3v Running Log for JobId '2021.apr07.bfe'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=192.33.118.251 (Wed Apr 7 15:00:45 2021)
  • converting pdb into xyzr (Wed Apr 7 15:00:45 2021)
  • completed conversion of PDB file: 2021.apr07.bfe.pdb (size: 578k) (Wed Apr 7 15:00:59 2021)
  • converted 18492 atoms of 18492 atoms (Wed Apr 7 15:00:59 2021)
  • found 18492 atoms in pdb (Wed Apr 7 15:00:59 2021)
  • running 3v all channel program (Wed Apr 7 15:00:59 2021)
  • created 2 channel files (Wed Apr 7 15:01:10 2021)
  • Download MRC files: 1 2 (Wed Apr 7 15:01:10 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Apr 7 15:01:10 2021)
  • UCSF Chimera created Jmol compatible file (Wed Apr 7 15:01:17 2021)
  • compressing channel-001.obj (Wed Apr 7 15:01:17 2021)
  • UCSF Chimera completed in 7.29 sec (Wed Apr 7 15:01:17 2021)
  • analyzing volume (Wed Apr 7 15:01:17 2021)
  • normal CoM (-66.1, -51.9, -72.9) Å (Wed Apr 7 15:01:17 2021)
  • reduced center failed (Wed Apr 7 15:01:17 2021)
  • volume analysis completed in 204.93 msec (Wed Apr 7 15:01:17 2021)
  • compressing channel-001.mrc (Wed Apr 7 15:01:17 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Apr 7 15:01:17 2021)
  • UCSF Chimera created Jmol compatible file (Wed Apr 7 15:01:24 2021)
  • compressing channel-002.obj (Wed Apr 7 15:01:24 2021)
  • UCSF Chimera completed in 7.12 sec (Wed Apr 7 15:01:24 2021)
  • analyzing volume (Wed Apr 7 15:01:24 2021)
  • normal CoM (-64.9, -51.5, -72.6) Å (Wed Apr 7 15:01:25 2021)
  • reduced center failed (Wed Apr 7 15:01:25 2021)
  • volume analysis completed in 205.52 msec (Wed Apr 7 15:01:25 2021)
  • compressing channel-002.mrc (Wed Apr 7 15:01:25 2021)
  • tarring file list (Wed Apr 7 15:01:25 2021)
  • compressing channel-001.mrc (Wed Apr 7 15:01:25 2021)

hit reload to refresh this page



Log file display

Show last lines of log file 
Terminal display
		
Message: analyzing volume 
Message: normal CoM (-64.9, -51.5, -72.6) Å 
Message: reduced center failed 
Message: volume analysis completed in 205.52 msec 
Message: compressing channel-002.mrc 
Message: tarring file list 
Message: compressing channel-001.mrc 
Traceback (most recent call last): 
File "/var/www/html/3vee/py/runChannelFinder.py", line 67, in  
runthreev.start() 
File "/var/www/html/3vee/py/runChannelFinder.py", line 57, in start 
self.threev.webMrcSection(mrcfiles, self.website, f, pdb=True, pymol=self.params['pymol']) 
File "/var/www/html/py/ThreeVLib.py", line 1033, in webMrcSection 
gzmrcfile = self.gzipFile(mrcfile, pymol) 
File "/var/www/html/py/ThreeVLib.py", line 853, in gzipFile 
header = mrc.readHeaderFromFile(fname) 
File "/var/www/html/py/pyami/mrc.py", line 666, in readHeaderFromFile 
f = open(filename) 
IOError: [Errno 2] No such file or directory: '/var/www/html/3vee/output/2021/apr07/bfe/channel-001.mrc' 

		


Citation:
'3V: cavity, channel and cleft volume calculator and extractor' (free text)
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W555–W562
by Neil R. Voss and Mark Gerstein
Download source code
Help
Site news and updates
If you find this useful or want more functionality please contact Neil <vossman77 [at] gmail [dot] com>
back to main page