3v Running Log for JobId '2017.aug10.c8d'

Program is still running, progress is shown below

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  • host ip address=104.34.216.132 (Fri Aug 11 00:34:59 2017)
  • converting pdb into xyzr (Fri Aug 11 00:34:59 2017)
  • completed conversion of PDB file: 2017.aug10.c8d.pdb (size: 490k) (Fri Aug 11 00:35:10 2017)
  • converted 15686 atoms of 17785 atoms (Fri Aug 11 00:35:10 2017)
  • found 15686 atoms in pdb (Fri Aug 11 00:35:10 2017)
  • running 3v all channel program (Fri Aug 11 00:35:10 2017)
  • created 2 channel files (Fri Aug 11 00:35:15 2017)
  • Download MRC files: 1 2 (Fri Aug 11 00:35:15 2017)
  • imaging volume (download mrc) with UCSF Chimera (Fri Aug 11 00:35:15 2017)
  • UCSF Chimera created Jmol compatible file (Fri Aug 11 00:35:22 2017)
  • compressing channel-001.obj (Fri Aug 11 00:35:22 2017)
  • UCSF Chimera completed in 6.43 sec (Fri Aug 11 00:35:22 2017)
  • analyzing volume (Fri Aug 11 00:35:22 2017)
  • normal CoM (-41.4, -62.4, -72.0) Å (Fri Aug 11 00:35:22 2017)
  • reduced center failed (Fri Aug 11 00:35:22 2017)
  • volume analysis completed in 32.78 msec (Fri Aug 11 00:35:22 2017)
  • compressing channel-001.mrc (Fri Aug 11 00:35:22 2017)
  • imaging volume (download mrc) with UCSF Chimera (Fri Aug 11 00:35:22 2017)
  • UCSF Chimera created Jmol compatible file (Fri Aug 11 00:35:29 2017)
  • compressing channel-002.obj (Fri Aug 11 00:35:29 2017)
  • UCSF Chimera completed in 6.93 sec (Fri Aug 11 00:35:29 2017)
  • analyzing volume (Fri Aug 11 00:35:29 2017)
  • normal CoM (-45.5, -53.4, -58.1) Å (Fri Aug 11 00:35:29 2017)
  • reduced center failed (Fri Aug 11 00:35:29 2017)
  • volume analysis completed in 148.08 msec (Fri Aug 11 00:35:29 2017)
  • compressing channel-002.mrc (Fri Aug 11 00:35:29 2017)
  • tarring file list (Fri Aug 11 00:35:29 2017)
  • compressing channel-001.mrc (Fri Aug 11 00:35:29 2017)

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Log file display

Show last lines of log file 
Terminal display
		
Message: analyzing volume 
Message: normal CoM (-45.5, -53.4, -58.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 148.08 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/2017/aug10/c8d/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
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