Regarding your paper entitled "3V: cavity, channel and cleft volume calculator and extractor", which I read carefully.
I’ve a question for you. In the abstract, it is written the following:"It rapidly finds internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces,…", but I think you mean "two imaginary rolling-probe solvent-excluded surfaces" because after looking at your code, I haven’t seen any analytic SES formulation therein. I guess you are just using two probe spheres of distinct radii to account for cavities, not the analytic SES themselves. Am I right?
I am not certain about your use of the term "imaginary", but I would say my method is a "discrete approximation" to the SES. And because it is discrete (i.e. a 3D grid) one can simply subtract one grid from another. See attached figures.
With small grid sizes (0.2 A), I see very little discrepancy to the analytical solution.
I have been running the channel extraction utility of the 3v and I was able to analyze the results successfully using chimera.
However now I want to run on the multiple files by using the local copy of the program. So I just rerun the calculation for the test case to check if I get the same results as the server. But i am not able to do so. I have tried various option but nothing is seems to be working.
Please let me know if you have any suggestion.
the command that was run is on the server is:
Channel.exe -i 2016.aug31.c64.xyzr -b 10.000 -s 3.000 -t 1.500 -g 1.000 -x -57.519 -y -8.258 -z -52.322 -m 2016.aug31.c64.mrc
Can you compare it to what you were running locally?
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=220.127.116.11 (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: