FAQ Frequently asked questions

First, upload a single-model protein data bank (PDB) file with hydrogens. It is highly recommended to energy minimize your protein using an all-atom forcefield before volume calculation, which will reduce steric clashes, standardize bond lengths, and also add the necessary hydrogens.

Then, modify any options (starting/ending probe size, and minimum surface distance) that you wish to change. These options will affect the accuracy and runtime of the calculation.

By default, all heteroatoms are ignored. To read heteroatoms, select the heteroatom checkbox on the webserver or pass the -het flag to the native ProteinVolume executable. Please note that not all heteroatom radii are included in bondi.rad. To expand upon ProteinVolume's heteroatom radius list, please edit bondi.rad.

The list of default heteroatoms and their radii are listed below:

C	1.7
O	1.52
S	1.8
H	1.2
N	1.55
P	1.8
F	1.47
NE	1.54
SI	2.10
LI	1.82
CL	1.75
AR	1.88
NA	2.27
MG	1.73
K	2.75
NI	1.63
CU	1.4
ZN	1.39
GA	1.87
AS	1.85
SE	1.90
BR	1.85
KR	2.02
TE	2.06
I	1.98
XE	2.16
PD	1.63
AG	1.72
CD	1.58
IN	1.93
SN	2.17
PT	1.72
AU	1.66
HG	1.55
TL	1.96
PB	2.02
U	1.86
FE	1.96

For the standalone version, Java runtime environment 1.7 and above is required. PV does not need to be compiled and is platform independent.

For the web server, there is a 2 hour job time limit that prevents malformed structures and extremely long submissions from hogging the queue.

All user data (PDBs, volume results) are deleted after calculation and are not stored. Job information (user, time stamp, email) and download information (user, time stamp, institution, email) are encrypted and stored for proof of usage for grant writing purposes. If you do not wish to disclose this data, anonymous use is possible.

Jan 17 2017 - Webserver update

• Moved webserver to another host with separate compute node(s). About 3x speedup.
• Increased structure max atom limit to 6000 atoms due to new compute node.

Dec 6 2017 - Webserver update

• Energy minimization routine no longer only operates on first chain detected.
• Updated webserver to check and warn for missing atoms (incomplete residues).
  If missing atoms are detected, the energy minimization function will automatically model them in with MODELLER.

May 24 2017 - Webserver update

• Updated webserver to allow spaces in PDB filenames
• Fixed download zip/tar.gz to remove the -v version flag from template scripts

Jan 10 2017 - PV 1.3

• 4x speed over 1.0
• Half the memory usage over 1.0
• More accurate volume numbers especially near surface
• Can handle multi-molecule systems such as unfolded DNA/RNA
• Webserver: Fixed bug with progress bar showing completed upon protein upload
• Webserver: Updated estimated calculation times to be much more accurate