- chemweb - imperial.ac.uk

Re: chime script problem
by Tim Maffett 04 Sep '96

04 Sep '96

At 08:25 AM 8/27/96 +0100, Alan Arnold wrote: >Greetings, > for those kind souls with a few spare minutes and a >chime-compatible browser, please check out > > http://www.ch.adfa.oz.au/ceramics/cscl.html > >save the html source and explain to me why the embedded application/x-spt >script (shamelessly transmogrified from MDL's chime scripting example) >doesn't work as expected. > >This was to be prototype for some 'live' unit cells for some common ceramic >crystal structures. I had hoped that it would display a CsCl unit cell >showing both cell outlines and Cs-Cl connections as a visual aid, and when >the script buttons were pressed, cpk shpheres of the appropriate sizes >would be displayed separately for Cl, Cs, ions then both together. Doesn't >seem to work with NS 3.0 on my Mac on NS 3.0 for Win95. The cell outlines >and 'bonds' are there (yay!!) but I don't seem to be able to get any cpk >display :-( I am not sure what the problem you are seeing is. When I visit your page the initial display is as I would expect from your embed tags for the chime plugin displaying the structure, and for the 4 chime buttons. I even tested your page with the new SGI version of Chime and it looks and works great. Your main structure embed tag: <<embed border=0 src="CsCl.mol" ALT="CsCl" align=abscenter width=400 bgcolor=#ffffff height=400 spiny=360 startspin=true name="CsCl" display3D=wireframe palette=foreground > The above is the embed that you are using, and everything you specify here is being displayed 'correctly' when I view your page. As far as the rasmol scripts (application/x-spt) embed tags which invoke 4 Chime 'buttons'... These scripts also work as I would expect them to. Rasmol (and chime) do not have a 'default' atom radii for 'spacefill' models, if none is specified after the 'spacefill' command than Van der Waals radii are used. The way you are specifying the radius after the spacefill commands ('spacefill ###') is correct for specifying a custom radius. (an example of one of your Rasmol scripts, this one attached to your Chime button "Display wireframe" "select all spacefill off wireframe on # only select (atomno>=1) and (atomno<<=8) colour atoms green spacefill 1.03 # select (atomno=9) colour atoms blue spacefill 0.732 " The above script (and your others) work exactly as I would expect. I will mention that in your initial 'structure' embed tag you can add a 'script="whatever rasmol script you want" ' argument to init your structure display with whatever specific rasmol commands you would like. For example you could use script= and the above script (in quotes) for your initializing rasmol script. You can also separate lines with '|' or ';' instead of hard carriage returns. (i.e. script="select all;spacefill off;wireframe on; select (atomno>=1) and atomno<<=8);colour atoms green;spacefill 1.03; select (atomno=9);colour atoms blue;spacefill 0.732" > >The weird cpk scaling factors are my attempt to force the Cl and Cs spheres >about the right size. I need a way of preventing the user from displaying >as cpk in chime with inappropriate default atom radii (Where are the >default sphere sizes hidden in the chime plug-in?) As I indicated above Rasmol and Chime both use Van der Waals radii when none is specified in the spacefill command. There is no default for the 'spacefill' command. > >On a related note, can someone please point me in the direction of the >specifications for MDL's .mol file format? (following extract from mail message from David Hughes of MDL) "CTfile Formats" is in Adobe Acrobat PDF format, suitable for reading by Adobe's Acrobat Reader (a free license for the Adobe Acrobat Reader can be obtained from Adobe's site.) You can download a copy of "CTfile Formats" from http://www.mdli.com/fileformats.html; this page also provides a link to Adobe's. > Any suggestions for the most >convenient file format to use as chime input for small inorganics of this >type - in particular, do any formats allow user-defined atom radii? > >Of course, if anyone has already done this before, I'd be every pleased to >be further enlightened... > >many thanks for listening. Hope I have been of *some* help. -Tim >---- >Alan Arnold, School of Chemistry, University College (UNSW) >Australian Defence Force Academy, CANBERRA ACT 2600 Australia >voice:+61 6 268 8080 fax:+61 6 268 8002 e-mail: apa(a)adfa.oz.au >WWW: http://apamac.ch.adfa.oz.au/apa/apa.html > >----- >chemweb: A list for Chemical Applications of the Internet. >Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ >To unsubscribe, send to listserver(a)ic.ac.uk the following message; >unsubscribe chemweb >List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk) > ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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browser profiles over the last 8 months
by M.Winter＠Sheffield.ac.uk 03 Sep '96

