vmdStore

vmdStore provides a user-friendly interface to free install VMD plugins. vmdStore also helps you keeping the plugins always updated.

Minimum Requirements

Operating System: macOS, Linux, or Windows

Visual Molecular Dynamics (VMD) 1.9.3 or later

wget (Linux and macOS)

Installation

The GUI installers for VMD Store were deprecated. Please, follow one of the following methods to install VMD Store.

1. You can install VMD Store through the Tk Console on VMD:

This installation process can be used on every machine running VMD 1.9.3 or later.

a. Download and unpack the VMD Store:

b. Launch VMD (1.9.3 or later) and open the Tk Console (Extensions > Tk Console);

c. Navigate to the downloaded directory on Tk Console. Example:

  [Linux/macOS]:

     cd /home/users/myname/Downloads/BioSIM-Research-Group-vmdStore-19131bc/

  [Windows]:

     cd C:/Users/myname/Downloads/BioSIM-Research-Group-vmdStore-19131bc/

d. Run the following command on Tk Console:

  ```
  play vmdStore-installer-tkconsole.tcl
  ```

e. Follow the instructions;

f. Done! Re-launch VMD and open VMD Store at Extensions > VMD Store > VMD Store.

  Video Tutorial (https://youtu.be/r6Ci2AS2uv0)

2. or the bash script (macOS and Linux only):

a. Download and unpack the VMD Store:

  [![Download vmdStore](https://a.fsdn.com/con/app/sf-download-button)](https://sourceforge.net/projects/vmdstore/files/latest/download)
  [![Download vmdStore](https://img.shields.io/sourceforge/dt/vmdstore.svg)](https://sourceforge.net/projects/vmdstore/files/latest/download)
  [![Download vmdStore](https://img.shields.io/sourceforge/dd/vmdstore.svg)](https://sourceforge.net/projects/vmdstore/files/latest/download)
  [![Download vmdStore](https://img.shields.io/sourceforge/dw/vmdstore.svg)](https://sourceforge.net/projects/vmdstore/files/latest/download)
  [![Download vmdStore](https://img.shields.io/sourceforge/dm/vmdstore.svg)](https://sourceforge.net/projects/vmdstore/files/latest/download)

b. Navigate to the download directory:

  ```
  cd /home/users/myname/Downloads/BioSIM-Research-Group-vmdStore-19131bc/
  ```

c. Run the following command:

      bash install-vmdStore.sh

d. Follow the instructions.

3. or manually according to the following tutorial.

Manual Installation

1. Download or clone the repository.

2. Copy the "vmdStore" directory, which is located inside the download package, to a Read&Write allowed directory on your system.

3. Edit the "vmdStore/vmdStore.rc" file to replace the "none" word by the path where the vmdStore directory is located. Example: "/home/users/name/vmdStore". (Attention: Enclose the path in quotation marks)

4. Add the following lines to your .vmdrc or vmd.rc file:

Replace the "none" word by the path where the vmdStore.rc file is located. Example: "/home/users/name/vmdStore/vmdStore.rc"

##### VMD Store ## START #####
play none
##### VMD Store ## END #####

5. Start VMD. It could be necessary to restart VMD on first launch after vmdStore installation.

Bug Report/Suggestions

If you want to report bugs or suggest features, please contact me: hfernandes@med.up.pt

If you want to include your own VMD plugin on VMD Store, send an email to hfernandes@med.up.pt

Available Plugins

Alanine Scanning Mutagenesis

• compASM (https://github.com/BioSIM-Research-Group/compASM)

Education

• vmdMagazine (https://github.com/BioSIM-Research-Group/vmdMagazine

Molecular Mechanics

• DelPhiForceVMD (https://github.com/delphi001/DelPhiForceVMD)
• pathways (https://github.com/balabin/pathways)
• energySplit (https://github.com/BioSIM-Research-Group/energySplit)

QM/MM

• molUP (https://github.com/BioSIM-Research-Group/molUP)

Tools

• toolBar (https://github.com/BioSIM-Research-Group/toolBar)
• selectionManager (https://github.com/BioSIM-Research-Group/selectionManager)
• chemPathTracker (https://github.com/BioSIM-Research-Group/chemPathTracker)
• volArea (https://github.com/BioSIM-Research-Group/volArea)

Molecular Docking

• vsLab (https://github.com/BioSIM-Research-Group/vsLab)