3v Running Log for JobId '2021.jul21.b3f'

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  • host ip address=141.161.133.94 (Wed Jul 21 14:09:58 2021)
  • converting pdb into xyzr (Wed Jul 21 14:09:58 2021)
  • completed conversion of PDB file: 2021.jul21.b3f.pdb (size: 170k) (Wed Jul 21 14:10:01 2021)
  • converted 5425 atoms of 5425 atoms (Wed Jul 21 14:10:01 2021)
  • found 5425 atoms in pdb (Wed Jul 21 14:10:01 2021)
  • running 3v all channel program (Wed Jul 21 14:10:01 2021)
  • created 1 channel files (Wed Jul 21 14:10:08 2021)
  • Download MRC files: 1 (Wed Jul 21 14:10:08 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Jul 21 14:10:08 2021)
  • UCSF Chimera created Jmol compatible file (Wed Jul 21 14:10:13 2021)
  • compressing channel-001.obj (Wed Jul 21 14:10:13 2021)
  • UCSF Chimera completed in 5.9 sec (Wed Jul 21 14:10:14 2021)
  • analyzing volume (Wed Jul 21 14:10:14 2021)
  • normal CoM (-19.8, -29.4, -33.3) Å (Wed Jul 21 14:10:14 2021)
  • reduced center failed (Wed Jul 21 14:10:14 2021)
  • volume analysis completed in 0.55 sec (Wed Jul 21 14:10:14 2021)
  • compressing channel-001.mrc (Wed Jul 21 14:10:14 2021)
  • compressing channel-001.mrc (Wed Jul 21 14:10:14 2021)

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Log file display

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Terminal display
		
OBJFILE /var/www/html/3vee/output/2021/jul21/b3f/channel-001.obj.gz 
Message: analyzing volume 
Message: normal CoM (-19.8, -29.4, -33.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 0.55 sec 
Message: compressing channel-001.mrc 
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/2021/jul21/b3f/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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