03 Sep '96

For your interest I enclose percentage browser stats for the last 6 months here. There's all sorts of reasons why these numbers aren't scientific but the apparent trends are interesting anyway. You may find these numbers helpful when deciding what features to implement on your pages. Browsers vers Jan Feb Mar Apr May Jun Jul Aug MSIE 3.9 3.6 5.8 6.4 5.2 5.7 7.3 7.5 Mosaic 3.1 3.1 2.9 3.0 2.4 2.0 1.8 1.6 NetScape 0.9 1.6 0.8 0.9 0.5 0.6 0.4 0.3 0.2 NetScape 1 7.0 4.2 3.0 2.5 2.8 2.0 1.1 0.9 NetScape 1.1 30.3 25.8 21.7 18.3 14.9 12.6 9.0 7.8 NetScape 1.2 22.7 19.1 16.9 11.8 13.4 9.8 6.7 6.8 NetScape 2 26.8 37.2 44.0 51.3 50.4 53.3 53.4 52.7 NetScape 3 0 0 0.1 2.2 6.0 11.1 17.8 20.2 All other browsers are very small. About 2000 variants of browsers were logged over the 8 months! Note the falling % for Moaic. Currently, NetScape seems to register 89% of hits but some browsers which are not NetScape register as such so 89% could be too high if I've missed some that show this behaviour. Version 3 was 20% last month. Version 2 is showing signs of dropping as version 3 picks up while the proportion of version 1 users is dropping slowly. My current favourite, MS InterNet Explorer is steady but less than 8%. Just over 80% of all hits come from [NetScape v2 or better + MSIE] and given that MSIE is at least as capable as NetScape 2, so we are fast approaching a point at which NetScape version 2 capabilities can be assumed. Platform Macintosh 23.2 23.5 24.9 25.5 19.6 22.3 26.7 19.8 PC 64.3 62.3 61.9 59.9 63.2 62.6 59.4 66.7 Unix 11.9 12.9 12.1 12.4 15.6 13.6 12.6 12.1 The percentages of the 3 main platforms are holding fairly steady, but it looks like Mac users take more holidays than PC users! (That doesn't sem to have included me unfortunately.) Dr Mark J Winter (Deputy Head of Department, Director of Studies) Department of Chemistry, The University, Sheffield S3 7HF, England tel: +44 (0)114 282 4498 fax: +44 (0)114 273 8673 e-m: M.Winter(a)Sheffield.ac.uk http://www.shef.ac.uk/~chem/staff/mjw/mark-winter.html WebElements is the periodic table on the world-wide web: http://www.shef.ac.uk/~chem/web-elements/ ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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MOTM
by Paul May 31 Aug '96

31 Aug '96

Hi, September's MOTM is now on-line. It's really 3 molecules, the various active ingredients of digitalis. URL: http://www.bris.ac.uk/Depts/Chemistry/MOTM/motm.htm I only have about 2 more definite MOTMs lined up, so if any of you are thinking of maybe one day contributing a MOTM, an offer now would be gratefully recieved :-) Regards, ----------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 9287667, fax: +44 (0)117 9251295 email: paul.may(a)bris.ac.uk WWW: http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm ----------------------------------------------------------------------------- ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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chemical mime / windows background
by Trevor Gilson 28 Aug '96

28 Aug '96

Some observations on Windows 3.11/netscape 2.x/chime: (stealth64 graphics 2001) 1) The "same" background colour for Netscape and chime does not always quite match; 2) If I switch from a chime page on the the CLIC chime-using paper (eg http://chemcomm.clic.ac.uk/c08349_9.htm) to my own trial chime web page (http://www.soton.ac.uk/~trg/acad/chimetry.html) the background comes up any old colour; minimising and re-vitalising brings it back to the near-match. NB the "correct" background appears on the transparent gif ; it is only the in-between bits that are wrong. Any similar experiences? Thanks, Trevor Gilson ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Report from ACS Orlando Meeting
by Rzepa, Henry 27 Aug '96

