- chemweb - imperial.ac.uk

Re: IE and "plugins": correction
by Rzepa, Henry 17 Aug '01

17 Aug '01

Ferenc Csizmadia wrote; ===== Please don't discourage people from using applets. :-) The situation is not so bad at all. Java applets may use the Java Plugin with IE (or Netscape). In the case of IE, this is actually a better solution then using built-in Java, since the Java Plugin is JRE 1.3 compatible. (Netscape 6 contains JRE1.3, previous versions of Netscape and IE include JRE1. ) ======== Of course, the Java "plugin with IE is not, I think, ActiveX and so it will not work with the latest IE. I have not tested (been away for my summer holiday!) but perhaps the most significant plugin to "break" would be the Java plugin. If anyone has tested the Java plugin with the recent IE, do let this list know. On a related note, Microsoft were asked to comment on the situation, particularly in regard to MacOS. Their quote was "MacIE will continue to support Netscape plug-ins at least through the next major release next year. ActiveX is the prefered technology for extending the functionality of WinIE, especially since Netscape itself is deprecating the old plug-in API in Netscape 6. You should also investigate Binary Behaviors as an alternative for your Windows plug-in." ======= It appears that they are citing Netscape API recommendations which deprecate the current way of doing things. I am not sure what the "new" API is. Is this perhaps a Microsoft "spin" on a Netscape dcument? I do note that for a long time, Chime did not display properly with Netscape 6.0 and Mozilla, but the latest release of Netscape 6.1 does now fix this (ie the fix was by Netscape, not MDL). -- Henry Rzepa. Imperial College, Chemistry Dept. +44 020 7594 5774 (Office) +44 020 7594 5804 (Fax) 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)

2 1

RE: IE and "plugins": correction
by Rick Hobson 17 Aug '01

17 Aug '01

My original comment was made in reply to ".... so perhaps we can encourage a project to develop an open source browser that supports XML, plugins, java, javascript?" I was simply pointing out that someone was already working on reinventing the wheel and there was no need for everyone to go into headless chicken mode just because Redmond would like to "encourage" us all to use their pet technologies. The following is from http://www.mozilla.org/projects/svg/ __________________________________________________________________________ The Future SVG support in Mozilla will be beneficial for both Mozilla and SVG. SVG is poised to become one of the most useful and fun Web technologies around. An open-source platform-independent SVG renderer ensures that the standard is kept clean and well-implemented. Help us out! __________________________________________________________________________ Much of this applies equally well to many other web based technologies. See http://www.mozilla.org/projects/ for a full list of current projects associated with Mozilla. The following clip from this page is pertinent to many of the comments which Henry makes below. "The primary mission of mozilla.org is to coordinate and integrate the work of others." So if there are holes then offer to "plug them" :-). Rick On Fri, 17 Aug 2001, Rzepa, Henry wrote: > >I stand to be corrected but doesn't Mozilla do all of these things? I > >strongly encourage all to support the Mozilla project - the more that do > >the less the likelihood that M$ will ultimately set the whole web agenda. > > > >http://www.mozilla.org/ > > > > The Mozilla project is opensource in the sense that many > separate developers appear to be contributing code to it. > > Thus http://www.croczilla.com/svg seems to be the main > thrust towards SVG (but this by a single person, who does it > in their "spare time"). As I have noted at this forum previously, > this offers one interesting way forward for rendering chemistry > from well specified data structures. > > > But Netscape/Mozilla seems to be developing with lots of what > one might call omissions, or holes, in their features. On another forum > for example, the lack of LDAP support was commented on, > implementation of which again seems to be coming from one particular > group in the opensource effort. I have a particular interest in the > use of X.509 certificates to authenticate, support for which was > excellent in Netscape 4.7, but only about 50% there in Netscape > 6.1 (remember, 6.1 is supposed to be a full release, not a beta, > and is not supposed therefore to have features missing). > > > The message that strongly comes over is that one must design > things such that the data, the logic and the rendering are kept > quite separate. This of course makes it particularly tricky > to design "friendly" sites where lots of JavaScript and > other content/logic/rendering is often used to create a usable > interface. Think of the amount of javascript (of unknown standard > or specification) in sites such as the > NCI or Protein Explorer databases. Most sites also have > a great deal of "CGI" hidden server side processing going > on. Once that server-side resource stops (or its domain > is purchased!) then all the data and content it represented > is lost! In that sense, we are back to where we were in > 1993, pre-web. > 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)

1 0

RE: IE and "plugins": correction
by Rzepa, Henry 17 Aug '01

17 Aug '01

>I stand to be corrected but doesn't Mozilla do all of these things? I >strongly encourage all to support the Mozilla project - the more that do >the less the likelihood that M$ will ultimately set the whole web agenda. > >http://www.mozilla.org/ > The Mozilla project is opensource in the sense that many separate developers appear to be contributing code to it. Thus http://www.croczilla.com/svg seems to be the main thrust towards SVG (but this by a single person, who does it in their "spare time"). As I have noted at this forum previously, this offers one interesting way forward for rendering chemistry from well specified data structures. But Netscape/Mozilla seems to be developing with lots of what one might call omissions, or holes, in their features. On another forum for example, the lack of LDAP support was commented on, implementation of which again seems to be coming from one particular group in the opensource effort. I have a particular interest in the use of X.509 certificates to authenticate, support for which was excellent in Netscape 4.7, but only about 50% there in Netscape 6.1 (remember, 6.1 is supposed to be a full release, not a beta, and is not supposed therefore to have features missing). The message that strongly comes over is that one must design things such that the data, the logic and the rendering are kept quite separate. This of course makes it particularly tricky to design "friendly" sites where lots of JavaScript and other content/logic/rendering is often used to create a usable interface. Think of the amount of javascript (of unknown standard or specification) in sites such as the NCI or Protein Explorer databases. Most sites also have a great deal of "CGI" hidden server side processing going on. Once that server-side resource stops (or its domain is purchased!) then all the data and content it represented is lost! In that sense, we are back to where we were in 1993, pre-web. -- Henry Rzepa. Imperial College, