eF-site Help: Difference between revisions

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== about eF-site ==
== about eF-site ==
eF-site (electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, for analyses of the molecular recognition mechanisms. The Connolly surfaces were made by using the [http://www.csb.yale.edu/userguides/graphics/msp/msu_local.html MSP program] (Connolly, M.L., J. Mol.Graph., 4, 93-96, 1986) and the electrostatic potentials were calculated by solving Poisson-Boltzmann equations with the self-consistent boundary method by Nakamura, H. & Nishida, S. (J. Phys. Soc. Jpn., 56, 1609-1622, 1987).
eF-site (electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, for analyses of the molecular recognition mechanisms. The molecular surfaces were made by using the [http://www.csb.yale.edu/userguides/graphics/msp/msu_local.html MSP program] (Connolly, M.L., J. Mol.Graph., 4, 93-96, 1986) or the [http://mgltools.scripps.edu/packages/MSMS MSMS program] (Sanner, M., Olson, A.J., Spehner, J.C., Biopolymers, 38, 305-320), and the electrostatic potentials were calculated by solving Poisson-Boltzmann equations with the self-consistent boundary method by Nakamura, H. & Nishida, S. (J. Phys. Soc. Jpn., 56, 1609-1622, 1987).


== seqinfo and efvet files ==
== seqinfo and efvet files ==
In this database system, two kinds of file, seqinfo file and efvet file, are used to keep all information for each entry. The seqinfo file describes biological functions of the molecule and chemical properties of each functional site on the molecular surface. The efvet file contains geometric information and coloring attributes of the molecular surface in the form of a set of polygons. Electrostatic potentials and hydrophobic properties are discribed together by the surface color in such a way that red to blue colors correspond negative to positive electrostatic potentials, and yellow color indicates the surface of the hydrophobic residue. The seqinfo file and efvet file are both written in XML and schema documents for them are available
In this database system, two kinds of file, seqinfo file and efvet file, are used to keep all information for each entry. The seqinfo file describes biological functions of the molecule and chemical properties of each functional site on the molecular surface. The efvet file contains geometric information and coloring attributes of the molecular surface in the form of a set of polygons. Electrostatic potentials and hydrophobic properties are discribed together by the surface color in such a way that red to blue colors correspond negative to positive electrostatic potentials, and yellow color indicates the surface of the hydrophobic residue. The seqinfo file and efvet file are both written in XML and schema documents for them are available
([http://ef-site.hgc.jp/eF-site/schema/seqinfo20.xsd seqinfo], [http://ef-site.hgc.jp/eF-site/schema/efvet30.xsd efvet]).
([https://pdbj.org/eF-site/schema/seqinfo20.xsd seqinfo], [https://pdbj.org/eF-site/schema/efvet41.xsd efvet]).


In eF-site Tools page, we provide a program that downloads efvet files as space separated values format.
In eF-site Tools page, we provide a program that downloads efvet files as space separated values format.
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with vertex lines being extended.
with vertex lines being extended.
The original vertex line has three placeholder columns for external programs, and the efvet file puts five values
The original vertex line has three placeholder columns for external programs, and the efvet file puts five values
(electrostatic potential, hydrophobicity temperature factor, minimum curvature and maximum curvature) there.
(electrostatic potential, hydrophobicity, temperature factor, minimum curvature and maximum curvature) there.
Each vertex line has also atom data (extracted from the corresponding PDB ATOM record) at the end.
Each vertex line has also atom data (extracted from the corresponding PDB ATOM record) at the end.


== jV ==
== Molmil ==
[http://ef-site.hgc.jp/wiki/jV/index.php jV] is used to display molecules and their surfaces as a Java applet program. The program 'jV' has been developed by Kengo Kinoshita (Graduate School of Information Sciences, Tohoku University) and Haruki Nakamura (Institute for Protein Research, Osaka Univeristy), as one of the activities of Protein Data Bank Japan (PDBj), supported by grant-in-aid from National Bioscience Database Center, Japan Science and Technology Agancy (JST-NBDC) and Institute for Protein Research IPR, Osaka University.
[https://pdbj.org/help/molmil Molmil] is used to display molecules and their surfaces for a web environment with the intent to be usable on as many platforms as possible. The program 'Molmil' has been developed by Gert-Jan Bekker (Institute for Protein Research, Osaka University), as one of the activities of Protein Data Bank Japan (PDBj), supported by grant-in-aid from National Bioscience Database Center, Japan Science and Technology Agency (JST-NBDC) and Institute for Protein Research IPR, Osaka University.


Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The mouse control is as follows.
Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The typical mouse control with two buttons and a wheel is as follows.
{| class="wikitable" border="1" style="margin:0 auto"  
{| class="wikitable" border="1" style="margin:0 auto"  
! Action !! Window, Linux !! Mac OS X
! Operation !! Method
|-
|-
! style="text-align:left" | rotate around X,Y axes
! style="text-align:left" | rotate around the current center
| left drag || drag
|
|-
* Left drag (drag with pressing the mouse left button)
! style="text-align:left" | rotate around Z axis
* Swipe (with the touch interface)
| Shift + right drag || Shift + command + drag
|-
|-
! style="text-align:left" | translate along X,Y axes
! style="text-align:left" | translate along X,Y axes
|
| right drag || command + drag
* Shift + Left drag (drag with pressing the Shift button and the mouse left button)
|-
* Left-right drag (drag with pressing the mouse left button and right button)
! style="text-align:left" | translate along Z axis (zoom in/out)
* Wheel drag (drag with pressing the mouse wheel button)
| Shift + left drag || Shift + drag
* Swipe with two fingers (with touch interface)
|}
|-
! style="text-align:left" | translate along Z axis (zoom in/out)
|
* Right drag (drag with pressing the mouse right button)
* Wheel (rotate the mouse wheel)
* Gesture to top/bottom direction with two fingers (move two fingers forward to top/bottom direction with keeping them touching to the trackpad and a bit space in between them)
* Pinch in/out (move two fingers closer/farther with keeping them touch to the touchpad/touch display)
|}


