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Topic: PyMOL

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	PyMOL scripts
		PyMOL tools to create the drawing commands to show the symmetry axes for a crystal, to draw a fancier unit cell and an attempt at drawing reciprocal space in 3D.
		Calculate the RMSD and fit one selection onto another within PyMOL without regard to matching residue names, etc. This script temporarily changes the selections to be fit into glycines and sets the residue names and chain identifiers to match so that the fit command can be used on non-identical sequences.
		Draw the Ewald sphere at the beginning and end of a data collection pass, as well as the limiting sphere and the reflections divided into categories (within the limiting sphere, outside the limiting sphere, collected, not collected and lastly part of one asymmetric unit).
	adelie.biochem.queensu.ca /~rlc/work/pymol (1257 words)

	Introduction to Molecular Visualization with PyMOL
		For use in a report or a presentation, PyMOL offers a ray-tracing feature to draw an image with a light source and shadows and other optical effects that provide an illusion that a physical, 3D model is held in the display.
		PyMOL is an powerful program that is increasingly being used for very advanced molecular graphics applications in research laboratories and in the pharmaceutical industry.
		Don't worry about learning all about PyMOL at this point; what we have shown here is enough to do all of the things we need you to be able to do.
	www.cem.msu.edu /~posey/cem181h/PyMOLtutorial05/tutorial05.htm (2720 words)

	Cameron Mura: PyMOL
		PyMOL is a powerful and versatile program for molecular graphics, based on the Python scripting language (which you don't need to know in order to use the program!).
		One PyMOL script produces both maps as separate panels (overlaying them in one panel is messy).
		We want a "sausage"-style cartoon representation of the backbones for one of the 14-mers, with the tube diameter scaled by values in the B-factor field (which, in the case of this crystal structure, are actual B-factors).
	mccammon.ucsd.edu /~cmura/PyMOL/index_no_frames.html (1373 words)

	nuccyl 1.5.2 Home Page
		However, currently PyMOL does not allow to sort the list of objects within the internal GUI itself, so that the advantage of using the latter becomes negligible if one is working with a large number of nucleotides - unless they enjoy scrolling thorugh a semi-random list of hundreds of nucleotides, that is.
		The reason is that this information can still be very useful if one wants, for example, to assign different colors to various regions of an RNA molecule; this is because, by inspecting the nuccyl3.pml file, one is able to immediately find out which pseudoatoms/cylinders correspond to a given range of nucleotides.
		Binary.pse files are much faster to load into PyMOL than command.pml ones; however, it is important to also keep the latter for reference, since they are invaluable for reconstructing the procedure that one followed to obtain a certain scene.
	www.biosci.ki.se /groups/ljo/software/nuccyl.html (3031 words)

	Some Useful PyMOL Scripts
		This is a PyMOL plugin which lets you run APBS from within PyMOL.
		This is a PyMOL plugin to aid in publication-quality rendering.
		PyMOL will zoom in on an Asn, Gln or His, showing the current residue with purple Carbons and Hydrogen bonds as yellow dotted lines.
	www-personal.umich.edu /~mlerner/Pymol (785 words)

	Linux Install - PyMolWiki
		PyMOL RPMs are available for Fedora Core 1 and 2, provided by Morten Kjeldgaard.
		The Ubuntu (http://www.ubuntu.com/) pymol package (http://packages.ubuntu.com/breezy/science/pymol) can be installed with minimal effort using the GUI package manager synaptic (http://en.wikipedia.org/wiki/Synaptic_Package_Manager), or on the command line, using the command
		PyMol also compiles from source on Ubuntu following the #Generic Linux instructions given above.
	www.pymolwiki.org /index.php/Linux_Install (823 words)

	PyMOL Home Page (Site not responding. Last check: 2007-10-31)
		PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation.
		DeLano Scientific announces immediate availability of the MacPyMOL Universal Binary for Intel/PPC Macs, and posts various benchmarks showing that PyMOL runs almost as fast on an entry-level iMac Core Duo as on a much more expensive dual-processor Opteron Linux workstation.
		Please test the latest 0.99 beta build and provide immediate feedback on any serious problems you encounter so that they can be corrected prior to the official release.
	pymol.sourceforge.net (163 words)

	Introduction to PyMOL
		PyMOL is a free, open-source tool to visualize molecules and the homepage is located at PyMOL Sourceforge homepage.
		When working on a molecule it is a good idea to have the script file and PyMOL open at the same time so that you can switch between the two.
		In the PyMOL molecular graphics system window (the one that doesn't show the molecule), a set_view command will be created for you and you simply cut and paste this text into your script.
	www.microbiology.ubc.ca /eltis/pymol (2513 words)

	Obtaining PyMOL
		is a platform-specific enhancement of PyMOL for Mac OS X that includes extra features such as an Aqua port of the user interface, direct copy-and-paste of images, and automatic QuickTime movie export.
		Since MacPyMOL is an incentive product, PyMOL sponsorship via a current PyMOL subscription is required for research use of MacPyMOL, but you are welcome to try a free 90-day evaluation.
		This free (sponsorship optional) version of PyMOL provides the cross-platform Tcl/Tk via X11, which means that you need Mac OS X 10.3 (Panther) with X11 installed in order to use it.
	pymol.sourceforge.net /obtaining.html (361 words)

	STRAP and Pymol (Site not responding. Last check: 2007-10-31)
		When a protein structure is opened STRAP sends the command to PyMol for loading a protein structure file.
		Picking an atom while the control and shift key is hold down, moves the alignment cursor to the respective residue.
		Pymol is currently the only protein viewer which is used in Strap to display 3D- superpositions:
	www.charite.de /bioinf/strap/pymol.html (240 words)

	Pymol (Site not responding. Last check: 2007-10-31)
		Pymol, which was not only open-source, but also worked on his Mac OS X when Rasmol would not.
		However, it took his faithful graduate student a while to become familiar enough with it to be able to actually DO something with the program.
		Unfortunately, Pymol's ability to determine secondary structure, well, simply sucks and is an admitted flaw of the software developer, Warren DeLano.
	hulab.tamu.edu /pymol.html (549 words)

	PyMOL 0.41 (Site not responding. Last check: 2007-10-31)
		PyMOL is a molecular graphics program which uses Python as its scripting language.
		PyMOL itself is free, open-source, and 100% unrestricted.
		Thus, PyMOL is ideally suited for corporate applications where license restrictions are of paramount concern.
	www.chem.ac.ru /Chemistry/Soft/PYMOL.en.html (476 words)

	How To Make an Electrostatic Surface with Delphi and PyMol (Site not responding. Last check: 2007-10-31)
		PyMol is a full featured molecular graphics program authored by Warren Delano of Delano Scientific.
		Versions of PyMol prior to 12/04 may not be able to read Linux generated DelPhi potential maps because of endian issues (byte-order differences between SGIs and Linux).
		If PyMol and DelPhi are not on the same computer, then copy the folder over to the computer on which you will run PyMol.
	keres.colorado.edu /howto/delphi-surface-pymol.html (470 words)

	Density Maps \| Pymol
		Pymol can also read and manipulate density maps - I feel it makes for much nicer density map pictures than O or Turbo Frodo, the maps can be easily manipulated and ray traced.
		The current version of pymol (0.95) supports CCP4, xplor/cns, and BRIX maps.
		So to start I'll ask pymol to show a modest 6 A sphere of the map about M1 using this command:
	morse.bio.jhu.edu /pymol/pymol_maps.htm (631 words)

	Brief PyMOL tutorial
		Files with pymol scripts are usually created with a text editor such as emacs or TextEdit and named with a ".pml" extension at the end.
		To control viewing the movie in pymol, use the movie controls on the bottom of the GUI window.
		The nice thing about pymol movies is that you can change the view and representation while the movie is playing.
	www.mrc-lmb.cam.ac.uk /rlw/text/MacPyMOL_tutorial.html (2845 words)

	CCP4 Newsletter Article: PyMOL: An Open-Source Molecular Graphics Tool
		The advantage of using PyMOL instead of Raster3D is that it allows users to orient and combine multiple objects in real-time 3D prior to rendering. The quality of the resulting images is comparable using either approach.
		PyMOL supports molecular editing at several different levels. At the simplest level, it allows the user to create new objects out of atom selections which may span any number of other objects. Thus, removing atoms from an object or combining separate objects is trivial. Bonds can then be formed between atoms in the combined object.
		PyMOL also enables rudimentary chemical editing of structures on an atomic basis using mouse clicks and CTRL-key combinations to delete, replace, or grow new molecular structures. For example, to make tyrosine out of phenylalanine, one would simply CTRL-middle-click on the para-hydrogen and type CTRL-O to replace it with a hydroxyl.
	www.ccp4.ac.uk /newsletters/newsletter40/11_pymol.html (1729 words)

	[No title] (Site not responding. Last check: 2007-10-31)
		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 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.
	www.vigyaancd.org /licenses/pymol.txt (171 words)

	PyMOL Tutorial (Site not responding. Last check: 2007-10-31)
		PyMOL is a molecular visualization and manipulation system based on an Open-Source software foundation.
		The program is designed to meet a variety of the molecular graphics, animation, and presentation needs of research scientists in academia and industry, including display of structure information over a LAN or the internet.
		Though most version of PyMOL may be obtained and used without licensing costs, all users are asked to purchase a PyMOL license and annual support subscription so that DeLano Scientific can develop, maintain, and support the package.
	www.daylight.com /meetings/mug04/DeLano (222 words)

	Creating a Panoramic view of your model with Pymol
		The Pymol software interactively displays molecular models and creates publication quality images.
		Adjust the front and rear clipping plane to focus on the area of the molecule you wish to display.
		I use "vi" on linux, or "wordpad" on the PC The next time you execute this script, you will automatically return to this view.
	www.doe-mbi.ucla.edu /~sawaya/tutorials/Graphics/pymol.html (732 words)

