View Parameters Auto Adjusted on PyMol

This section provides a tutorial to demonstrate how PyMol automatically calculate viewing parameters to ensure that the molecule structure is displayed in the center and enclosed entirely inside the viewing window.

When you load a molecule structure into PyMol, it will automatically adjust viewing parameters, so that the molecule structure will be displayed in the center of the screen and enclosed entirely inside the viewing window.

Here are atom locations of the molecule specified in the Molecule-HY-001.sdf file:

0.8400   -0.1600    0.0000 N   0  0     0  0  0  0  0  0
1.4800    0.4300    0.0000 N   0  0     0  0  0  0  0  0
0.0900    0.2700    0.0000 N   0  0     0  0  0  0  0  0
1.1100    1.2100    0.0000 C   0  0     0  0  0  0  0  0
0.2700    1.1200    0.0000 C   0  0     0  0  0  0  0  0
0.8400   -1.0300    0.0000 C   0  0     0  0  0  0  0  0
1.5300    1.9900    0.0000 C   0  0     0  0  0  0  0  0
1.0700    2.7400    0.0000 Cl  0  0     0  0  0  0  0  0
1.5900   -1.4600    0.0000 C   0  0     0  0  0  0  0  0
0.0800   -1.4600    0.0000 C   0  0     0  0  0  0  0  0
1.5900   -2.3300    0.0000 C   0  0     0  0  0  0  0  0
0.0700   -2.3200    0.0000 C   0  0     0  0  0  0  0  0
0.8400   -2.7600    0.0000 C   0  0     0  0  0  0  0  0

If I load the molecule into PyMol, the viewing parameters will be adjusted as shown below

PyMOL>load /Users/herong/Molecule-HY-001.sdf

PyMOL>get_view

### cut below here and paste into script ###
set_view (\
     1.000000000,    0.000000000,    0.000000000,\
     0.000000000,    1.000000000,    0.000000000,\
     0.000000000,    0.000000000,    1.000000000,\
     0.000000000,    0.000000000,  -17.179622650,\
     0.876923084,   -0.289230824,    0.000000000,\
    13.544545174,   20.814699173,  -20.000000000 )
### cut above here and paste into script ###

The output tells us that:

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Molecule Mass and Weight

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 DNA Sequencing

 Gene Mutation

 SDF (Structure Data File)

 PyMol Installation

PyMol GUI and CLI

 PyMol Screen Layout

 Load Molecule from File into PyMol

 Virtual Trackball Rotation on PyMol

 Zoom In and Out on PyMol

 PyMol Command Line Interface

 "load" and "delete" Commands on PyMol

 "log_open" and "log_close" Commands on PyMol

 Model Space and Camera Space on PyMol

 "get_view" and "set_view" on PyMol

View Parameters Auto Adjusted on PyMol

 Zoom In/Out by Moving Camera

 Rotation with Transformation Matrix

 Rotation with "turn" Command

 Difference of "turn" and "rotate" Commands

 Difference of "move" and "translate" Commands

 "center", "zoom" and "reset" Commands

 Model-to-Camera Space Coordinates Mapping

 Camera-to-Model Space Coordinates Mapping

 Turn Structure around Camera

 "show lines" Presentation Command

 "show sticks" Presentation Command

 "show spheres" Presentation Command

 "show surface" Presentation Command

 "show mesh" Presentation Command

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 HGNC (HUGO Gene Nomenclature Committee)

 Relocated Tutorials

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB