF extremely slow when RCSB Ligand-expo site is down

[Tristan Croll]

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
Looks like the RCSB Ligand-expo site is down, which makes opening a mmCIF with lots of ligands (that aren't locally cached) agonisingly slow - attempting to open 6tx0 took a couple of minutes, attempting to fetch (and timing out on) each ligand. That should be improved a lot by #3317, but unless I'm mistaken that just caches failures for each residue - not a failure of the whole *server*.

Might also be worth looking at a backup plan for when this server's down. The PDBe runs a similar server, PDBeChem: https://www.ebi.ac.uk/pdbe-srv/pdbechem/.

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 6tx0 format mmcif fromDatabase pdb

Summary of feedback from opening 6tx0 fetched from pdb  
---  
warnings | Unable to fetch template for 'DZ4': might have incorrect bonds  
Unable to fetch template for 'CZF': might have incorrect bonds  
Unable to fetch template for 'DZ4': might have incorrect bonds  
Unable to fetch template for 'DZ4': might have incorrect bonds  
Unable to fetch template for 'DZ4': might have incorrect bonds  
2 messages similar to the above omitted  
Missing or invalid residue template for DZ4 /A:705  
Unable to fetch template for 'CZF': might have incorrect bonds  
Missing or invalid residue template for CZF /A:706  
Unable to fetch template for 'DZ4': might have incorrect bonds  
Missing or invalid residue template for DZ4 /A:707  
Unable to fetch template for 'DZ4': might have incorrect bonds  
Missing or invalid residue template for DZ4 /B:701  
Unable to fetch template for 'DZ4': might have incorrect bonds  
Missing or invalid residue template for DZ4 /B:706  
Unable to fetch template for 'CZF': might have incorrect bonds  
Missing or invalid residue template for CZF /B:707  
  
6tx0 title:  
Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with
XTP, dAMPNPP and Mg [more info...]  
  
Chain information for 6tx0 #1  
---  
Chain | Description  
A B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1  
  
Non-standard residues in 6tx0 #1  
---  
CZF —
[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl] phosphono hydrogen phosphate  
DZ4 —
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine  
FE — Fe (III) ion  
MG — magnesium ion  
  
6tx0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  




OpenGL version: 3.3.0 NVIDIA 450.36.06
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        5.1G         48G        263M        8.6G         56G
	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

[pett]

Also reported in #3443

[pett]

As mentioned in #3443, for entries also available in PDB format opening the PDB version is still fast.

[Greg Couch]

Will extend negative caching to include the fact that the network is down. Will limit it to the current invokcation of ChimeraX.

[Tristan Croll]

A related thought: would it be worth offering users the ability to cache 
a local copy of the full chemical components dictionary 
(http://www.wwpdb.org/data/ccd)?

On 2020-06-26 17:55, ChimeraX wrote:

[Greg Couch]

The full chemical components dictionary is constantly being updated, so in general it wouldn't work. But it would be possible to use a snapshot, so in practice it could work.

[Greg Couch]

Added negative caching of data files. If a data fetch fails, the hostname in the URL is cached, and all attempts to fetch data from that hostname will immediately fail for the next 10 minutes.