Search results

''Changed in PyMOL 1.6: Added return code'' == Python API ==

...ed state without performing any fitting. The rms values are returned as a python array. ===PYMOL API===

''New in PyMOL 1.7.2. See the [[center_of_mass]] script for older PyMOL versions.'' PyMOL> fetch 1ubq, async=0

...of the built-in wizards. There are special Python scripts which work with PyMOL in order to obtain direct user interaction and easily peform complicated ta <source lang="python">

* Since PyMOL 2.5: Changes the named global setting to the default value. * Before PyMOL 2.5: Changes the named global setting to a zero or off value.

...to an atom selection in the specified state. It returns the rms values to python as an array. <source lang="python">

This page is about an API function. For the selection operator with the same name, see [[extend (sele ...PI-only function which binds a user defined function as a command into the PyMOL scripting language.

'''set_key''' binds a Python function or PyMOL command to a key press. ''Changes with PyMOL version:''

...on of the current atom. One common usage is to extract the positions as a python list to alter then write back to the molecule using alter_state. ...ression in valid [http://en.wikipedia.org/wiki/Python_syntax_and_semantics python syntax]

...so, there's a [[Pymolrc | .pymolrc]] file that initializes PyMOL each time PyMOL is executed. * More on launching PyMOL

...aring proteins with lower sequence identity, the [[super]] and [[cealign]] commands perform better. * '''quiet''' = 0/1: suppress output {default: 0 in command mode, 1 in API}

|type = Python Module |download = https://github.com/speleo3/pymol-psico

...ymol''' module namespace, and thus exposes objects like '''cmd''' and '''[[pymol.stored|stored]]'''. The order of iteration is that of the internal atom ord ...modification of '''x, y, z''' (and atom-state level settings in Incentive PyMOL 1.7+).

'''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in <source lang="python">

'''PyTMs''' is a PyMOL plugin that enables to easily introduce a set of common post-translational ..., or together with the [https://github.com/Pymol-Scripts/Pymol-script-repo pymol-script-repository]<br>

...ust end in ".ccp4", Raster3D input (Molscript output) must end in ".r3d", PyMOL session files must end in ".pse", and pickled ChemPy models with a ".pkl" c <source lang="python">

'''Fetch''' retrieves a protein structure from the PDB and loads it into PyMOL. ...tch_Path|fetch_path]], which defaults to the current working directory for PyMOL.

For those who are making movies with PyMOL, '''Ray''' is one of the most commonly used last steps before stitching the ==PyMol API==

...or report a bug, please fill a ticket at [http://sourceforge.net/projects/pymol/| sourceforge] === Ideas for PyMOL Development ===

...ng <nowiki><PRE>code here</PRE></nowiki> use <nowiki><source lang="python">python code</source></nowiki> or <nowiki><source lang="language-name-here">some co ..., starting data (''e.g.'', PDB files) to ''(ii)'' actual, working PyMOL or Python scripts and ''(iii)'' final output image files.