From flicker%colloid.engin.umich.edu@srvr4.engin.umich.edu Sun Jan 30 14:45:42 1994 Received: from srvr4.engin.umich.edu for flicker%colloid.engin.umich.edu@srvr4.engin.umich.edu by www.ccl.net (8.6.4/930601.1506) id OAA28306; Sun, 30 Jan 1994 14:42:52 -0500 Received: from colloid.engin.umich.edu by srvr4.engin.umich.edu (5.67/1.35) id AA07520; Sun, 30 Jan 94 14:42:52 -0500 From: Received: by colloid.engin.umich.edu (5.67/1.35) id AA15460; Sun, 30 Jan 94 14:42:51 -0500 Date: Sun, 30 Jan 94 14:42:51 -0500 Message-Id: <9401301942.AA15460@colloid.engin.umich.edu> To: chemistry@ccl.net Subject: amber parm file I would like to modify my Amber parameters files. I have c routines to read in the files "rdprm.c", however I don't have any to write out a modified file. Does anybody have a c file that can accomplish this task? Thanks Scott From seibel%phmms0.mms.smithkline.com@smithkline.com Sun Jan 30 17:45:51 1994 Received: from phmms0.mms.smithkline.com for seibel%phmms0.mms.smithkline.com@smithkline.com by www.ccl.net (8.6.4/930601.1506) id QAA28929; Sun, 30 Jan 1994 16:59:11 -0500 Received: by phmms0.mms.smithkline.com (920330.SGI/911001.SGI) for CHEMISTRY@ccl.net id AA13772; Sun, 30 Jan 94 16:58:40 -0500 Date: Sun, 30 Jan 94 16:58:40 -0500 From: seibel%phmms0.mms.smithkline.com@phinet.smithkline.com (George Seibel) Message-Id: <9401302158.AA13772@phmms0.mms.smithkline.com> To: CHEMISTRY@ccl.net Subject: Color Plates in Electronic Journals >Dr. Rzepa wrote on Jan 15: > >> c) Whether www might be suitable for otherwise VERY expensive >> color plates? and Rainer Stumpe of Springer-Verlag replied: >Well, if you consider a 10 square centimeter (4 by 4 inches) >color illustration, printed with a resolution of 14.000 dpi, 16 >bit colors, you will either have to sacrifice resolution (300 >dpi, 8 bit colors), or you will have to handle VERY large >files. I feel, the technology to match color prints is only >emerging; it might take another 5 years to become generally >available. The technology is here today. First of all, we need to understand the difference between the use of the term "dpi" (dots per inch) in printing and in computer image processing. The printer creates subtle variations in color by combining many small dots of primary colors (1 bit color) into a much larger cell. The cell is somewhat analogous to a pixel that is displayed on a CRT (where the primary colors come from the phosphor dots on the inner surface of the CRT). The effective (pixel) resolution of printed color images in most journals is in the small numbers of hundreds of dpi, not thousands. The source of most molecular graphics images is a workstation screen of about 100 dpi. If you displayed a full screendump from an Iris at 14,000 dpi, it would be about 0.09 inches tall. Modern image compression software is quite effective at reducing the storage requirements of images. In order to demonstrate this, I generated two images typical of the molecular graphics that are popular in scientific journals today. I used UCSF MidasPlus to display a backbone trace of IL-8, including carbonyl oxygens, amide hydrogens, and disulfides. This was colored by atom and depthcued appropriately on a 24 bit Iris. I captured a 560x544 pixel screen dump using imgsnap. This image was identical to the 24 bit, depthcued image on the screen. There were four different colors of atoms (red, yellow, blue, and gray), yet the variations in intensity due to depth cueing resulted in a total of only 44 different colors of pixels in the image. This may seem surprising but it represents about 4 bits of depth cueing per color, which is what GL was effectively providing. I used free software (toppm from SGI and Jef Poskanzer's pbmplus package) to convert this image to GIF format. GIF uses a form of Lempel-Ziv compression and is a good choice for a mostly monochrome image such as this. The resulting file was 11,814 bytes. This was not a grainy, postage-stamp sized image. It was about 6 inches square at 100 dpi, and was identical in appearance to the original image. I would not consider 12 kilobytes to be huge. The second test image was a 666 by 590 pixel ribbon rendering, sized such that there was more continuous tone content than black background. This image had over 4000 colors. I compressed it using public domain JPEG compression software written by Tom Lane's Independent JPEG Group. JPEG compression is designed for real-world photographic images, which have a lot of tonal variation. JPEG discards from the image some information to which humans are not very sensitive. The amount of information discarded is a user-selected parameter and may range from a great deal of information loss, resulting in a degraded image but an extremely small file, to essentially no information loss, in which case the image is identical in appearance to the original, but there is not as much compression as is possible. Normally one sets the parameter such that the file is as small as possible while still looking good. When compressed, the ribbon image (6.25 x 7 inches on my Iris screen) occupied 39,809 bytes. Once again, this is a large, beautiful image, very similar in appearance to the original. There were some compression artifacts visible, although they were fairly subtle and did not in my opinion detract from the image. So there you have it. 12K for a stick figure and 40K for a ribbon rendering, both of which looked very good when displayed. All of the image processing was done with software available for free on the net. The decompression and display of the JPEG image took about 3 seconds on my R4000 indigo using xli for image display. GIF images can be displayed very quickly. I believe that there are no *technical* barriers to fully electronic scientific journals today. The barriers are largely political. If the text and graphics are compressed with the best currently available (not to mention free) software, then conventional networking, storage, and display hardware is adequate for the task. Much of it is already in place. The profusion of journal titles, many of which are egregiously overpriced, has forced us into a situation where something has to give. What gives today is usually our access to the scientific literature. George Seibel, SmithKline Beecham seibelgl@sb.com From eslone@mason1.gmu.edu Sun Jan 30 22:45:48 1994 Received: from mason1.gmu.edu for eslone@mason1.gmu.edu by www.ccl.net (8.6.4/930601.1506) id WAA01217; Sun, 30 Jan 1994 22:09:25 -0500 Received: by mason1.gmu.edu (5.65/DEC-Ultrix/4.3/GMUv3) id AA01208; Sun, 30 Jan 1994 22:09:25 -0500 Message-Id: <9401310309.AA01208@mason1.gmu.edu> Subject: In Search Of... To: chemistry@ccl.net Date: Sun, 30 Jan 1994 22:09:25 -0500 (EST) From: "J. Eric Slone" X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 805 Is anyone aware of a program for the IBM PC that will allow entering IUPAC nomenclature and will display the appropriate structure (and/or visa versa)? I have seen a program like this for the Mac but not the IBM PC. Thanks, Eric ________________________________________________________________________________ J. Eric Slone Scientific Consulting Services Serving Government & Industry Since 1982 Internet: eslone@mason1.gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Voice: (703) 461-7078 Miguel do Unamuno ________________________________________________________________________________ From JSMCM@jazz.ucc.uno.edu Sun Jan 30 23:45:49 1994 Received: from jazz.ucc.uno.edu for JSMCM@jazz.ucc.uno.edu by www.ccl.net (8.6.4/930601.1506) id WAA01415; Sun, 30 Jan 1994 22:58:08 -0500 Received: from jazz.ucc.uno.edu by jazz.ucc.uno.edu (PMDF #2820 ) id <01H8B4M5675U8X06QZ@jazz.ucc.uno.edu>; Sun, 30 Jan 1994 21:57:48 CST Date: 30 Jan 1994 21:57:48 -0600 (CST) From: JORGE Subject: H2SO4 Help To: chemistry@ccl.net Message-id: <01H8B4M5675W8X06QZ@jazz.ucc.uno.edu> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: JSMCM MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT I am passing this message from another list. Jorge M. Seminario jsmcm@uno.edu ps Can anyone suggest a theoretical approach to help to solve the problem? -------------------------------------------------------------------- Dear Sirs, We are writing to ask for information regarding non-expensive methods to use or transform the sulfuric acid (H2SO4) contained in the waste water coming from the mining industry in Peru, and is going to the sea. We are interested in productive methods to reduce the costs of treatment. Any information (Procedures, Addresses, Names of environmental institutes, etc.) will be appreciated. Yours sincerely, M.Sc. Alejandro Pino; Ch.Eng. Oswaldo Carrillo. Faculty of Processes Enginering. San Agustin University of Arequipa, Peru E. Mail: P.O. Box 23, Fax 0051-54-237808. Arequipa - Peru ---------------------------------------------end of message---