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'''util.mroll''' issues mdo commands to create full rotation util.mroll(1,120,1) # issues [[mdo]] commands to create full rotation over 120 frames

# create a selection [[Category:Commands]]

...'' creates a new molecule object from a selection. It can also be used to create states in an existing object. create name, (selection) [, source_state [, target_state ]]

* name = string: name of object to create or modify {default: obj??} # Create default (B-DNA) chain

The [[Keyboard Shortcut Menu]] is a GUI panel that can create, modify, delete, and reset keyboard shortcuts. This functionality mimics th New shortcuts can be created by clicking the "Create New" button. This will open a new dialog that will fill the first box with

...ailable in open-source version). Given a two-state object, '''morph''' can create an interpolated trajectory from the first to the second conformation. * target = string: name of output object to create

Commands line [[load]], [[fetch]] and [[create]] have a '''discrete=-1/0/1''' argument. create discreteobj, ala, 1, 1, discrete=1

...passed to the used method, so you can for example adjust outlier cutoff or create an alignment object. There are several similar commands/scripts for this job, like "A > align > all to this" from the PyMOL panel,

This command can be used to create low-resolution surfaces of protein structures. * name = string: name of the map object to create or modify

will create an 1600-pixel wide image with an aspect ratio equal to that of will create a 2000 by 1500 pixel image with antialiasing disabled

...ween maps. For example, with [[Map_set]] you can add two maps together or create a consensus map from a series of maps or even take a difference map. This example shows you how to create a consensus map of the bound ligand in a conserved pocket.

Use [[align]] or [[super]] to create an alignment object (without fitting) and then use the alignment object in # create alignment object

...ent sequence similarity, the [[align]] command is preferred, because these commands are much faster than [[cealign]]. ...arget''' arguments are swapped with respect to the [[align]] and [[super]] commands.

# create the new entry called ".protein" in group 1hpv # create ".ligand in the 1hpv group

We will create a plugin which consists of [[PluginArchitecture#More than one file per plug The callback may do arbitrary stuff. Here we're going to create a dialog and show it to the user.

...contribute an explanation of the symexp command and link it to the 'PyMOL commands' page. Where do I go start this new page?<br>

::string: name of the distance object to create * This neat example shows how to create distance measurements from an atom in a molecule to all other atoms in the

Convenience shortcut to create selection with name "sele": [[Category:Commands|Select]]

...rmations, either as two objects or one multi-state object, '''morph''' can create an interpolated trajectory from the first to the second conformation. * name = string: name of object to create

=Invoking PyMOL and reading startup commands from a file= ...eate ".pymolrc.py" which contains actual Python code instead of just PyMOL commands. See an [[Inchoates_pymolrc|example .pymolrc]]).

# create the fake trajectory (of states) for a in range(2,31): cmd.create("obj","obj",1,a)

will create a new color that will appear in the GUI list. From the [[Category:Commands|Get Color Indices]]

** mode=3: don't move and don't create a bond, just combine into single object [[Category:Commands|Fuse]]

* name = string: name of object to create or modify {default: obj??} [[Category:Commands]]

*'''name''' = string: name of the ramp object to create * create a new object from the atoms for which you just measured a property

* '''object''' = string: name of alignment object to create {default: None} [[Category:Commands|Fit]]

You can create mesh around the center of the view by specifying "center" as the selection When [[map_auto_expand_sym]] is ON, you can create mesh beyond the precalculated volume. In this

...aring proteins with lower sequence identity, the [[super]] and [[cealign]] commands perform better. * '''object''' = string: name of alignment object to create {default: (no alignment object)}

# this will create a one-to-one mapping of states to movie frames. useful for making movies fr [[Category:Commands|Mset]]

...ctor values and color by the new values. This example is possible because commands PyMOL does not recognize are passed to the Python interpreter --- a very p # create the global, stored array

If the [[auto_indicate_flags]] setting is true, then PyMOL will automatically create a selection called "indicate" which contains all atoms with that flag after [[Category:Commands]]

..., '''Edit''', '''Help''', '''Display''', etc), shortcut buttons for common commands, and the command line. .... But, it's complex, and page upon page of PyMOL documentation cover these commands, so we're going to ignore them as much as possible.

...ovie in PyMOL is a series of frames stitched together in some way so as to create the desired animation. Once a movie is made in PyMOL, we have a few option == Movie Making Commands ==

subsequent "create" and "byres" operations. [[Category:Commands|Alter]]

First, [[Special:Userlogin|Create a New Account or Login]]. We have to block anonymous users from editing pa ...ing]] needs nice example usage. Feel free to expound (and comment on) the commands.

# 1) Load or create content for three scenes (this could just as easily ...red frames may not be up to date. I suggest calling "refresh" between the commands.

The util.cba* ("Color By Atom") commands color atoms according to type: oxygen in red, nitrogen in blue, hydrogen in ...nc command will color all the atoms according to type, as in the util.cba* commands stated above, except for the C-atoms.

# create phosphate spheres create phos, elem p;

Each of these two windows contain a command line, where we can enter commands into the program. <br> ...an, however, get really far without ever having to worry about writing any commands.

* [[psico]] is a python module which extends PyMOL with many commands * Create objects for each molecule or chain in selection with [[split_object]] and [

...ize these libraries (for this you could run "import wx" and "import numpy" commands in PyMOL: there should be no mistakes). * Load/create the models of spin labels (reference objects). The models of several common

...n can be accomplished through standalone Python scripts, through new PyMOL commands, through PyMOL Wizards, or via Tkinter plugins. * Create a plugin-manager GUI in the style of Firefox, Rythmbox, Gedit, Eclipse. A G

...If you want to save the position of your labels, the best way might be to create a new object and move the atoms in this object. Since the labels are positi [[Category:Commands|Label]]

'''Note:''' PyMOL has built-in commands to do RMSD fitting. This script is typically not needed. # Create the 3x3 matrix

# Create the coordinate system matrix (3x3 in R3) that corresponds to a set of basis ...that particular type of illustration. The principles and practices used to create superb static figures (''i.e.'', M_sV_s) also apply to