27 Aug '96

Some of the high (low?) points of the ACS meeting that I encountered. a) Three new "you only need to visit this site for all your chemical needs" sites announced; http://chemweb.com http://sciquest.com http://www.ChemCenter.org The quality and focus varies enormously (but I will leave you to decide which is what yourselves). b) A new chemistry viewer called WebLab from MSI is launched, initially as a stand-alone application, but within three weeks as a Netscape plug-in. Its focus is on representation of "materials", ie unit cells, polymers, etc, although it can also handle e.g. pdb files etc. The plug-in will be free, as is Chime. It has features that Chime does not have (and vice versa). Anyone want to produce a Molecule-of-the-Month display using WebLab ? c) Java is BIG! But there are concerns about its security (perhaps misfounded?) and its slow performance (even with just-in-time compilation). People are waiting for Java3D, but to quote "Java is not ready today, tomorrow will be too late". VRML by the way was very little discussed, except by SGI! d) At the presentations about the Web, almost all were by commercial developers. Few "academics" produced memorable presentations (I reserve comment about my own, which you can see on http://www.ch.ic.ac.uk/talks/intranets/ ) When I asked in one such presentation as to who was going to control standards in the chemical Internet, the reply was almost always evasive to the extreme. Chemical MIME by the way is being widely adopted, although the situation with Java classes is less clear!! P.S. Don't tell the gang at work, but I'm skipping the next two days of lectures to hang out with Goofy at DisneyWorld. ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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chime script problem
by apa＠adfa.oz.au 27 Aug '96

27 Aug '96

Greetings, for those kind souls with a few spare minutes and a chime-compatible browser, please check out http://www.ch.adfa.oz.au/ceramics/cscl.html save the html source and explain to me why the embedded application/x-spt script (shamelessly transmogrified from MDL's chime scripting example) doesn't work as expected. This was to be prototype for some 'live' unit cells for some common ceramic crystal structures. I had hoped that it would display a CsCl unit cell showing both cell outlines and Cs-Cl connections as a visual aid, and when the script buttons were pressed, cpk shpheres of the appropriate sizes would be displayed separately for Cl, Cs, ions then both together. Doesn't seem to work with NS 3.0 on my Mac on NS 3.0 for Win95. The cell outlines and 'bonds' are there (yay!!) but I don't seem to be able to get any cpk display :-( The weird cpk scaling factors are my attempt to force the Cl and Cs spheres about the right size. I need a way of preventing the user from displaying as cpk in chime with inappropriate default atom radii (Where are the default sphere sizes hidden in the chime plug-in?) On a related note, can someone please point me in the direction of the specifications for MDL's .mol file format? Any suggestions for the most convenient file format to use as chime input for small inorganics of this type - in particular, do any formats allow user-defined atom radii? Of course, if anyone has already done this before, I'd be every pleased to be further enlightened... many thanks for listening. ---- Alan Arnold, School of Chemistry, University College (UNSW) Australian Defence Force Academy, CANBERRA ACT 2600 Australia voice:+61 6 268 8080 fax:+61 6 268 8002 e-mail: apa(a)adfa.oz.au WWW: http://apamac.ch.adfa.oz.au/apa/apa.html ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Test for Browser support for e.g. chemical/x-pdb
by Rzepa, Henry 26 Aug '96

26 Aug '96

Although plug-ins such as Chime have helped to facilitate molecule display, its still a pain to the user who does not have it installed getting "broken" plugin icons etc. To help solve this problem, Dave Riddick and I have written some javascript which tests to see what the user has on their system. http://www.ch.ic.ac.uk/motm/pdb_test.html It turns it this is quite a challenge, given that Netscape 2 and 3 differ in what can be tested for, and Internet Explorer is similarly variable. Coping with all permutations is quite complex. Anyway, I enclose the HTML document as it currently stands. If you want to try it for yourself, substitute the refs to pdb files and .gif files in this script for ones of your own. This version tests only for .pdb support, but could easily be extended to cope with other MIME types. The document shows how to produce a table of such types as supported by your own browser. Bug reports etc of course gratefully received. Henry Rzepa. +44 171 594 5774 (Office) +44 594 5804 (Fax)

