From chemistry-request@server.ccl.net Mon Mar 18 17:00:19 2002 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2IM0Jp10730 for ; Mon, 18 Mar 2002 17:00:19 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.4712.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: plotting 3D electron density difference maps Date: Mon, 18 Mar 2002 13:59:59 -0800 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: plotting 3D electron density difference maps Thread-Index: AcHOreQ9lvZboKRlRVSQ9nR3OF2bLQAEdbyg From: "DeLano, Warren" To: "Anik Peeters" , Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g2IM0Jp10731 > From: Anik Peeters [mailto:anik@uia.ua.ac.be] > I am looking for software, preferably freeware, to plot 3D electron > density or electron density difference maps for large molecules (appr. > 500 atoms). The program may run on a unix workstation or on pc. PyMOL is ideal for this kind of project, where you might be able to do a bit of development in order to enable efficient transfer of your 3D dataset into the visualization program. http://www.pymol.org > We have our own programs to calculate the value of the > electron density > (difference) in the grid points of a given 3D lattice. > Therefore, we can > generate the results in any format needed, but we do need to know what > the input format is for a given plotting program, so > therefore we would > prefer a program that comes along with its source code or sample input > files. We also welcome programs for converting one 3D data set into > another. > PyMOL can read XPLOR and CCP4 format electron density files, but you can also create a 3D volume "brick" from within Python (using the high-perfomance "Numeric" package) to display volume data like electron density. Mesh isosurfaces are supported by the current binary release, and the impending release supports solid isosurfaces too (source code in current CVS). These are great for MO diagrams and/or electrostatic potential plots. Python is rapidly becoming a standard programming language for computational chemistry, so I encourage everyone to learn it. PyMOL's capabilities provide you with a specific reward for doing so. > I already donwloaded Molden, but it seems a bit slow when I am looking > at our molecular system interactively. Provided that you can access a graphics accelerator card, PyMOL's performance meets or beats any other package, and it is cross-platform (Windows, Unix, MacOSX). It can display any 3D map that will fit into available RAM. And now for the best part... PyMOL is unrestricted open-source software (even for commercial usage), meaning that it is free, modifiable, and redistributable in modified form. If you find PyMOL useful, then you are asked to help advance the project through development, documentation, or funding. PyMOL's users (hundreds of scientists distributed around the globe) are working together to make it a better and better package each and every day. Everyone is welcome to join the effort. The goal of PyMOL is to create the "Linux" of molecular modeling: a Python environment, (including PyMOL and other powerful packages), that is free, open-source, interoperable, and suited for an unlimited variety of tasks in computational chemistry and structural biology. - Warren PyMOL Founder -- mailto:warren@sunesis.com Warren L. DeLano, Ph.D.