In order to use jV, the [http://java.com/download/ Java Runtime Environment (JRE)] 1.6 or later must be installed on your computer. jV is freely distributed and can be used as a stand-alone program as well as an applet. In addition to mouse controls, a command line interface is provided.
Molmil is freely distributed and can be used as a stand-alone program as well as an applet. In addition to mouse controls, a command line interface is provided and the Pymol-like commands are also available. See the [https://github.com/gjbekker/molmil/wiki/Simple-CLI-examples GitHub page] for several examples.


'''Download jV'''
Please see the following pages for usage of Molmil.
* [http://service.ipr.pdbj.org/eF-site/servlet/DownloadViewerBinary binary (4.5.3)]
* [https://pdbj.org/help/molmil-manual Molmil User Manual]
* [http://service.ipr.pdbj.org/eF-site/servlet/Registration source code (4.5.3)] (registration will be required)
* [https://github.com/gjbekker/molmil/wiki/Molmil-usage Molmil usage（GitHub）]
* [https://github.com/gjbekker/molmil/wiki/Integrate-Molmil Integrate Molmil（GitHub）]
* [https://github.com/gjbekker/molmil/wiki/Molmil-API Molmil API（GitHub）]
* [https://github.com/gjbekker/molmil/wiki/FAQ Molmil FAQ（GitHub）]
 
When you use Molmil, please cite our paper: [https://doi.org/10.1186/s13321-016-0155-1 Bekker, GJ., Nakamura, H. & Kinjo, A.R. Molmil: a molecular viewer for the PDB and beyond. J Cheminform 8, 42 (2016)].

Latest revision as of 15:21, 9 May 2023

about eF-site

eF-site (electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, for analyses of the molecular recognition mechanisms. The molecular surfaces were made by using the MSP program (Connolly, M.L., J. Mol.Graph., 4, 93-96, 1986) or the MSMS program (Sanner, M., Olson, A.J., Spehner, J.C., Biopolymers, 38, 305-320), and the electrostatic potentials were calculated by solving Poisson-Boltzmann equations with the self-consistent boundary method by Nakamura, H. & Nishida, S. (J. Phys. Soc. Jpn., 56, 1609-1622, 1987).

seqinfo and efvet files

In this database system, two kinds of file, seqinfo file and efvet file, are used to keep all information for each entry. The seqinfo file describes biological functions of the molecule and chemical properties of each functional site on the molecular surface. The efvet file contains geometric information and coloring attributes of the molecular surface in the form of a set of polygons. Electrostatic potentials and hydrophobic properties are discribed together by the surface color in such a way that red to blue colors correspond negative to positive electrostatic potentials, and yellow color indicates the surface of the hydrophobic residue. The seqinfo file and efvet file are both written in XML and schema documents for them are available (seqinfo, efvet).

In eF-site Tools page, we provide a program that downloads efvet files as space separated values format. The format is based on that of the vet file of the MSP program described here with vertex lines being extended. The original vertex line has three placeholder columns for external programs, and the efvet file puts five values (electrostatic potential, hydrophobicity, temperature factor, minimum curvature and maximum curvature) there. Each vertex line has also atom data (extracted from the corresponding PDB ATOM record) at the end.

Molmil

Molmil is used to display molecules and their surfaces for a web environment with the intent to be usable on as many platforms as possible. The program 'Molmil' has been developed by Gert-Jan Bekker (Institute for Protein Research, Osaka University), as one of the activities of Protein Data Bank Japan (PDBj), supported by grant-in-aid from National Bioscience Database Center, Japan Science and Technology Agency (JST-NBDC) and Institute for Protein Research IPR, Osaka University.

Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The typical mouse control with two buttons and a wheel is as follows.

Operation Method
rotate around the current center
  • Left drag (drag with pressing the mouse left button)
  • Swipe (with the touch interface)
translate along X,Y axes
  • Shift + Left drag (drag with pressing the Shift button and the mouse left button)
  • Left-right drag (drag with pressing the mouse left button and right button)
  • Wheel drag (drag with pressing the mouse wheel button)
  • Swipe with two fingers (with touch interface)
translate along Z axis (zoom in/out)
  • Right drag (drag with pressing the mouse right button)
  • Wheel (rotate the mouse wheel)
  • Gesture to top/bottom direction with two fingers (move two fingers forward to top/bottom direction with keeping them touching to the trackpad and a bit space in between them)
  • Pinch in/out (move two fingers closer/farther with keeping them touch to the touchpad/touch display)

Molmil is freely distributed and can be used as a stand-alone program as well as an applet. In addition to mouse controls, a command line interface is provided and the Pymol-like commands are also available. See the GitHub page for several examples.

Please see the following pages for usage of Molmil.

When you use Molmil, please cite our paper: Bekker, GJ., Nakamura, H. & Kinjo, A.R. Molmil: a molecular viewer for the PDB and beyond. J Cheminform 8, 42 (2016).

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