3v Running Log for JobId '2019.aug08.07e'

Program is still running, progress is shown below

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  • host ip address=129.67.69.149 (Thu Aug 8 05:26:50 2019)
  • downloading pdb file (Thu Aug 8 05:26:50 2019)
  • failed to download pdb id: 2b5h (Thu Aug 8 05:26:50 2019)
  • trying download pdb id again without bio unit (Thu Aug 8 05:26:52 2019)
  • completed download of PDB id 2b5h (size: 180 k, 2279 lines) (Thu Aug 8 05:26:52 2019)
  • converting pdb into xyzr (Thu Aug 8 05:26:52 2019)
  • completed conversion of PDB file: 2b5h-2019.aug08.07e.pdb (size: 47k) (Thu Aug 8 05:26:53 2019)
  • converted 1512 atoms of 1512 atoms (Thu Aug 8 05:26:53 2019)
  • found 1512 atoms in pdb (Thu Aug 8 05:26:53 2019)
  • running 3v all channel program (Thu Aug 8 05:26:53 2019)
  • created 2 channel files (Thu Aug 8 05:26:54 2019)
  • Download MRC files: 1 2 (Thu Aug 8 05:26:54 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Aug 8 05:26:54 2019)
  • UCSF Chimera created Jmol compatible file (Thu Aug 8 05:26:57 2019)
  • compressing channel-001.obj (Thu Aug 8 05:26:57 2019)
  • UCSF Chimera completed in 2.93 sec (Thu Aug 8 05:26:57 2019)
  • analyzing volume (Thu Aug 8 05:26:57 2019)
  • normal CoM (-35.8, -37.1, -35.2) Å (Thu Aug 8 05:26:57 2019)
  • volume analysis completed in 40.25 msec (Thu Aug 8 05:26:57 2019)
  • compressing channel-001.mrc (Thu Aug 8 05:26:57 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Aug 8 05:26:57 2019)
  • UCSF Chimera created Jmol compatible file (Thu Aug 8 05:27:00 2019)
  • compressing channel-002.obj (Thu Aug 8 05:27:00 2019)
  • UCSF Chimera completed in 2.86 sec (Thu Aug 8 05:27:00 2019)
  • analyzing volume (Thu Aug 8 05:27:00 2019)
  • normal CoM (-33.6, -36.3, -41.7) Å (Thu Aug 8 05:27:00 2019)
  • reduced center failed (Thu Aug 8 05:27:00 2019)
  • volume analysis completed in 27.05 msec (Thu Aug 8 05:27:00 2019)
  • compressing channel-002.mrc (Thu Aug 8 05:27:00 2019)
  • tarring file list (Thu Aug 8 05:27:00 2019)
  • compressing channel-001.mrc (Thu Aug 8 05:27:00 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: analyzing volume 
Message: normal CoM (-33.6, -36.3, -41.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 27.05 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/2019/aug08/07e/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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