December 2002 - chemweb - imperial.ac.uk

[svg-developers] Re: Re: SVG and Visio, XML and Office (fwd)
by Eugen Leitl 13 Dec '02

13 Dec '02

Peter/Henry, can you please comment on that? ---------- Forwarded message ---------- Date: Fri, 13 Dec 2002 11:42:53 -0000 From: Jim Ley <jim(a)jibbering.com> Reply-To: svg-developers(a)yahoogroups.com To: svg-developers(a)yahoogroups.com Subject: [svg-developers] Re: Re: SVG and Visio, XML and Office "Eugen Leitl" <eugen(a)leitl.org> wrote in message news:Pine.LNX.4.33.0212131125070.22354-100000@hydrogen.leitl.org... > On Fri, 13 Dec 2002, Breare, David wrote: >> Now look at this: > <atomArray> > - > <atom id="a1"> > <string builtin="elementType">C</string> > <float builtin="x2">-2.8313</float> > <float builtin="y2">0.3645</float> > </atom> Yes, it's a rather poor quality XML serialisation, seemingly designed to be as verbose as possible, perhaps a better serialisation would help, since there's a presumably perfectly good text format anyway, the only reason to go for XML is the free investment you get in parsers - is this really a key issue? > The resulting SVG from this is even more verbose. You seem to be mistaking poor quality tools, for the technology itself. > > do not take a great deal of time to download, in fact, in many cases > > they can be smaller than their raster equivalent. > > We're usually generating compressed b/w PNGs which tend to be pretty > small. I will have to play around with SVG rendering over limited > bandwidth to see how it renders. The advantage of an svg view, would be the interactivity you could provide, animations, zoom etc. not the bandwidth, the bandwidth is likely to be higher than the PNG, however the SVG is likely to have advantages in many cases, I don't know enough of the uses of your application to suggest if it would be or not, but the reasons you've given, don't really stand up. Of course if the XML you have is the standard representation, then you have every right to complain vigourously to the developers of the vocabulary. Jim. ------------------------ Yahoo! Groups Sponsor ---------------------~--> Get 128 Bit SSL Encryption! http://us.click.yahoo.com/CBxunD/vN2EAA/xGHJAA/1U_rlB/TM ---------------------------------------------------------------------~-> ----- To unsubscribe send a message to: svg-developers-unsubscribe(a)yahoogroups.com -or- visit http://groups.yahoo.com/group/svg-developers and click "edit my membership" ---- Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/ chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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Re: [MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd)
by Eugen Leitl 13 Dec '02

13 Dec '02

---------- Forwarded message ---------- Date: 13 Dec 2002 10:41:30 +0100 From: Konrad Hinsen <hinsen(a)cnrs-orleans.fr> To: gamercier(a)yahoo.com Cc: pyquante-users(a)lists.sourceforge.net, pymol-users(a)lists.sourceforge.net, mmtk(a)python.net, chemistry(a)ccl.net Subject: Re: [MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd) Gustavo Mercier <gamercier(a)yahoo.com> writes: > to the chemistry of a problem. In advanced undergraduate course, an > instructor may wish to breakthrough the "black box". The scripting *Should* wish to do so. Understanding what one is doing is the difference between a scientist and a lab technician. > this effort. Unfortunately, the issue is one of leadership to > initiate such a project. May be those who mantain MMTK, PyQuante, > PyMol, etc. may be willing to take the initiative. This issue has been addressed at a meeting on OpenSource software for atomistic simulations (which includes physics and chemistry) this year. The result is the formation of an informal organization called "FSAtom": http://www.fsatom.org/ Among the goals of this organizations is the design of common interfaces to ensure the interoperability of OpenSource codes. There will be more meetings (not committee style, but scientific workshops) as well as mailing list discussions. Everybody is welcome to join. > may go along way to make development not only easier but useful. It > would be best not to rediscover the wheel. And come up with a hexagon ;-) > As a suggestion, let's consider the chemistry implementation of XML > -- CML. Whatever the details of the object "molecule", it would be > beneficial to input and output to/from CML. A specification of I don't agree. I looked at CML a while ago, thought about implementing it in MMTK, but quickly found out that almost none of the information I needed to store about molecules could be represented in CML, except by adding "conventions" of my own - but then I could just as well define my own XML format. CML is based on the right intentions, but is too weak as an implementation. BTW, common file formats are another goal of the FSAtom organization. Konrad. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen(a)cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- ------------------------------------------------------- This sf.net email is sponsored by: With Great Power, Comes Great Responsibility Learn to use your power at OSDN's High Performance Computing Channel http://hpc.devchannel.org/ _______________________________________________ PyMOL-users mailing list PyMOL-users(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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Announcing VEGA1.4.3
by Giulio Vistoli 11 Dec '02

11 Dec '02

Dear collegues, As a christmas gift, we are glad to announce the new release of VEGA1.4.3 (http://www.ddl.unimi.it/) our well known program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). New features of release 1.4.3: - Alchemy loader & saver. - MDL Molfile saver. - CSV and Raw surface format. - Gromacs .xtc support for the trajectory analysis. - Multi-model PDB support for the trajectory analysis. - ILM calculation in the trajectory analysis. - The IFF file format was expanded in order to support the surface maps. - Win32: new geometry transformation engine. - Win32: added By segment coloring method. - Win32: surface calculation for selected atoms. - Win32: trajectory analysis for selected atoms. - Win32: interactive selection of the conformations trough the graph editor. - Win32: added the Data De/compressor Engine support in the graph editor. - Win32: now the graph editor supports Gromacs log files. - Win32: REBOL/View instead of REBOL/Core scripting language. - Win32: new extended commands (BioDock, GraphAdd, GraphCalc, GraphClose, GraphDelete, GraphGet, GraphLabelX, GraphLabelY, GraphLoad, GraphNew, GraphOpen, GraphSave, GraphSet, GraphTitle, GraphWin, MonitorPower). - Win32: new system variables (CPUs, GLRenderer, GLVendor, GLVersion, GraphLabelX, GraphLabelY, GraphPoints, GraphPosX, GraphPosY, GraphSizeX, GraphSizeY, GraphTitle, GraphVisible, TmpFile, TmpDir). - Win32: WinDD 1.4. Giulio Vistoli & Alessandro Pedretti --------------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli(a)unimi.it http://www.ddl.unimi.it

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request
by hossein karimi 09 Dec '02

09 Dec '02

Dear all members In my reaserch I want to measure the amounts of humic and fulvic acids in soil but I faced to a problem.I have extracted and fractionated them by means of NaOH and changes in pH but I can not measure the amount of fulvic and humic acid in final solution with low pH (fulvic acid) and precipitated materials (humic acid) because I do not access to necessary tools and I am seeking for a simple presedure.Is it a true method to measure by drying and weighting final solution and precipitated materials. I shall be greatful if you will help me with your advices and comments. Regards Hossein Karimi Department of Soil Science Agricultural College,Ferdowsi University,Mashhad,IRAN P.O.Box 91775-1163 E-Mail http://skarimi343@yahoo.com --------------------------------- Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now

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