3v Running Log for JobId '2019.jul11.278'

Program is still running, progress is shown below

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  • host ip address=171.65.184.67 (Thu Jul 11 15:48:30 2019)
  • converting pdb into xyzr (Thu Jul 11 15:48:31 2019)
  • completed conversion of PDB file: 2019.jul11.278.pdb (size: 86k) (Thu Jul 11 15:48:33 2019)
  • converted 2766 atoms of 2766 atoms (Thu Jul 11 15:48:33 2019)
  • found 2766 atoms in pdb (Thu Jul 11 15:48:33 2019)
  • running 3v all channel program (Thu Jul 11 15:48:33 2019)
  • created 2 channel files (Thu Jul 11 15:48:45 2019)
  • Download MRC files: 1 2 (Thu Jul 11 15:48:45 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jul 11 15:48:45 2019)
  • UCSF Chimera created Jmol compatible file (Thu Jul 11 15:48:48 2019)
  • compressing channel-001.obj (Thu Jul 11 15:48:48 2019)
  • UCSF Chimera completed in 3.0 sec (Thu Jul 11 15:48:48 2019)
  • analyzing volume (Thu Jul 11 15:48:48 2019)
  • normal CoM (-43.2, -36.8, -38.5) Å (Thu Jul 11 15:48:48 2019)
  • reduced center failed (Thu Jul 11 15:48:48 2019)
  • volume analysis completed in 72.74 msec (Thu Jul 11 15:48:48 2019)
  • compressing channel-001.pdb (Thu Jul 11 15:48:48 2019)
  • compressing channel-001.mrc (Thu Jul 11 15:48:49 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jul 11 15:48:49 2019)
  • UCSF Chimera created Jmol compatible file (Thu Jul 11 15:48:51 2019)
  • compressing channel-002.obj (Thu Jul 11 15:48:51 2019)
  • UCSF Chimera completed in 2.92 sec (Thu Jul 11 15:48:52 2019)
  • analyzing volume (Thu Jul 11 15:48:52 2019)
  • normal CoM (-44.5, -38.0, -40.8) Å (Thu Jul 11 15:48:52 2019)
  • reduced center failed (Thu Jul 11 15:48:52 2019)
  • volume analysis completed in 49.89 msec (Thu Jul 11 15:48:52 2019)
  • compressing channel-002.pdb (Thu Jul 11 15:48:52 2019)
  • compressing channel-002.mrc (Thu Jul 11 15:48:52 2019)
  • tarring file list (Thu Jul 11 15:48:52 2019)
  • compressing channel-001.pdb (Thu Jul 11 15:48:52 2019)
  • compressing channel-001.mrc (Thu Jul 11 15:48:52 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: reduced center failed 
Message: volume analysis completed in 49.89 msec 
Message: compressing channel-002.pdb 
Message: compressing channel-002.mrc 
Message: tarring file list 
Message: compressing channel-001.pdb 
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/2019/jul11/278/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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If you find this useful or want more functionality please contact Neil <vossman77 [at] gmail [dot] com>
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