Getting Started

The short tutorial below explains how to run Capsid Mesh using a small example distributed with the program. If you already know how to use Capsid Mesh but just want to get it quickly installed on your Windows/Linux OS, the easiest way to do so is:

Download

The example/test distributed with Capsid Mesh is included with the binaries we distribute with the program:

  • For Win OS download the Capsid Mesh bundle from here

  • For Ubuntu download the Capsid Mesh bundle from here

Install

Uncompress the file capsid_mesh_win_v1.0.zip on win OS or capsid_mesh_linux_v1.0.tar.gz on linux OS.

dir capsid_mesh

You should be able to see:

..
data_in
results
temp
capsid_mesh.exe
chonps.atoms
config.conf
t3_cage.bin

Input data files

Capsid Mesh needs a VDB file from VIPERdb the which has to be put in the folder data_in

The setup is read through the file config.conf, and an important aspect to take careful is the T-number of the virus to be meshed.


#PDB_FILE_NAME 
1cwp
#T_NUMBER 
3
#RESOLUTION 
3
#SURFACE(1:vdw,2:sas)
2
#PROBE_RADIUS
3

Run

To run Capsid Mesh execute capsid_mesh.exe

capsid_mesh.exe

Results

The results of a Capsid Mesh run are placed in the output directory results, and intermediate files are generated in the output directory temp, this files can be discarded when the program finish

Results of capsid_mesh on example 1cwp

capsid_mesh.exe output:

 capsid_mesh.exe

                 CAPSID MESH: A program to generate viral capsid meshes suitable for FEA


         CAPSID MESH: RVGIAU construction
version                       : 1.0
file_name_in                  : data_in/1cwp.vdb
T_index_number                : 3
resolution                    : 3.00 Angstroms
enclosed volume by surface    : SAS
probe radius                  : 3.00 Angstroms
Van der Waals radii used
C                             : 1.78 Angstroms
H                             : 1.60 Angstroms
O                             : 1.60 Angstroms
N                             : 1.80 Angstroms
P                             : 1.83 Angstroms
S                             : 1.20 Angstroms
Generating viral capsid mesh...
Number of nodes               : 745300
Number of elements            : 660780
file_name_out_mesh            : results/1cwp_full.msh
Time Elapsed                  : 409.22 seconds