I would really appreciate if your could assist me with an issue I encounter by using your online 3V software.
I am trying to compute the cavity size of a host (which I also did two years ago, see Org. Biomol. Chem., 2013, 11,
7667) but am receiving the message: "failed to create an MRC file”.
Program is still running, progress is shown below
host ip address=188.8.131.52 (Tue Mar 31 17:13:16 2015)
converting pdb into xyzr (Tue Mar 31 17:13:16 2015)
completed conversion of PDB file: 2015.mar31.8dd.pdb (size: 4k) (Tue Mar 31 17:13:16 2015)
converted 128 atoms of 128 atoms (Tue Mar 31 17:13:16 2015)
found 128 atoms in pdb (Tue Mar 31 17:13:16 2015)
running 3v channel program (Tue Mar 31 17:13:16 2015)
failed to create an MRC file (Tue Mar 31 17:13:16 2015)
The program stops and does not provide me with any result.
I looked at the log file and the program does not find a cavity at coordinate 0,0,0. I tried it again with a high resolution grid size.
I used the cached PDB that you uploaded and I managed to get a channel using channel finder:
It missed the channel, I think if you use the coordinates, 5,0,0 it will work better: