From owner-chemistry@ccl.net Sat Apr 28 05:54:01 2007 From: "Hans De Winter hans.dewinter===silicos.com" To: CCL Subject: CCL: Alternative protein surface representation Message-Id: <-34150-070428055242-3550-bW0zFpvDG8MFrZmRLTn3vQ.@.server.ccl.net> X-Original-From: "Hans De Winter" Date: Sat, 28 Apr 2007 05:52:37 -0400 Sent to CCL by: "Hans De Winter" [hans.dewinter*silicos.com] Dear, I would like to represent the surface of a protein with a graphics pattern projected onto it. In particular, I have a series of points representing a protein surface, and I would like to render the surface of this protein as a solid surface consisting of a repeating pattern of a user-defined image, for example as a wood or brick structure. Any idea what kind of software I could use to achieve this? Thanks in advance, Hans De Winter Silicos NV From owner-chemistry@ccl.net Sat Apr 28 11:36:00 2007 From: "Rick Venable venabler(~)nhlbi.nih.gov" To: CCL Subject: CCL: Alternative protein surface representation Message-Id: <-34151-070428113333-29380-hSeqCdGRdtsQeb5E4Ov3nw],[server.ccl.net> X-Original-From: Rick Venable Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Sat, 28 Apr 2007 11:00:27 -0400 Mime-version: 1.0 Sent to CCL by: Rick Venable [venabler()nhlbi.nih.gov] I'd probably try POV-Ray [www.povray.org], a free, open source ray tracing program with binary executables available for Windows, Mac OS X, and Linux. It has advanced texture features, a variety of "finite patch primitives" that could be used to define a renderable object from points on a surface, and fairly good documentation. A fair number of molecular display programs can create POV-Ray files as well, as a means of producing high quality molecular images. -- Rick Venable 29/500 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-8014 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 4/28/07 5:52 AM, "Hans De Winter hans.dewinter===silicos.com" wrote: > Sent to CCL by: "Hans De Winter" [hans.dewinter*silicos.com] > Dear, > > I would like to represent the surface of a protein with a graphics pattern > projected onto it. In > particular, I have a series of points representing a protein surface, and I > would like to render the > surface of this protein as a solid surface consisting of a repeating pattern > of a user-defined image, for > example as a wood or brick structure. Any idea what kind of software I could > use to achieve this? > > Thanks in advance, > > Hans De Winter > Silicos NV From owner-chemistry@ccl.net Sat Apr 28 22:45:01 2007 From: "Markus Dittrich dittrich]![psc.edu" To: CCL Subject: CCL: NRBSC Workshop on Microphysiological Simulations Message-Id: <-34152-070427033749-22345-Hn8UzV3N3uiBa2JvLbsOYA:+:server.ccl.net> X-Original-From: Markus Dittrich Date: Thu, 26 Apr 2007 10:34:23 -0400 Sent to CCL by: Markus Dittrich [dittrich._._.psc.edu] Dear Colleagues, The National Resource for Biomedical Supercomputing at the Pittsburgh Supercomputing Center will host a workshop entitled \Computational Methods for Spatially Realistic Microphysiological Simulations\ during June 25-29, 2007. This workshop will cover theory and practice for the design and simulation of models focused on diffusion-reaction systems such as neurotransmission, signaling cascades, and other forms of biochemical networks (e.g., Coggan et al., 2005, Science 309:446-451; He et al., 2006, Nature 444:102-105). Current versions of the MCell/DReAMM simulation environment ( and ) will be introduced, including new Monte Carlo methods for 3-D simulation of reactions in solution and on arbitrarily shaped biological surfaces, as well as new tools for model design and visualization. Models created from both anatomical reconstruction tools and computer-aided design tools will be covered. Based on feedback from a similar highly successful workshop in June 2006, this workshop has been extended to five full days, and attendees will be strongly encouraged to bring ideas/data for their own simulation projects. The daily schedule will include theoretical and practical lectures, instructor-guided hands-on tutorials, and opportunities for one-on-one interaction with the instructors on individual project development. APPLICATION Application deadline is May 15, 2007. Workshop content will be targeted to graduate student, postdoctoral, and faculty-level attendees. Space is limited. Openings will be assigned based on evaluation of information provided by applicants. To apply online or for more information, visit or contact Christal Banks (cbanks^psc.edu). INSTRUCTORS Organizer: Joel Stiles, M.D., Ph.D., Center for Quantitative Biological Simulation at PSC Thomas Bartol, Ph.D., Computational Neurobiology Laboratory at Salk Institute Rex Kerr, Ph.D., HHMI Janelia Farm FINANCIAL INFORMATION This workshop is funded by grants from the NIH National Center for Research Resources. These grants provide tuition and hotel costs, supercomputing time, and workshop materials for US academic participants. ALL participants are responsible for paying their own travel expenses. Complimentary continental breakfasts and lunches will be provided the days of the workshop. A few positions may be available for US government employees and corporate and industrial researchers. These participants are responsible for their own hotel accommodations, and tuition costs are as follows: a) Tuition for US government employees is $350 in advance to cover the workshop materials and supercomputing time. Contract government employees will be considered an academic participant and therefore their tuition costs will be waived if they submit a letter from their department head. Letters can be sent to the NRBSC contact. b) Tuition for corporate and industrial participants is $975 in advance to cover the workshop materials and supercomputing time. ABOUT NRBSC The National Resource for Biomedical Supercomputing (an NIH NCRR Resource Center) pursues leading edge research and education in high performance computing and the life sciences, with focus areas in microphysiology, visualization and analysis of massive volumetric datasets, and computational structural biology. For additional information, please see . -- **************************************************************** Markus Dittrich, Ph.D. Center for Quantitative Biological Simulation Pittsburgh Supercomputing Center Carnegie Mellon University 300 South Craig, Rm 401 Pittsburgh, PA 15213 phone : (412) 268-1688 fax : (412) 268-8200 email : dittrich_._psc.edu web : http://www.psc.edu/~dittrich ****************************************************************