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Protein Data Bank Viewer |
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· Download · Examples |
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1. The program is viewer for PDB-Standard files and 3D
visualization of the included Atom Structures. 2. Several files in the same time can be open and
displayed in the best way on the screen. 3. The Atom Structure locates in two ways: a.
As the Tree of Model – Chain – Residue – Atom, including “Het Atoms” (since
version 2009.2.20.3). “Het Atom”, Residue, Chain and Model contained “Het
Atoms” are selected by the font of red color. b. Bold font shows that atom has a
anthers ones have been got from CONECT section (since version 2009.3.20.4). c.
As 3D Scene of selected objects. 4. One model or one Chain or list of Residues can be
selected in the Tree and this selection will be shown at the scene. The
Residues can be selected by usual Windows way using muse left key clicks with
Shift or Ctrl keys on keyboard. Only Residues of the same Model can be multi
selected. a. Selected Atom is shown on 3D-scene with the Residue
owned the atom. b. If the Selected Atom has connected atoms 3D scene shows
the Selected Atom Residue and all connected Residues (since version
2009.3.20.4). 5. Double click on any Atom on the scene will show the
Atom in the Tree without changing the Tree Selection for its best
recognizing. 6. Three buttons on the scene control panel “Chain”,
“Models” and “Residues” show the current screening object and switch to
parent object without changing selection in the Tree. 7. The buttons “Atoms Color” or “Residue Color” change the
colors of the Atoms on the scene. 8. The buttons “All Atoms” or “N-CA-C” change 3D screening
way of Residues – only main N, CA and C Atoms or all ones. 9. The seven buttons “Head”, “Top”, “Bottom”, “Front”,
“Back”, “Left”, “Right” switch on or off the corresponding lamps on the scene
for the best screening. The button “Visible” switches on or off the
visibility of all the lamps except headlight lamps which is visible all time
as white transparent cube in the center of coordinate system. 10. There are two ways of managing scene and moving the object
on it. Pay your attention that both ways can be used only if the cursor is
located on the scene. a. The simple way is moving and rotating the object around
the coordinate system center. i.
Press “Best” button for better object position. ii. Chose one or more lights around the object. iii. Press left mouse button and drag the object while
keeping button pressed. iv. Use mouse wheel to make the object position
closer or further to you. b. The more difficult and more useful way is to manage the
scene as a driver in 3D space. The following options help you walk around the
atoms. i.
Put the cursor on any point of scene. ii. Image that you are driver on small space
shuttle. iii. Transparent white cube in front of you is your
headlights. iv. Press “Up Arrow” and “Down Arrow” for moving
yourself forward and backward. v. Press “Left Arrow” and “Right Arrow” for
rotating yourself around the line going from your eyes to the headlights. vi. Press “Shift + Up Arrow”, “Shift + Down Arrow”,
“Shift + Left Arrow” or “Shift + Right Arrow” for turning up, down, left or
right around the point of headlights. vii. Press “Ctrl + Up Arrow”, “Ctrl + Down Arrow”, “Ctrl +
Left Arrow” or “Ctrl + Right Arrow” for sliding up, down, left or right
without any turning or rotation. viii. At last, press “Alt + Up Arrow”
or “Alt + Down Arrow” for changing the focus distance between your eye and
headlights. ix. Two special controls on scene tool bar “Linear
Speed” and “Angular Speed” help you to change speed for linear or angular
moving. c. In any case if you lost yourself in scene space press
button “Best” and you should immediately find the object. 11. When the scene is closing the tree selection, object
position, lights and some others parameters are automatically saving until
next open the PDB-file for the parameters restoring and work starting with
the best way of screening. But for the same PDB-file user can save and
restore different scenes using the “Open Scene” and “Save Scene” commands in
the main menu. 12. License: a. This program is free software: you can redistribute it
and/or modify it under the terms of the GNU General Public License as
published by the Free Software Foundation, either version 3 of the License,
or (at your option) any later version. b. This program is distributed in the hope that it will be
useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. c. See the GNU General Public License for more details
<http://www.gnu.org/licenses/>. 13. History: a. January
16, 2009. i.
Start. b. February
20, 2009. i.
Remote version check. ii. Fixed bug of reading float number with decimal
divider different from point. iii. HETATM section to visualization. c. March
20, 2009. i.
CONECT section to visualization added. ii. Bug of pressing “Best” button with empty list of
object fixed. iii. Some visual effects (Long process, Tree element
names, etc.) сhanged. iv. The atoms selection show on 3D-scene сhanged. d. May
19, 2010. i.
Small bugs fixed. |