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greek literals
by thomas＠chem.uni-potsdam.de 25 Aug '96

25 Aug '96

Hallo, I am searching for a source for greek literals as .gif or .jpg pictures. Can anybody help me ? St. Thomas

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ChemComm E-journal Project
by GRIFFITHSJ＠rsc.org 20 Aug '96

20 Aug '96

<cross posting> CLIC ONCE FOR PROGRESS Whilst the modern chemical laboratory would be barely recognisable to the scientific time traveller from the turn of the century, the chances are that they would feel entirely at home in the traditional periodical library. In spite of the sheer volume of printed periodicals available, much useful chemical information is not included in journals. For example, 3D molecular coordinates, dynamic and time dependent behaviours translate inadequately to the printed page. The Royal Society of Chemistry, in association with the other members of the CLIC Consortium, is in the process of producing an electronic version of ChemComm, its flagship primary journal, incorporating new ways of presenting molecular information by visual and interactive displays. The CLIC Consortium takes its name from its four participants (Cambridge University, Leeds University, Imperial College London, and The RSC at Cambridge), and its primary objective is to introduce and set standards for fundamentally new ways of communicating chemistry. The World Wide Web has been used to deliver an enhanced presentation of conventionally submitted and reviewed articles in ChemComm. For the first time in a chemistry journal, articles are available with colour-coded models which readers can rotate and inspect. The first article to be given this treatment deals with the intrinsically three-dimensional subject of supermolecular chemistry. The CLIC project has also introduced other electronic journal features such as enhanced illustrated contents lists and feature articles. In the near future, other methods of presenting complex molecular information will be introduced, including wavefunctions and molecular surfaces, dynamics, spectra, and mathematical symbolism. As the CLIC project develops, it will explore new ways of presenting chemical information which have no printed equivalent - in effect to transform the conventional scientific journal into an interactive and highly visual experience. Further information is available from: http://chemcomm.clic.ac.uk/ ---------- Dr Jonathan Griffiths, NewMedia, The Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge, United Kingdom. Tel: +44 (0)1223 432136; Fax: +44 (0)1223 420247. Email: griffithsj(a)rsc.org http://chemistry.rsc.org/rsc/ ---------- ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Graphical Chemical Structure Standards
by RANDALL BRINKHUIS 17 Aug '96

17 Aug '96

This message is being cross-posted to CHMINF-L, CHEMIND-L, and CHEMWEB. Please reply to me directly unless you think your response might be of value to others on the list. If desired, I can summarize the responses. I have recently started a new position and I am trying to come up to speed quickly on chemical structure searching. I am not necessarily interested in searching any one system (STN, DIALOG, etc.). What I am interested in is being able to pull together bits of disparate information from a variety of sources in such a way that they can be related to other pieces of information. I apologize for not being more precise, but to be honest, I am pretty new at this and all I know about the information is that some of it is textual and some is graphic. What standards exist regarding graphics packages? Are these compatible with standard graphics formats (TIFF, GIF, JPEG, etc.)? If a propietary system, how widely used is it? Can the graphics be linked to data in database systems that are SQL or ODBC compliant? In other words, can they be imported into or have links created from Oracle databases (relational) or Lotus Notes databases (non-relational)? Do they allow OLE, or can they be packaged as objects? In either case, could structure searching be conducted within the Oracle or Notes database, or would it have to be done within the originating application? Or, perhaps more appropriately, does this list (whichever one you are reading this on) have a searchable archive? Or can someone provide me with citations for authoritative journal articles, texts, or Web sites regarding standards for management of graphics and databases? Much obliged, Randall Brinkhuis Environmental Protection Specialist U.S. Environmental Protection Agency brinkhuis.randall(a)epamail.epa.gov ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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