3v Running Log for JobId '2019.jan09.953'

Program is still running, progress is shown below

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  • host ip address=158.227.41.160 (Wed Jan 9 10:56:49 2019)
  • downloading pdb file (Wed Jan 9 10:56:49 2019)
  • failed to download pdb id: 2oar (Wed Jan 9 10:56:49 2019)
  • trying download pdb id again without bio unit (Wed Jan 9 10:56:51 2019)
  • completed download of PDB id 2oar (size: 451 k, 5703 lines) (Wed Jan 9 10:56:51 2019)
  • converting pdb into xyzr (Wed Jan 9 10:56:51 2019)
  • completed conversion of PDB file: 2oar-2019.jan09.953.pdb (size: 149k) (Wed Jan 9 10:56:55 2019)
  • converted 4755 atoms of 4755 atoms (Wed Jan 9 10:56:55 2019)
  • found 4755 atoms in pdb (Wed Jan 9 10:56:55 2019)
  • running 3v all channel program (Wed Jan 9 10:56:55 2019)
  • created 1 channel files (Wed Jan 9 10:56:58 2019)
  • Download MRC files: 1 (Wed Jan 9 10:56:58 2019)
  • imaging volume (download mrc) with UCSF Chimera (Wed Jan 9 10:56:58 2019)
  • UCSF Chimera created Jmol compatible file (Wed Jan 9 10:57:02 2019)
  • compressing channel-001.obj (Wed Jan 9 10:57:02 2019)
  • UCSF Chimera completed in 4.6 sec (Wed Jan 9 10:57:02 2019)
  • analyzing volume (Wed Jan 9 10:57:02 2019)
  • normal CoM (-40.7, -39.5, -25.7) Å (Wed Jan 9 10:57:03 2019)
  • reduced center failed (Wed Jan 9 10:57:03 2019)
  • volume analysis completed in 348.46 msec (Wed Jan 9 10:57:03 2019)
  • compressing channel-001.pdb (Wed Jan 9 10:57:03 2019)
  • compressing channel-001.mrc (Wed Jan 9 10:57:03 2019)
  • compressing channel-001.pdb (Wed Jan 9 10:57:03 2019)
  • compressing channel-001.mrc (Wed Jan 9 10:57:03 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: normal CoM (-40.7, -39.5, -25.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 348.46 msec 
Message: compressing channel-001.pdb 
Message: compressing channel-001.mrc 
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/jan09/953/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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