a question about 3V

Q:
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?

A:
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.

Help with Voronoi software

Q:
I have a protein PDB structure I’ve seen you this text,,I want to use Voronoia software to find the cavity of the protein and the amino acids of the cavity ,Can you help me to analyse it? I want to use the SURFNET software to find my cavity,can you help me to analyse? the following is my protein PDB structure.

A:
My apologies for the confusion, but SURFNET was not written by our group. SURFNET was written by Laskowski. Perhaps you could reach out to that team, and they may be able to help:

https://www.ncbi.nlm.nih.gov/pubmed/8603061
SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions.
Laskowski RA1.

If you’re interested in using a similar software, you may want to try our 3V server:
http://3vee.molmovdb.org/

If you experience difficulties using 3V, please do not hesitate to let us know.

ps — By the way, I just ran 3v on your pdb. Feel free to set whatever parameters you like, but I used 2 and 6 as probe radii. See attached results.

Need help on 3v

Q:
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.

A:
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?

Trouble installing libproteingeometry on Ubuntu 12.04

Q1:
I am trying to set up your software package (libproteingeometry) on a lab
desktop. I having trouble during the Make step. After running for a while,
one of the packages is unable to link to the appropriate math header files,
causing make to exit with an error. I am able to understand some C++ coding,
but am not proficient enough to come up with a solution to this problem
independently. I would like to use your program, so is there anyway that you
can put me in contact with someone in your lab who might be able to help me
finish installing this software?

A1:
Apologies again for the delay. May I ask how many structures you plan on running? Customizing libprotgeometry for your machine’s settings may be pretty tricky, especially from our end. If you’re not running too many structures, I’d highly suggest using the Online version of this tool (assuming you’re calculating residue-level packing metrics), linked here:

http://www.molmovdb.org/cgi-bin/voronoi.cgi

Q2:
Unfortunately, I plan on using you program in some molecular dynamics analysis, so the number of structures would be on the order of thousands. I fee like this is too much to run on your server (unless your server has a MD analysis option that I missed, which would be great).

I can send you specific error messages I have upon trying to run the make command. Please let me know what would help you. I saw this error on a forum somewhere where it looked like the problem had been solved, but the solution was not posted.

A2:
Yes, please do send us specific error messages upon trying to run make, as well as any other error messages that you obtain. The more info we have, the better. We’ll try to sort things out. Also, what type of OS is your machine running?

Q3:
I run ubuntu 12.04. I’m pretty sure the system is a converted dell. i5 processor, with nvidia graphics card. I’ll send the error messages in the morning.

Volume calculations w/3V

Q:
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=164.107.224.25 (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.

A:
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:
http://3vee.molmovdb.org/viewResults.php?jobid=2015.apr04.e5b

It missed the channel, I think if you use the coordinates, 5,0,0 it will work better:
http://3vee.molmovdb.org/viewResults.php?jobid=2015.apr04.e64