	Description of PyMOL
		PyMOL is also available on the Core Macintosh in the "Applications" folder, and is installed on most of the Windows PCs.
		Luca Jovine has made available the program nuccyl, which allows PyMOL to display atomic models of nucleic acids in a highly simplified representation.
		A customized version of PyMOL that supports electrostatic potential calculation and display is also available.
	www.csb.yale.edu /userguides/graphics/pymol (424 words)

	Debian -- pymol
		PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
		Although a newcomer to the field, PyMOL can already be used to generate stunning images and animations with unprecedented ease.
		It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.
	packages.debian.org /unstable/science/pymol (167 words)

	[MMTK] PyMol (Site not responding. Last check: 2007-10-31)
		Back at the beginning of the year, I wrote a little xml-rpc server thing for PyMol which allows molecules to be loaded from other processes.
		The server itself is basically at the "proof-of-concept" stage, but it is functional and pretty easy to expand.
		I believe Warren is distributing this with PyMol now, but if not I can dig around and find it.
	starship.python.net /pipermail/mmtk/2002/000432.html (274 words)

	PyMOL Sponsorship Request (Site not responding. Last check: 2007-10-31)
		The effects of your purchases will be cumulative and directly measured by PyMOL's ever-increasing capabilities.
		Corporate users, reflect for a moment on the very high price of comparable commercial software, and then consider the question, "Can our company afford not to fund PyMOL?" The project cannot succeed without you, so not funding our efforts implies a willingness to accept huge and unnecessary future costs in meeting essential software needs.
		PyMOL is a promising low-cost alternative, so why not help it to succeed?
	www.pymol.org /donate.html (220 words)

	Input devices for PyMOL: 3d_controller.py (Site not responding. Last check: 2007-10-31)
		The 3d_controller.py PyMOL extension provides a few commands to start the eventio.py class for certain devices.
		To configure how a certain device works, ie which PyMOL commands a certain button will trigger, look inside the 3d_controller.py file and change it as you will.
		If you have a different device, try using the evio_test.py file from the eventio page to read all type/code it generates and then duplicate one of the *_reader functions in the 3d_controller.py file and modify it to understand your device's type/codes.
	atb.slac.stanford.edu /~zac/pymol (235 words)

	[MMTK] PyMol (Site not responding. Last check: 2007-10-31)
		When you run MMTK from PyMol, all the "view" operations automatically use PyMol.
		If anyone wants a copy, just tell me. However, at the moment the only way to use this combination is to run MMTK scripts from within PyMol.
		For a visualization session this is fine, but not really for development of MMTK scripts in which visualization play only a minor role.
	starship.python.net /pipermail/mmtk/2002/000431.html (178 words)

	Main Page - PyMolWiki
		However, due to massive amount of spamming, we've changed the registration process, until further notice.
		It describes pymol and apbs issues specific to Mac OS X. page has been established.
		APBS How to set this up on OS X and on Linux has been started but needs contributions.
	www.pymolwiki.org /index.php/Main_Page (195 words)

	Electrostatics in PyMOL
		Michael Lerner at the University of Michigan has written some PyMOL add-ins that allow PyMOL to interface with the electrostatic calculation program APBS.
		Use the website at the San Diego Supercomputing Center to convert a PDB file into the PQR format needed for APBS.
		At the PyMOL command line, use "load_pqr [file].pqr" to read in the PQR created above.
	www.csb.yale.edu /userguides/graphics/pymol/electro.html (436 words)

	Structure Morphing Movie
		for this movie, I used LSQMAN to generate a series of intermediate structures, then used Pymol to make a movie from them.
		The Pymol manual says not to trust its secondary structure assignment procedure (which is slow anyway).
		In Pymol, each morphed structure is considered one state of a molecule.
	ginsberg.med.virginia.edu /~dcoop/Help/morph.html (757 words)

	The GNU-Darwin Distribution
		The PyMOL Molecular Graphics System has been ported to GNU-Darwin and Mac OSX.
		PyMOL is a powerful molecular graphics package for structural biology and other sciences.
		Pymol is an effective molecular builder, but it can also produce stunningly beautiful and realistic
	gnu-darwin.sourceforge.net /gdc/mol.html (850 words)

	Pymol Quick Howto (Site not responding. Last check: 2007-10-31)
		pdb file into pymol, select and color the domains, and make an output image.
		Longer and more comprehensive pymol tutorials are available.
		After loading in the pdb coordinates, three objects were created.
	compbio.berkeley.edu /people/ed/pymol_tut/Pymol_Quick_Howto.html (153 words)

	ScienceSoft
		The PyMOL source code is copyrighted, but you can freely use and copy
		PyMOL is Copyright 1998-2003 by Warren L. DeLano of
		Sie können entweder nach einer PDB ID suchen lassen, oder sie können die PDB Daten direkt eingeben indem Sie mit dem Schaltfläche Dateneingabe in den entsprechenden Modus umschalten.
	sciencesoft.at /index.jsp?link=pymol&lang=en (430 words)

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