PyMOL Wiki - User contributions [en]

Ramp update

2022-05-25T18:29:52Z

Cchem: 1 revision imported

[[ramp_update]] updates range and/or color of a color ramp.

''New in PyMOL 1.8''

== Usage ==

ramp_update name [, range [, color ]]

== Example ==

ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]
ramp_update e_pot_color, range=[-15,0,15]
ramp_update e_pot_color, color=[green,white,orange]

== See Also ==

* [[ramp_new]]

[[Category:Commands]]

Cluster mols

2022-05-25T18:29:52Z

Cchem: 3 revisions imported

[[File:cluster_mols_py_pymol.png|450px|right]]
cluster_mols is a PyMOL plugin that allows the user to quickly select compounds from a virtual screen to be purchased or synthesized.

It helps the user by automatically clustering input compounds based on their molecular fingerprints [http://openbabel.org/wiki/FP2] and loading them into the PyMOL window. cluster_mols also highlights both good and bad polar interactions between the ligands and a user specified receptor. Additionally there are a number of keyboard controls for selecting and extracting compounds, as well as functionality for searching online to see if there are vendors for a selected compound.

= Description =
The basic work flow of cluster_mols.py can be broken up into three parts.
# Computing a similarity matrix from the input compounds
# Performing hierarchical clustering on the results from 1)
# Cutting the tree at a user-specified height and creating and sorting clusters

The results of 1 and 2 are saved to python pickle files so you do not have to recompute them in subsequent runs.

In addition, it also highlights both good and bad polar contacts between the ligand and a user specified protein using the 'show_contacts' module described below.

This script also integrates keyboard controls which allows for WASD movement through the clusters as well as keyboard shortcuts for pulling out compounds.
See below for usage.

= Download =
The most up to date version (recommended) of cluster_mols is available through BitBucket at: https://bitbucket.org/mpb21/cluster_mols_py/overview

= Installation =

This plugin has a number of dependencies that are required. And it is currently only supported on Linux and OSX.

Python packages (install using easy_install or pip)
# openbabel
# numpy
# scipy
# Tkinter
# fastcluster
# Pmw-py3 '''Important:''' Pmw 2.0.1 does not work; install the Pmw-py3 package instead of Pmw to get version 2.1

Command line tools (These must be accessible through your PATH environment variable):
# obabel -- from http://openbabel.org

Recent versions of cluster_mols do not require sdsorter, but it is still a very useful tool for dealing with sdf files.
# sdsorter -- https://sourceforge.net/projects/sdsorter/

Once you have the required dependencies, install it through PyMOL's Plugin menu.

PyMOL > Plugin > Install Plugin

= Usage =

The GUI is relatively straightforward, if you follow it from top to bottom, and then then left to right through the tabs.

The program requires that the input be a '.sdf' or '.sdf.gz' file. If your compounds are not in that format, use the 'babel' tool from OpenBabel to convert them.

== GUI Options ==
[[File:cluster_mols_screen_1_desc.png|200px|thumb]]
[[File:cluster_mols_screen_2_desc.png|200px|thumb]]

In the 'Compute Similarities' tab, there are options for selecting a new ligand and for specifying how many CPUs you want to run the similarity calculation on. Clicking the 'Compute Similarity' button will start the similarity calculations. If you check the 'Ignore saved results?' box it will ignore any saved intermediate results files. This could be useful if you change the contents of the original input file while keeping the file name the same.

Depending on how many compounds there are, the similarity calculations may take between 1 and 10 minutes. If you launched PyMOL from the command line, you will be able to see the progress printing out in the console. The similarity results are saved to a file so if you want to re-cluster the same input file, you do not need to wait to recompute the similarities.

The first option on the Cluster Compounds tab defines how the clusters will be sorted. The default is to sort by the 'minimizedAffinity' which is inserted into the output sdf file after minimization with 'smina' (An enhanced version of AutoDock Vina. Available at: http://www.smina.sf.net). You can also sort the clusters by any SD tag that exists in the input file, or by the Title (alphabetically) or by the size of the cluster.

The second option is the height at which the hierarchical clustering tree is cut. The units are arbitrary, but a higher number leads to a small number of large clusters of less similar compounds, and lower cutoffs lead to more small clusters of more similar compounds. Play around with the cutoff until you get a clustering that you like. The third option is a check box for whether to group clusters with only one compound into one ‘singletons’ cluster. The forth option enables the show_contacts tool that is described below. There is also a field to enter a PyMOL selection string to compute the hydrogen bonds to. Finally, there is a button to create the clusters and load them into PyMOL.

== Keyboard Controls ==
Once you have finished the similarity calculations and clustering mentioned above, you can navigate the clusters using the keyboard. Familiar to gamers, you can move through clusters using the WASD keys, (W for up, S for down, A for left, D for right).
The one important caveat is that due to [[Set_Key#KEYS_WHICH_CAN_BE_REDEFINED|limitations]] in PyMOL, the WASD movement needs to be used with the Control (or Alt) key. Meaning Ctrl-W moves up. It seems weird, but you quickly get used to it.

Navigation Controls

Ctrl-W – Move up a cluster

Ctrl-S – Move down a cluster

Ctrl-A – Move to the previous compound in a cluster

Ctrl-D – Move to the next compound in the cluster

Ctrl-F -- Check for vendors

If you acquired your compounds from ZINCPharmer (http://zincpharmer.csb.pitt.edu/) and/or your compounds have title that start with a ZINC ID (http://www.docking.zinc.org) or a MolPort ID (http://www.molport.com), you can hit 'Ctrl-F' to see if there are any vendors available.

Compound selection

In addition to moving through the clusters, you can also extract compounds that you like for later viewing using the following controls. Pressing F3 will append the current compounds into a new object with the suffix '_selected'.

F1 – Print title of currently selected molecule

F2 – Remove most recently added compound

'''F3 – Add currently visible compound to list''' (Most commonly used)

F4, F12 – Print List

== show_contacts ==
show_contacts is an expanded version of list_hbonds[http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/] that shows both favorable and unfavorable contacts between ligands and a protein receptor. show_contacts has been integrated into cluster_mols as a function and is executed automatically when clustering. It can also be run by itself, not in the context of cluster_mols. In the standalone case, the usage is as follows:

show_contacts(selection,selection2,result="contacts",cutoff=3.6, bigcutoff = 4.0):

The arguments are as follows:
#selection -- pymol selection string for the protein
#selection2 -- pymol selection string for the ligands
#results -- prefix of the object that the distances should be shown in. (Default "contacts")
#cutoff -- Distance cutoff for what is considered an ideal hydrogen bond.
#bigcutoff -- Distance cutoff for a non-ideal hydrogen bond.

Output:
The output of show_contacts are a set of pymol distance objects. They are color-coded and size coded to indicate different interactions between the ligand and protein. They are controlled by the parameter indicated.

# thin-purple lines -- all possible polar contacts (acc-acc, don-don, acc-don) -- bigcutoff
# thick-yellow lines -- All ideal hydrogen bonds -- cutoff
# thin-yellow lines -- Non ideal hydrogen bonds -- bigcutoff
# thick-red lines -- Polar clashes, i.e. Donor-Donor, Acceptor-Acceptor -- cutoff

= Citing ClusterMols =
If you use ClusterMols in your work, please cite the following.

Baumgartner, Matthew (2016) IMPROVING RATIONAL DRUG DESIGN BY INCORPORATING NOVEL BIOPHYSICAL INSIGHT. Doctoral Dissertation, University of Pittsburgh.

= Authors =
The main cluster_mols.py script was conceived of by Matthew P Baumgartner (mpb21 [at] pitt.edu) and Dr. David Koes while working in the lab of Dr. Carlos Camacho at the University of Pittsburgh. The cluster_mols.py script was implemented (and later rewritten) by MPB. The show_contacts functionality and the first version of the objectfocus.py keyboard controls was written by DK.

Please send questions/comments/bug reports to matthew.p.baumgartner [at] gmail.com.

[[Category:Plugins]]

Jupyter

2021-12-06T03:43:04Z

Cchem: 1 revision

Some PyMOL functionality can be used inside [https://jupyter.org/ Jupyter Notebooks]. Since PyMOL's nature is primarily that of an application and not of a library, there are various ways to do PyMOL+Jupyter integration, each way with its own limitations.

== Ways of Integration ==

* Directly using the PyMOL API
** Running PyMOL and Jupyter in the same interpreter
*** Same thread (headless only)
*** Asynchronous thread (GUI possible)
** Running PyMOL standalone, with [[RPC]] communication (GUI possible)
* Using third party libraries which add their own intermediate layer
** [https://pypi.org/project/ipymol/ IPyMOL] controls a PyMOL instance via [[RPC]]
** [https://www.rdkit.org/docs/source/rdkit.Chem.PyMol.html RDKit] controls a PyMOL instance via [[RPC]]

== Installation ==

If PyMOL and Jupyter should run in the same interpreter, they need to be installed into the same Python environment. [[RPC]] also works with two independent environments.

=== Incentive PyMOL ===

Install [https://docs.conda.io/en/latest/miniconda.html Miniconda] or [https://www.anaconda.com/ Anaconda] (or grab a bundle from [https://pymol.org/#download pymol.org] which includes conda). Then install:

conda install jupyter schrodinger::pymol

=== Open-Source PyMOL ===

[[Linux Install|Compile and install]] PyMOL with the same Python that you use with Jupyter, into the same environment.

== Example 1: Same interpreter, same thread ==

This example will render an image and display it inside the Jupyter notebook.

Open a notebook, then execute:

<syntaxhighlight lang="python">
from pymol import cmd
cmd.fragment('ala')
cmd.orient()

# since PyMOL 2.5
cmd.ipython_image()

# before PyMOL 2.5
cmd.png('/tmp/foo.png', ray=1)
from IPython.display import Image
Image(filename='/tmp/foo.png')
</syntaxhighlight>

== Example 2: Same interpreter, asynchronous thread ==

''Note: This doesn't work on macOS, see https://github.com/schrodinger/pymol-open-source/issues/28 ''

This example will control a PyMOL window (see also [[Launching_From_a_Script#STDOUT|stdout notice]]).

Open a notebook, then execute:

<syntaxhighlight lang="python">
# open a PyMOL window
import sys
import pymol
_stdouterr = sys.stdout, sys.stderr
pymol.finish_launching(['pymol', '-q'])
sys.stdout, sys.stderr = _stdouterr

# load something into the PyMOL window
from pymol import cmd
cmd.fragment('ala')
</syntaxhighlight>

== Example 3: RPC ==

Launch PyMOL with the "-R" option:

<source lang="bash">
pymol -R
</source>

Open a Python 3 notebook, then execute:

<syntaxhighlight lang="python">
# load something into the PyMOL window
import xmlrpc.client as xmlrpclib
cmd = xmlrpclib.ServerProxy('http://localhost:9123')
cmd.fragment('ala')
</syntaxhighlight>

== See Also ==

* [[Launching From a Script]]
* [[RPC]]

Get Area

2021-12-06T03:43:03Z

Cchem: 1 revision

#REDIRECT [[Get area]]

Talk:Get Area

2021-12-06T03:43:03Z

Cchem: 1 revision

#REDIRECT [[Talk:Get area]]

Contact map visualizer

2021-12-06T03:43:03Z

Cchem: 1 revision

{{Infobox script-repo
|type = plugin
|filename = plugins/contact_map_visualizer.py
|author = [[User:Venky|Venkatramanan Krishnamani]]
|license = -
}}

'''Enhanced version of this plugin is now available at [[CMPyMOL]]'''

The '''contact map visualizer''' plugin can link contact map images to the residues in PyMOL in a interactive way. Contact maps are pixel graphics where each protein residue corresponds to one line and one row of pixels. Thus for a 100 residue protein, such a image has 100x100 pixels. A common tool to generate such images is '''g_mdmat''' from the [http://www.gromacs.org gromacs] package.

== Usage ==

contact_map_visualizer [ image_file [, selection ]]

== Required Dependencies ==

* [http://pygame.org/ pygame]
* [http://wiki.python.org/moin/TkInter Tkinter] (optional and usually included with PyMOL)
* [http://www.pythonware.com/products/pil/ PIL] (optional, for automatically converting XPM images)

Example for installing all dependencies on a Ubuntu like system:

<source lang="bash">
sudo apt-get install python-tk python-imaging python-pygame
</source>

== Installation ==

* Navigate to plugins > install
* Locate the downloaded '''contact_map_visualizer.py''' file in the dialogbox and select 'OK'
* Quit and Restart 'pymol'

Alternative way: Just [[run]] the script, it will provide a command but no menu plugin entry.

== Generate Contact Map ==

[[File:Contact-Map-of-a-Trajectory.png|thumb|200px|right|Mean contact map of a protein trajectory generated from g_mdmat tool in the Gromacs analysis package.]]

Use the command [http://manual.gromacs.org/online/g_mdmat.html g_mdmat] from [http://www.gromacs.org Gromacs] analysis package. A typical contact map looks like the figure on the right.

To generate contact map of a single PDB. For example contact map for a PDB from RCSB, use the following command
g_mdmat -f <protein.pdb> -s <protein.pdb> -mean contact-map.xpm
To generate a mean contact map form a protein trajectory
g_mdmat -f <trajectory.pdb> -s <starting-frame.pdb> -mean contact-map.xpm

For Gromacs 2021
To generate contact map of a single PDB. For example contact map for a PDB from RCSB, use the following command
gmx g_mdmat -f <protein.pdb> -s <protein.pdb> -mean contact-map.xpm
To generate a mean contact map form a protein trajectory
gmx g_mdmat -f <trajectory.pdb> -s <starting-frame.pdb> -mean contact-map.xpm
To convert XPM to PNG format
convert contact-map.xpm contact-map.png

== Screenshot ==

[[File:Screenshot.png|thumb|800px|center]]

== Copyright ==
<source lang="text">
# Copyright Notice
# ================
#
# The PyMOL Plugin source code in this file is copyrighted, but you are
# free to use and copy it as long as you don't change or remove any of
# the copyright notices.
#
# -----------------------------------------------------------------------------------
# This PyMOL Plugin Contact Maps Visualizer is
# Copyright (C) 2012 by Venkatramanan Krishnamani <venks@andrew.cmu.edu>
#
# 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 name(s) of the author(s) not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
#
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN
# NO EVENT SHALL THE AUTHOR(S) 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.
#
</source>

[[Category:Plugins]]
[[Category:Pymol-script-repo]]

Get sasa relative

2021-12-06T03:43:03Z

Cchem: 1 revision

[[get_sasa_relative]] calculates the [https://en.wikipedia.org/wiki/Relative_accessible_surface_area relative per-residue solvent accessible surface area] and optionally labels and colors residues.
The value is relative to full exposure of the residue, calculated by removing all other residues except its two next neighbors, if present.

The command loads a value beteween 0.0 (fully buried) and 1.0 (fully exposed) into the b-factor property, available in [[iterate]], [[alter]] and [[label]] as '''b'''.

''New in Incentive PyMOL 1.8 and Open-Source PyMOL 2.1''

''Changed in PyMOL 2.6: Added '''subsele''' argument''

== Usage ==

get_sasa_relative [ selection [, state [, vis [, var [, quiet [, outfile [, subsele ]]]]]]]

== Example ==

fetch 1ubq
get_sasa_relative polymer

Side-chain exposure, including C-alpha atom, using '''subsele''' argument (new in PyMOL 2.6):

get_sasa_relative polymer, subsele=sidechain guide

== See Also ==

* [[get_area]]

[[Category:Commands|get_sasa_relative]]

PICv

2021-08-16T02:55:03Z

Cchem: 1 revision

{{Infobox script-repo
|type = plugin
|download = [http://vidyaniranjan.co.in/PICv/PICv.py '''PICv''']
|author = [https://akshayuttarkar.wixsite.com/akshay Akshay Uttarkar], [https://vpdesai2020.github.io/vasanth.github.io/ Vasanth Kumar Desai], Namitha P, John Berrisford, [https://www.ebi.ac.uk/about/people/sameer-velankar Sameer Velankar], [http://www.vidyaniranjan.co.in/ Vidya Niranjan]*
|license = GNU Free Documentation License 1.2
}}

== '''About PICv''' ==

[[File:PICv.png]]

Protein interaction clustering and visualization is an pioneer attempt in understanding protein-protein interaction at a residue level. For any given protein the interaction is purely dependent on its charges and surface-structural modifications. The clustering of proteins based on there preferential amino acid interactions provides a biological insight on both the above mentioned aspects. The clusters such obtained can be used to infer the interaction behavior for a class or family of proteins. Such interpretation can be useful in understanding structural protein chemistry. The interactions also provide information on the crucial amino acids required for interactions to remain stable. This information can be used to design antibody or induce mutations to depreciate its functionality

[[File:PICv_home_screen.PNG]]

== '''Code''' ==
Download the plugin from the following URL:

[http://vidyaniranjan.co.in/PICv/PICv.py '''PICv Source Code''']

== '''Installation and Demo video''' ==

Visit the below mentioned link for detailed installation followed by demo.

[https://youtu.be/3bxpASy-FV0 '''PICv (Video)''']

== '''Developed by''' ==

The plugin was developed by '''Center of Excellence Computational Genomics''', R V College of Engineering, Bangalore, India in collaboration with '''Protein Data Bank in Europe (PDBe), UK'''

'''For more details visit'''

[http://www.vidyaniranjan.co.in/ '''Center of Excellence Computational Genomics''']

== '''Copyright''' ==
<source lang="text">
# Copyright Notice
# ================
#
# The PyMOL Plugin source code in this file is copyrighted, but you are
# free to use and copy it as long as you don't change or remove any of
# the copyright notices.
#
# -----------------------------------------------------------------------------------
# This PyMOL Plugin PICv is
# Copyright (C) 2021 by Vidya Niranjan <vidya.n@rvce.edu.in>
#
# 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 name(s) of the author(s) not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
#
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN
# NO EVENT SHALL THE AUTHOR(S) 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.
#
</source>

[[Category:Plugins]]
[[Category:Pymol-script-repo]]

3Dstrut

2021-08-16T02:55:03Z

Cchem: 14 revisions

{|class = infobox
|-
!style="width: 120px;" |Type
|Plugin
|-
!Download
|https://github.com/
|-
!Author
|George Phillips
|-
!Other authors
|Tony Kamenick, Stuart Ballard
|-
!Contributors
|Shashank Ravichandran, Gautham Krishna, [[User:Ragothaman|Ragothaman Yennamalli]]
|}

3Dstrut is an external plugin for the molecular visualization program PyMOL. The plugin generates struts at optimal positions and thus enables 3D printing of any structure visualized using PyMOL. This software is distributed freely for Windows, Linux and macOS platforms.

== Version history ==
Version history goes here

== Installation ==
Installation details goes here

Windows Install

2021-06-22T03:21:08Z

Cchem: 3 revisions

This page describes how to install PyMOL on Microsoft Windows.

== Incentive PyMOL ==

[http://www.schrodinger.com Schrödinger] provides an installer to paying sponsors (EXE for PyMOL 2.0, MSI for previous version). The bundle also includes ready-to-use [[APBS]], [[morph|RigiMOL]], an MPEG encoder for movie export, and a small molecule energy minimization engine.

Download: https://pymol.org/#download

== Open-Source PyMOL ==

Open-Source PyMOL is available [https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/LICENSE free of charge]. It also allows sponsors to create highly customized PyMOL installations which might not be possible with the MSI installer.

Pre-compiled Open-Source PyMOL is available free from [http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol Christoph Gohlke of the Laboratory for Fluorescence Dynamics, University of California, Irvine].

# Install the latest version of Python 3 for Windows (e.g., by going to http://www.python.org/downloads/ and choosing the x64 EXE installer). Use the standard options, which should mean that the installation directory is most likely C:\Users\<Your Username>\AppData\Local\Programs\Python\Python38). Make sure the option to add environment variables is selected.
# Do install [https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads the current Microsoft Visual C++ Redistributable for Visual Studio 2015, 2017 and 2019]. Otherwise the installed PyMOL binary may fail to run (without any error message!).
# Download the [http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol-open-source appropriate wheel files], along with all requirement wheel files (including [http://www.lfd.uci.edu/~gohlke/pythonlibs/#pip pip], [http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy Numpy] and [http://www.lfd.uci.edu/~gohlke/pythonlibs/#pmw PMW]) into a single file directory, e.g., <code>C:\Users\<Your Username>\Downloads\PyMOL_installation</code>

Navigate to the installation directory in a CMD window <source lang = python>cd C:\Users\<Your Username>\Downloads\PyMOL_installation</source> (or where ever you put the files) and begin the installation using the command:
<source lang = python>python.exe pip-20.x.x-py2.py3-none-any.whl/pip install --no-index --find-links="%CD%" pymol_launcher</source> If your python install is part of your PATH variable, then running (where x refers to the version number of pip): <source lang = python>python pip-20.x.x-py2.py3-none-any.whl/pip install --no-index --find-links="%CD%" pymol_launcher</source>
should suffice.

To update PyMOL update the files in the PyMOL install directory and run: <source lang = python>pip install --upgrade --no-deps pymol.whl</source> where <code>pymol.whl</code> is replaced by the PyMOL wheel file name (not the launcher, the launcher should not require updating). To use the newer single-window Qt interface, also install the optional PyQt5 dependency for your Python installation: <source lang=python> pip install pyqt5 </source>

=== Extend PyMOL with additional scripts ===
If you now want to extend the capabilities of PyMOL, and take advantage of all the available plugins+scripts "out there", then do the following. <br>
# First install "numpy" as an available module to Python. [http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy Select appropriate installer from here]
# Download the script/plugin collection [[Git | Pymol-script-repo]] from [https://github.com/Pymol-Scripts/Pymol-script-repo/zipball/master a .zip file from here]
git clone https://github.com/Pymol-Scripts/Pymol-script-repo
# Unpack it to here: '''C:\Python27\Lib\site-packages\pymol\pymol_path\Pymol-script-repo''' Double check that the folder name is correct and the same.
Open "Notepad" and write.
<syntaxhighlight lang="python">
# Add paths to sys.path so PyMOL can find modules and scripts
import sys, os
pymol_git = os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

# Make setting changes to Plugin Manager
import pymol.plugins
pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
pymol.plugins.autoload = {'apbs_tools': False}
pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])
pymol.plugins.preferences = {'instantsave': True, 'verbose': False}
</syntaxhighlight>
'''Then "File->Save as->All files-> C:\Python27\Lib\site-packages\pymol\pymol_path\run_on_startup.py'''

Now start pymol, and enjoy all the plugins available from the menu.

'''PyMOL''' shortcut<br>
Make a '''pymol''' directory in your homepath. '''mkdir %HOMEPATH%\pymol''' Then make sure, PyMOL starts here, when you open the shortcut.<br>
Make a shortcut to the .cmd file, and modify it. <br>
Target: C:\python27\PyMOL\pymol.cmd <br>
Start in: %HOMEPATH%\pymol

== See Also ==

* [[pymolrc]]
* [[Linux Install]]
* [[MAC Install]]

[[Category:Installation|Windows]]
[[Category:Technical Issues|Windows Install]]
[[Category:Windows]]

Redo

2021-06-22T03:21:07Z

Cchem: 1 revision

''(Incentive PyMOL only feature)''

See [[undo]] for guidance on PyMOL's undo feature.

== Usage ==
redo [, steps]

* '''steps''' = integer: number of steps to undo

== PyMOL API ==
<source lang="python">
cmd.redo(int steps=1)
</source>

== Example ==
redo
redo 5

== SEE ALSO ==
[[Undo]]

[[Category:Commands|Redo]]
[[Category:Editing Module|Redo]]

Builder

2021-06-22T03:21:07Z

Cchem: 2 revisions

= Overview =
The [[Builder]] is a PyMOL GUI menu that allows you to easily build up structures by hand from various elements like atoms, fragments, rings, amino acids, etc. You can also assign charge, secondary structure, etc.

To access the [[Builder]] simply select the "Builder" option from the PyMOL GUI (see images).

<gallery>
Image:Builder0.png|Builder button in the GUI
Image:Builder1.png|Builder activated.
</gallery>

= Nucleic Acid Builder =

As of '''Incentive PyMOL 2.3''', building can also be done with nucleic acids.

[[File:DNA_Builder1.png]]

Click the 'Builder' button in the top-right panel.

[[File:DNA_Builder2.png]]

Once selecting "Nucleic Acids", you will presented options for building either DNA or RNA. For DNA, you can specify the custom DNA's form (A-DNA or B-DNA) and whether the DNA should be single- or double-stranded.

[[File:DNA_Builder3.png]]

When ready, select the base type for the nucleic acid by clicking on the button with its specified one-letter code (e.g. A, T, U, C, or G) and select "Create As New Object".

[[File:DNA_Builder4.png]]

To extend the DNA, select a terminal 5' phosphate or 3' oxygen.

You can see the change in the nucleic acid's sequence in real-time (Display-> Sequence). For double-stranded DNA, positive residue indices are base-paired to its negative counterpart (5 base-paired with -5, 12 base-paired with -12, etc...).

Once finished, click the "Done" button.

[[File:DNA_Builder5.png]]

Here is an example finished product from the DNA builder.

''New in Incentive PyMOL 2.5''

As of Incentive PyMOL 2.5, builder can attach nucleic acids to existing structures. Double stranded structures are automatically detected based on distance cutoff and base pairing. Additionally, a phosphate group will be automatically added to the 5' end if missing from the structure.

The "Residue: Remove" button will remove the residue currently selected based on PyMOL's Selection Algebra. This means the entire residue of the atom selected will be removed. This works for both proteins and nucleic acids.
[[File:Remove-Residue-Button.png]]

[[Category:Builder]]
[[Category:Building]]
[[Category:Modeling]]
[[Category:Editing]]

Keyboard Shortcut Menu

2021-06-22T03:21:06Z

Cchem: 3 revisions

The [[Keyboard Shortcut Menu]] is a GUI panel that can create, modify, delete, and reset keyboard shortcuts. This functionality mimics the [[Set_Key]] function.

''New in PyMOL 2.5''

== Usage ==
The Keyboard Shortcut Menu is located in the "Setting" menu heading.

[[File:Keyboard-Shortcut-Menu-Location.png]]

From this table, shortcuts can be edited directly by clicking and typing in the new command.

[[File:Shortcut-Menu-Edit.png]]

New shortcuts can be created by clicking the "Create New" button. This will open a new dialog that will fill the first box with the key you press (e.g. CTRL-K). The desired command can then be typed in the "Command" box. Click the "Help" button for useful tips for making new shortcuts.

[[File:Shortcut-Menu-Create-New.png]]

Selected commands can also be deleted or reset to their default values with the "Delete Selected" and "Reset Selected" buttons respectively.

[[File:Shortcut-Menu-Delete-Reset.png]]

The "Reset All" button will restore all commands to their default values and remove any new shortcuts that have been created.

The "Save" button will save the current shortcut configuration to a file. This configuration will be automatically loaded in when you open PyMOL.

== See Also ==
* [[Set_Key]]

[[Category:GUI]]

Main Page

2021-06-22T03:21:05Z

Cchem: 2 revisions

__NOTOC__
{| align="center" width="100%" style="background: #B22222; margin-bottom: 4em; border-bottom: 1px solid #B22222; border-left: 1px solid #B22222; border-right: 1px solid #B22222;"
|+ style="font-size: 1.0em; font-weight: normal; color: #FFFFFF; text-align:right; background: #B22222; padding-top:0.5em; padding-bottom: 0.25em; padding-right: 0.60em; border-top: 2px solid #B22222; border-bottom: 1px solid #fff;" |hosted by [[File:SBGridlogo2.jpg|140 px|link=https://sbgrid.org/]]
|}
{| align="center" style="padding-bottom: 3em;"
|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
| To request a new account, email SBGrid at: accounts (@) sbgrid dot org
|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
|}

{| align="center" width="45%" style="background: #FFFFFF; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
|+ style="font-size: 1.4em; font-weight: bold; color: #FFFFFF; text-align:center; background: #000000; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #000000; border-bottom: 1px solid #fff;" |Quick Links
|-
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
|-
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
|-
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[PyMOL_mailing_list|Getting Help]]'''
|}

{| width="100%"
| style="vertical-align: top; width: 40%" |
{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
! Official Release
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
! POSF
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
|-
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
! New Plugin
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
! Selection keywords
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
! Plugin Update
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
|-
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
! Older News
| See [[Older_News|Older News]].
|}
|style="vertical-align: top; width: 40%"|
{| class="jtable" style="float: right; width: 90%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|<div class="didyouknow" >
<DynamicPageList>
randomcount=1
category=Commands|Plugins|Script_Library|Settings
includepage=*
includemaxlength=1050
escapelinks=false
allowcachedresults=false
resultsheader=__NOTOC__ __NOEDITSECTION__
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
</DynamicPageList>
</div>
<div style="clear: both;"></div>
|}
|
|style="vertical-align: top; width: 18%"|
<DynamicPageList>
imagecontainer=Covers
randomcount=1
escapelinks=false
openreferences=true
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n
ordermethod=none
allowcachedresults=false
</DynamicPageList>

|}

Undo

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Cchem: 4 revisions

''(Incentive PyMOL only feature)''

Most actions as of '''Incentive PyMOL 2.5''' are undoable.

Actions are undoable via GUI menu (Edit -> Undo). The undo feature may be manually disabled by unchecking `Edit -> Undo Enabled`, and can be re-enabled by rechecking the same menu item.

== Usage ==
undo [, steps]

* '''steps''' = integer: number of steps to undo

== PyMOL API ==
<source lang="python">
cmd.undo(int steps=1)
</source>

<code>undo_enable</code> is an API-only feature that allows you enable undo.

<source lang="python">
cmd.undo_enable()
</source>

<code>undo_disable</code> is an API-only feature that allows you disable undo.

<source lang="python">
cmd.undo_disable()
</source>

== Example ==
undo
undo 5

== Comments ==

Currently, the undo stack supports the previous 25 actions or up to 1GB memory used. These will later be configurable in an upcoming release.

Currently, undo support for builder is not available but will be supported in a later patch release.

While movie is playing, the undo manager is paused and will save the current session's state when the user ends the movie.

During wizards, the undo manager is paused, and the current session's state is saved when the user clicks 'Done' for active wizards.

For larger sessions, it may be suitable to manually turn off undo to save on memory usage (commands such as set will incur a high memory cost). Add <code>cmd.undo_disable()</code> in your pymolrc if you need to disable undo automatically upon startup.

For '''Incentive PyMOL''', all previous undo features are deprecated and will now be superseded by the one introduced in '''Incentive PyMOL 2.5'''.

== SEE ALSO ==
[[Redo]]

[[Category:Commands|Undo]]
[[Category:Editing Module|Undo]]

Isosurface

2021-06-22T03:21:02Z

Cchem: 2 revisions

'''isosurface''' creates a new surface object from a map object.

== Usage ==

<source lang="python">
isosurface name, map, [,level [,(selection) [,buffer [,state [,carve [,source_state [,side [,mode ]]]]]]]]
</source>

* name = the name for the new mesh isosurface object.
* map = the name of the map object to use for computing the mesh.
* level = the contour level. (default=1.0)
* selection = an atom selection about which to display the mesh with an additional "buffer" (if provided). (default="")
* state = the state into which the object should be loaded (default=1) (set state=-2 to append new surface as a new state)
* carve = a radius about each atom in the selection for which to include density. If "carve= not provided, then the whole brick is displayed. (default=None)
* source_state = the state of the map from which the object should be loaded. (default=0)
* Front or back face. Triangle-winding/normal direction. (default=1)
* mode = surface geometry (0: dots; 1: lines; 2: triangle triangle-normals; 3: triangle gradient-normals) (default=3)

== Algorithm ==

PyMOL offers three different algorithms for isosurface generation. Each of these can be activated by the <code>isosurface_algorithm</code> setting

* 0: Marching Cubes via VTKm (default) (requires VTKm)
* 1: Marching Cubes basic (fallback if VTKm not installed)
* 2: Marching tetrahedra (legacy)

== Examples ==

fetch 1oky, type=2fofc, async=0
isosurface 1okySurf, 1oky_2fofc

With carving at 2 Angstrom around the molecular model:

fetch 1oky, async=0
fetch 1oky, type=2fofc, async=0
isosurface 1okySurf, 1oky_2fofc, 1.0, (1oky), carve=2.0

== Notes ==

If there exists a non-map object with the same name, then the new surface will overwrite that object. Surface objects can be appended onto existing surface objects using the aforementioned state argument.

== See Also ==

* [[volume]]
* [[isodot]]
* [[isomesh]]
* [[load]]
* [[Dynamic_mesh]]

[[Category:Commands|Isosurface]]
[[Category:States|Isosurface]]
[[Category:Electron_Density]]
[[Category:Maps]]

PICv

2021-03-01T03:38:08Z

Cchem:

{{Infobox script-repo
|type = plugin
|download = [http://vidyaniranjan.co.in/PICv/PICv.py '''PICv''']
|author = [https://akshayuttarkar.wixsite.com/akshay Akshay Uttarkar], [http://vasanthdesai.me/?i=1 Vasanth Kumar Desai], Namitha P, John Berrisford, [https://www.ebi.ac.uk/about/people/sameer-velankar Sameer Velankar], [http://www.vidyaniranjan.co.in/ Vidya Niranjan]*
|license = GNU Free Documentation License 1.2
}}

== '''About PICv''' ==

[[File:PICv.png]]

Protein interaction clustering and visualization is an pioneer attempt in understanding protein-protein interaction at a residue level. For any given protein the interaction is purely dependent on its charges and surface-structural modifications. The clustering of proteins based on there preferential amino acid interactions provides a biological insight on both the above mentioned aspects. The clusters such obtained can be used to infer the interaction behavior for a class or family of proteins. Such interpretation can be useful in understanding structural protein chemistry. The interactions also provide information on the crucial amino acids required for interactions to remain stable. This information can be used to design antibody or induce mutations to depreciate its functionality

[[File:PICv_home_screen.png]]

== '''Code''' ==
Download the plugin from the following URL:

[http://vidyaniranjan.co.in/PICv/PICv.py '''PICv Source Code''']

== '''Installation and Demo video''' ==

Visit the below mentioned link for detailed installation followed by demo.

[https://youtu.be/3bxpASy-FV0 '''PICv (Video)''']

== '''Developed by''' ==

The plugin was developed by '''Center of Excellence Computational Genomics''', R V College of Engineering, Bangalore, India in collaboration with '''Protein Data Bank in Europe (PDBe), UK'''

'''For more details visit'''

[http://www.vidyaniranjan.co.in/ '''Center of Excellence Computational Genomics''']

== '''Copyright''' ==
<source lang="text">
# Copyright Notice
# ================
#
# The PyMOL Plugin source code in this file is copyrighted, but you are
# free to use and copy it as long as you don't change or remove any of
# the copyright notices.
#
# -----------------------------------------------------------------------------------
# This PyMOL Plugin PICv is
# Copyright (C) 2021 by Vidya Niranjan <vidya.n@rvce.edu.in>
#
# 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 name(s) of the author(s) not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
#
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN
# NO EVENT SHALL THE AUTHOR(S) 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.
#
</source>

[[Category:Plugins]]
[[Category:Pymol-script-repo]]

File:PICv home screen.png

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Cchem: Cchem uploaded a new version of "File:PICv home screen.png"

File:PICv home screen.png

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Cchem: Cchem uploaded a new version of "File:PICv home screen.png"

File:Modevector.png

2021-03-01T03:34:50Z

Cchem:

Annotate v

2021-03-01T03:33:42Z

Cchem:

{{Infobox script-repo
|type = script
|filename = annotate_v.py
|author = [[User:XinYu|Xin Yu]]
|license = BSD
}}

== Description ==

''Version: 1.0''

A simple-to-use script for annotation of VH or VL sequence of an antibody. It creates a Pymol object for each FR or CDR region. It utilizes the REST API interface of ''Abnum'' (http://www.bioinf.org.uk/abs/abnum/) from Dr Andrew Martin's group at UCL

== Annotation Schemes ==

Currently supports '''Kabat, Chothia, Contact, IMGT'''<sup>1</sup>

<sup>1</sup>Definitions for Kabat, Chothia, Contact, and IIMGT are same as listed in the table (http://www.bioinf.org.uk/abs/info.html#kabatnum), except that for IMGT, H-CDR2 is defined as '''H51-H57''' in this script, as opposed to of '''H51-H56''' in the table. This slight revision generates result that matches that from ''IMGT website'' (http://www.imgt.org/)

== Dependencies and Limitations ==

1. Import '''request''' module

2. Relies on internet connection to ''Abnum''

3. Incomplete VH or VL sequence might not be annotated

== How to use ==

1. Create a selection object for the V region, (such as '''VH''' and '''VL''' shown here). Only 1 V-region (VH OR VL) can be annotated each time. Alternatively, simply select the residues into the default '''<sele>''' group.

[[Image:Annotate_v_pic1.png|center|thumb|800px|Create a selection group for input seq, or use the default sele]]

2. Copy the entire script and create a `.py` file. Run script.

3. The general syntax is:

<source lang="python">annotate_v("selection_group_name", "scheme")</source>

'''selection_group_name:''' name of the selection group where you have the input sequence. Must be single-letter amino acid coded. Either VH or VL but not both

'''scheme:''' currently supports Kabat, Chothia, Contact, IMGT. Must be lowercase

For example:

<syntaxhighlight lang="python">
annotate_v("VH", "kabat") #input sequence from VH selection group, annotate using "kabat"
annotate_v("sele", "imgt") #input sequence from the default sele group, annotate using "imgt". You can also try "contact", "chothia"
</syntaxhighlight>

4. In the output window, the script will print the FR and CDR regions (if found). It also automatically creates a selection group for each of the FR and CDR region.

[[File:Annotate_v_pic2.png|center|thumb|400px|example output from command lines]]

[[File:Annotate_v_pic3.png|center|thumb|800px|new FR and CDR selection groups are created]]

== Contact ==
For bugs & questions, emai @ xinyu18018@gmail.com. Enjoy!

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Pymol-script-repo]]

File:Annotate v pic2.png

2021-03-01T03:33:11Z

Cchem:

File:Annotate v pic3.png

2021-03-01T03:33:11Z

Cchem:

File:Annotate v pic1.png

2021-03-01T03:26:36Z

Cchem:

Annotate v

2021-03-01T03:25:46Z

Cchem:

{{Infobox script-repo
|type = script
|filename = annotate_v.py
|author = [[User:XinYu|Xin Yu]]
|license = BSD
}}

== Description ==

''Version: 1.0''

A simple-to-use script for annotation of VH or VL sequence of an antibody. It creates a Pymol object for each FR or CDR region. It utilizes the REST API interface of ''Abnum'' (http://www.bioinf.org.uk/abs/abnum/) from Dr Andrew Martin's group at UCL

== Annotation Schemes ==

Currently supports '''Kabat, Chothia, Contact, IMGT'''<sup>1</sup>

<sup>1</sup>Definitions for Kabat, Chothia, Contact, and IIMGT are same as listed in the table (http://www.bioinf.org.uk/abs/info.html#kabatnum), except that for IMGT, H-CDR2 is defined as '''H51-H57''' in this script, as opposed to of '''H51-H56''' in the table. This slight revision generates result that matches that from ''IMGT website'' (http://www.imgt.org/)

== Dependencies and Limitations ==

1. Import '''request''' module

2. Relies on internet connection to ''Abnum''

3. Incomplete VH or VL sequence might not be annotated

== How to use ==

1. Create a selection object for the V region, (such as '''VH''' and '''VL''' shown here). Only 1 V-region (VH OR VL) can be annotated each time. Alternatively, simply select the residues into the default '''<sele>''' group.

[[Image:Annotate_v_pic1.png|center|thumb|800px|Create a selection group for input seq, or use the default sele]]

2. Copy the entire script and create a `.py` file. Run script.

3. The general syntax is:

<source lang="python">annotate_v("selection_group_name", "scheme")</source>

'''selection_group_name:''' name of the selection group where you have the input sequence. Must be single-letter amino acid coded. Either VH or VL but not both

'''scheme:''' currently supports Kabat, Chothia, Contact, IMGT. Must be lowercase

For example:

<syntaxhighlight lang="python">
annotate_v("VH", "kabat") #input sequence from VH selection group, annotate using "kabat"
annotate_v("sele", "imgt") #input sequence from the default sele group, annotate using "imgt". You can also try "contact", "chothia"
</syntaxhighlight>

4. In the output window, the script will print the FR and CDR regions (if found). It also automatically creates a selection group for each of the FR and CDR region.

[[File:Annotate_v_pic2.jpg|center|thumb|400px|example output from command lines]]

[[File:Annotate_v_pic3.jpg|center|thumb|800px|new FR and CDR selection groups are created]]

== Contact ==
For bugs & questions, emai @ xinyu18018@gmail.com. Enjoy!

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Pymol-script-repo]]

File:PICv home screen.png

2021-03-01T03:18:56Z

Cchem:

File:PDF.png

2021-03-01T03:18:55Z

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File:860px-Modevector.png.jpeg

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File:Views.png

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File:1600px-Annotate v pic1.jpg.png

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Cchem: Cchem uploaded a new version of "File:1600px-Annotate v pic1.jpg.png"

File:1600px-Annotate v pic3.jpg.png

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File:Flags-ignore-exfoliate.png

2021-03-01T03:15:59Z

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File:Geo measures.png

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File:Isomesh-buffer-carve.png

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File:6sps-mesh-all.png

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File:Pincer Angle.png

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File:6sps-mesh-ligand-carved.png

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File:Properties-Inspector.png

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File:6sps-mesh-ligand.png

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2021-03-01T03:12:32Z

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File:PICv.png

2021-03-01T03:08:21Z

Cchem:

Geo Measures Plugin

2021-03-01T03:06:23Z

Cchem: 1 revision

{{Infobox script-repo
|type = plugin
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Caceres and Vera Lucia Eifler-Lima
|license = GNU General Public License v3.0
}}

The [[Geo Measures Plugin]] can carry out geometric analysis on protein structures.In addition, it makes other trajectory analyzes such as Probability Density Function (PDF), Root Mean Square Deviation (RMSD), Radius of Gyration (RG), Free Energy Landscape (FEL), Principal Component Analysis (PCA), Ramachandran map, Root Mean Square Fluctuation (RMSF), Define Secondary Structure of Proteins (DSSP), and Modevectors. Altogether there are 14 tools, which can be easily used by the graphical interface.
{|
|[[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]]
||[[Image:figure_4.png|thumb|300px|left|Free Energy Landscape]]
||[[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]]
|-
|[[Image:PDF.png|thumb|300px|left|Probability Density Function]]
||[[Image:Modevector.png|thumb|300px|left|Modevectors]]
||[[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]]
|}

== Video Tutorial ==
----
https://youtu.be/YKmIcU5weI0
----

== Installation ==

----
Requirements:

PyMOL version higher than 2.0.

It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].

You need to install python packages.

To do this use the command:

pip install pandas matplotlib scipy mdtraj sklearn

----

Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]

[[Category:Plugins]]

== References ==

----

Kagami LP, das Neves GM, Timmers LFSM, Caceres RA,Eifler-Lima VL, Geo-Measures: A PyMOL plugin for protein structure ensembles analysis,Computational Biology and Chemistry(2020)
doi.org/10.1016/j.compbiolchem.2020.107322

----
'''Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM'''

Unset

2021-03-01T03:05:59Z

Cchem: 1 revision

'''unset''' behaves in two ways.

If selection is not provided:

* 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.

If a selection is provided, then "unset" undefines object-specific or state-specific settings so that the global setting will be in effect.

== Usage ==

unset name [,selection [,state ]]

== Python API ==

<source lang="python">
cmd.unset ( string name, string selection = '',
int state=0, int updates=1, int log=0 )
</source>

== See Also ==

* [[unset_deep]]
* [[set]]

[[Category:Commands|Unset]]
[[Category:States]]

Spaceball plugin

2021-03-01T03:05:59Z

Cchem: 1 revision

{{Infobox script-repo
|type = plugin
|download = http://divites.de/files/pymol/spaceball.tar.gz
|author = [[User:RaphaelDives|Raphael Dives]]
|license = BSD-3-Clause
}}

<div style="background-color: #9f9; padding: 10px; margin-bottom: 20px; text-align: center">
'''Note:''' Incentive PyMOL 2.1 has built-in SpaceNavigator support for all platforms, see https://pymol.org/spacenavigator
</div>

== Description ==
This plugin integrates Spaceball devices on Linux Systems.

It was developed and tested with the SpaceNavigator(TM) by 3DConnexion.

But it *should* work with other (Linux based) systems and Spacenav Driver compatible devices as well.

The used software was:
:PyMOL version 1.7
:Ubuntu-12.04 / 14.04

== Installation ==
[http://divites.de/files/pymol/spaceball.tar.gz Download] the plugin and install it using the PyMOL plugin wizard.

Please consider the following requirements:
#Install the "libspnav0" and "libspnav-dev" packages from the repositories
#Obtain and install the current version of the Spacenav driver from [http://www.spacenav.sourceforge.net/ http://www.spacenav.sourceforge.net/]

== Important ==

The name "SpaceMouse" is registered trademark of 3DConnexion.

This plugin uses the spnav-0.9 package
:Copyright (c) 2011, Stanley Seibert
:All rights reserved.
:The BSD-License agreement and the Readme for this package are located in the spnav_docs folder.
:Please see the http://bitbucket.org/seibert/spnav/ for more information.

[[Category:Plugins]]
[[Category:Pymol-script-repo]]

Properties Inspector

2021-03-01T03:05:59Z

Cchem: 1 revision

The [[Properties Inspector]] panel lets you inspect and modify object, object-state, atom, and atom-state properties and settings. It opens when clicking the "Properties" button in the upper right.

''New in PyMOL 2.0''

== Screenshot ==

Screenshot of PyMOL with the properties panel open, after applying "A > preset > pretty" to PDB 1rx1:

[[File:Properties-Inspector.png]]

== Notes ==

* The panel doesn't refresh automatically. After loading new objects, press the refresh button (next to the atom index field).

== See Also ==

* [[iterate]]
* [[get]], [[set]], [[unset]]
* [[Get_Title|get_title]], [[set_title]]

[[Category:GUI]]

Pmlbeta

2021-03-01T03:05:59Z

Cchem: 3 revisions

{{Infobox script-repo
|type = plugin
|download = https://gitlab.com/awacha/pmlbeta/-/raw/binaries/pmlbeta_latest.zip
|author = András Wacha
|license = [https://choosealicense.com/licenses/bsd-3-clause/ BSD 3-clause]
|homepage = https://pmlbeta.readthedocs.io
}}

[[Pmlbeta]] is primarily a plugin for creating and manipulating molecular models of β-peptides, but works for α-peptides as well. In other words, the [[Fab]] command on steroids. Its central piece is the betafab2 command, but a graphical user interface is also supplied.

== Installation ==

Install the current version from [https://gitlab.com/awacha/pmlbeta/-/raw/binaries/pmlbeta_latest.zip pmlbeta_latest.zip] using the PyMOL [[Plugin Manager]]

== On-line documentation ==

On-line documentation is available at https://pmlbeta.readthedocs.io

== See Also ==

* [[Fab]]

[[Category:Plugins]]

PICv

2021-03-01T03:05:58Z

Cchem: 33 revisions

{{Infobox script-repo
|type = plugin
|download = [http://vidyaniranjan.co.in/PICv/PICv.py '''PICv''']
|author = [https://akshayuttarkar.wixsite.com/akshay Akshay Uttarkar], [http://vasanthdesai.me/?i=1 Vasanth Kumar Desai], Namitha P, John Berrisford, [https://www.ebi.ac.uk/about/people/sameer-velankar Sameer Velankar], [http://www.vidyaniranjan.co.in/ Vidya Niranjan]*
|license = GNU Free Documentation License 1.2
}}

== '''About PICv''' ==

[[File:PICv.png]]

Protein interaction clustering and visualization is an pioneer attempt in understanding protein-protein interaction at a residue level. For any given protein the interaction is purely dependent on its charges and surface-structural modifications. The clustering of proteins based on there preferential amino acid interactions provides a biological insight on both the above mentioned aspects. The clusters such obtained can be used to infer the interaction behavior for a class or family of proteins. Such interpretation can be useful in understanding structural protein chemistry. The interactions also provide information on the crucial amino acids required for interactions to remain stable. This information can be used to design antibody or induce mutations to depreciate its functionality

[[File:PICv_home_screen.PNG]]

== '''Code''' ==
Download the plugin from the following URL:

[http://vidyaniranjan.co.in/PICv/PICv.py '''PICv Source Code''']

== '''Installation and Demo video''' ==

Visit the below mentioned link for detailed installation followed by demo.

[https://youtu.be/3bxpASy-FV0 '''PICv (Video)''']

== '''Developed by''' ==

The plugin was developed by '''Center of Excellence Computational Genomics''', R V College of Engineering, Bangalore, India in collaboration with '''Protein Data Bank in Europe (PDBe), UK'''

'''For more details visit'''

[http://www.vidyaniranjan.co.in/ '''Center of Excellence Computational Genomics''']

== '''Copyright''' ==
<source lang="text">
# Copyright Notice
# ================
#
# The PyMOL Plugin source code in this file is copyrighted, but you are
# free to use and copy it as long as you don't change or remove any of
# the copyright notices.
#
# -----------------------------------------------------------------------------------
# This PyMOL Plugin PICv is
# Copyright (C) 2021 by Vidya Niranjan <vidya.n@rvce.edu.in>
#
# 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 name(s) of the author(s) not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
#
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN
# NO EVENT SHALL THE AUTHOR(S) 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.
#
</source>

[[Category:Plugins]]
[[Category:Pymol-script-repo]]

Main Page

2021-03-01T03:05:55Z

Cchem: 1 revision

__NOTOC__
{| align="center" width="100%" style="background: #B22222; margin-bottom: 4em; border-bottom: 1px solid #B22222; border-left: 1px solid #B22222; border-right: 1px solid #B22222;"
|+ style="font-size: 1.0em; font-weight: normal; color: #FFFFFF; text-align:right; background: #B22222; padding-top:0.5em; padding-bottom: 0.25em; padding-right: 0.60em; border-top: 2px solid #B22222; border-bottom: 1px solid #fff;" |hosted by [[File:SBGridlogo2.jpg|140 px|link=https://sbgrid.org/]]
|}
{| align="center" style="padding-bottom: 3em;"
|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
| To request a new account, email SBGrid at: accounts (@) sbgrid dot org
|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
|}

{| align="center" width="45%" style="background: #FFFFFF; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
|+ style="font-size: 1.4em; font-weight: bold; color: #FFFFFF; text-align:center; background: #000000; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #000000; border-bottom: 1px solid #fff;" |Quick Links
|-
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
|-
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
|-
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[PyMOL_mailing_list|Getting Help]]'''
|}

{| width="100%"
| style="vertical-align: top; width: 40%" |
{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
! Official Release
| [https://pymol.org PyMOL v2.4 has been released] on May 20, 2020.
|-
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
! Official Release
| [https://pymol.org PyMOL v2.3 has been released] on February 11, 2019.
|-
! POSF
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
|-
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
! New Plugin
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
! Selection keywords
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
! Plugin Update
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
|-
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
! Older News
| See [[Older_News|Older News]].
|}
|style="vertical-align: top; width: 40%"|
{| class="jtable" style="float: right; width: 90%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|<div class="didyouknow" >
<DynamicPageList>
randomcount=1
category=Commands|Plugins|Script_Library|Settings
includepage=*
includemaxlength=1050
escapelinks=false
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resultsheader=__NOTOC__ __NOEDITSECTION__
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
</DynamicPageList>
</div>
<div style="clear: both;"></div>
|}
|
|style="vertical-align: top; width: 18%"|
<DynamicPageList>
imagecontainer=Covers
randomcount=1
escapelinks=false
openreferences=true
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n
ordermethod=none
allowcachedresults=false
</DynamicPageList>

|}

Get Symmetry

2021-03-01T03:05:51Z

Cchem: 1 revision

'''get_symmetry''' can be used to obtain the crystal and spacegroup parameters for a molecule or map object.

===USAGE===
get_symmetry object-name-or-selection

===DESCRIPTION===

Returns a tuple containing the following 7 values:

* The unit cell lengths (a,b,c)
* The unit cell angles (alpha, beta, gamma)
* The space group name (e.g. "P 21 21 21")

===PYMOL API===
<source lang="python">
cmd.get_symmetry(string selection)
</source>

===See Also===

* [[Set_Symmetry|set_symmetry]]
* [[symmetry_copy]]
* [[Supercell]]

[[Category:Commands|Get Symmetry]]

Symmetry

2020-12-07T04:05:37Z

Cchem: 6 revisions

There are many ways that symmetry can be important/useful/beautiful to look at in macromolecular structures. A typically application is the reconstruction of a symmetric oligomer from a few subunits. PyMOL has tools that can help with this type of analysis or depiction.

== Expanding crystallographic symmetry ==
Structures determined by X-ray crystallography are typically deposited as files containing the coordinates for one asymmetric unit (ASU). Knowledge of the symmetry operators that describe how the ASUs are arranged relative to each other allows the arrangement of the crystal lattice to be recreated. PyMOL can read this symmetry information from the input coordinate file and recreate the neigbouring copies of the ASU using symmexp.

PyMOL's built in symmetry expansion functionality is available as A->generate->symmetry mates for an object or as the [[symexp]] command.

The [[SuperSym]] plugin has additional unit cell and symmetry axis tools.

== Displaying symmetry axes ==
Often it is necessary to be able to find and draw symmetry axes. There are some contributed scripts that help do this including [[Symmetry Axis]], for which you need to know the coordinates and direction of the axis you would like to draw, and [[RotationAxis]], which does an excellent job of displaying symmetry relationships between selections.

[[Category:Objects_and_Selections|Displaying Biochemical Properties]]
[[Category:Nucleic_Acids|Displaying Biochemical Properties]]
[[Category:Biochemical_Properties]]