3v Running Log for JobId '2018.feb13.9dc'

Program is still running, progress is shown below

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  • host ip address=128.103.94.226 (Tue Feb 13 11:32:47 2018)
  • converting pdb into xyzr (Tue Feb 13 11:32:47 2018)
  • completed conversion of PDB file: 2018.feb13.9dc.pdb (size: 589k) (Tue Feb 13 11:33:01 2018)
  • converted 18834 atoms of 18834 atoms (Tue Feb 13 11:33:01 2018)
  • found 18834 atoms in pdb (Tue Feb 13 11:33:01 2018)
  • running 3v all channel program (Tue Feb 13 11:33:01 2018)
  • created 2 channel files (Tue Feb 13 11:33:08 2018)
  • Download MRC files: 1 2 (Tue Feb 13 11:33:08 2018)
  • imaging volume (download mrc) with UCSF Chimera (Tue Feb 13 11:33:08 2018)
  • UCSF Chimera created Jmol compatible file (Tue Feb 13 11:33:26 2018)
  • compressing channel-001.obj (Tue Feb 13 11:33:26 2018)
  • UCSF Chimera completed in 18.4 sec (Tue Feb 13 11:33:27 2018)
  • analyzing volume (Tue Feb 13 11:33:27 2018)
  • normal CoM (-24.0, -58.9, -66.4) Å (Tue Feb 13 11:33:28 2018)
  • reduced center failed (Tue Feb 13 11:33:29 2018)
  • volume analysis completed in 1.9 sec (Tue Feb 13 11:33:29 2018)
  • compressing channel-001.mrc (Tue Feb 13 11:33:29 2018)
  • imaging volume (download mrc) with UCSF Chimera (Tue Feb 13 11:33:29 2018)
  • UCSF Chimera created Jmol compatible file (Tue Feb 13 11:33:45 2018)
  • compressing channel-002.obj (Tue Feb 13 11:33:45 2018)
  • UCSF Chimera completed in 17.18 sec (Tue Feb 13 11:33:46 2018)
  • analyzing volume (Tue Feb 13 11:33:46 2018)
  • normal CoM (-33.4, -67.2, -62.8) Å (Tue Feb 13 11:33:48 2018)
  • reduced center failed (Tue Feb 13 11:33:48 2018)
  • volume analysis completed in 1.75 sec (Tue Feb 13 11:33:48 2018)
  • compressing channel-002.mrc (Tue Feb 13 11:33:48 2018)
  • tarring file list (Tue Feb 13 11:33:48 2018)
  • compressing channel-001.mrc (Tue Feb 13 11:33:48 2018)

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Log file display

Show last lines of log file 
Terminal display
		
Message: analyzing volume 
Message: normal CoM (-33.4, -67.2, -62.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.75 sec 
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/2018/feb13/9dc/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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