PyMol-Demo Online Help
This is a short description of the scripting language incorporated in PyMol. This demonstration supports only a part of these very powerful commands. All the examples are based on the protein hemoglobin.
List of commands:
show view
rotate axis,angle
turn axis,angle
move axis,distance
set property,value
set_color name,[red,green,blue]
color name
zoom
show view
- the parameter view can take the following values:
show lines
|
show sticks
|
show spheres
|
show dots
|
show cartoon
|
show ribbon
|
show surface
|
show mesh
|
|
Special scripts:
Script: Cartoon (color)
|
Script: Transparency
|
rotate axis,angle
- rotation around a spatial axis: The parameter axis stands for
x,y and z, the three spatial axes. angle indicates the rotation angle in degrees.
show sticks
rotate x,45
|
show sticks
rotate y,45
|
show sticks
rotate z,45
|
turn axis,angle
- rotation of the camera around a spatial axis: The parameter axis stands for
x,y and z, the three spatial axes. angle indicates the rotation angle in degrees.
move axis,distance
- camera movement along a spatial axis: The parameter axis stands for x,y and z, the three spatial axes. distance indicates the distance covered.
show sticks
move x,10
|
show sticks
move z,50
|
set property,value
- sets a PyMol-status variable
set_color name,[red,green,blue]
- defines a colour: name colour name defined by the user.
red,green,blue floating point values within
the range of 0.0-1.0 that stand for the amount of red, green and blue in the self-defined colour.
Example: set_color red,[1.0,0.0,0.0]
color name
- sets a colour: name existing colour name.
Table with pre-defined colours
| white | |
black | |
blue | |
green | |
red | |
| cyan | |
yellow | |
magenta | |
salmon | |
lime | |
| slate | |
hotpink | |
orange | |
yellowgreen | |
bluegreen | |
| blueviolet | |
marine | |
olive | |
purple | |
teal | |
| ruby | |
forest | |
deep | |
grey | |
carbon | |
| nitrogen | |
oxygen | |
hydrogen | |
brightorange | |
pink | |
| firebrick | |
chocolate | |
wheat | |
violet | |
density | |
color yellow
show ribbon
|
set_color water,[0.72,0.67,0.94]
color water
show ribbon
|
zoom
- matches the molecule to the size of the graphic representation.
PyMOL Copyright Notice
The PyMOL source code is copyrighted, but you can freely use and copy
it as long as you don't change or remove any of the copyright notices.
----------------------------------------------------------------------
PyMOL is Copyright 1998-2003 by Warren L. DeLano of
DeLano Scientific LLC, San Carlos, CA, USA (
www.delanoscientific.com).
All Rights Reserved
Permission to use, copy, modify, distribute, and distribute modified
versions of this software and its documentation for any purpose and
without fee is hereby granted, provided that the above copyright
notice appear in all copies and that both the copyright notice and
this permission notice appear in supporting documentation, and that
the names of Warren L. DeLano or DeLano Scientific LLC not be used in
advertising or publicity pertaining to distribution of the software
without specific, written prior permission.
WARREN LYFORD DELANO AND DELANO SCIENTIFIC LLC DISCLAIM ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL WARREN LYFORD DELANO
OR DELANO SCIENTIFIC LLC BE LIABLE FOR ANY SPECIAL, INDIRECT OR
CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE
USE OR PERFORMANCE OF THIS SOFTWARE.
----------------------------------------------------------------------
Where indicated, portions of the PyMOL system are instead protected
under the copyrights of the respective authors. However, all code in
the PyMOL system is released as non-restrictive open-source software
under the above license or an equivalent license.
PyMOL Trademark Notice
======================
PyMOL(TM) is a trademark of DeLano Scientific LLC. Derivate software
which contains PyMOL source code must be plainly distinguished from
the PyMOL package distributed by DeLano Scientific LLC in all publicity,
advertising, and documentation.
The slogans, "Includes PyMOL(TM).", "Based on PyMOL(TM) technology.",
"Contains PyMOL(TM) source code.", and "Built using PyMOL(TM).", may
be used in advertising, publicity, and documentation of derivate
software provided that the notice, "PyMOL is a trademark of DeLano
Scientific LLC.", is included in a footnote or at the end of the
document.
All other endorsements employing the PyMOL trademark require specific,
written prior permission.
--
e-mail:
warren@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
This demo enables you to to represent molecules three-dimensionally, using the PymMol-Package
(v0.99)
This powerful Python-Program with a Tcl-Tk-GUI does, however do considerably more, than
just offer this link-up feature. For large-scale projects, it is advisable to purchase the
package via the PyMol-Homepage.
All examples on this site were taken from this package. The PDB ID query is
based on data from the Research Collaboratory for Structural Bioinformatics (RCSB).
The local copy of this database contains 36042
files and was last updated on 02.05.2006 18:39:00.
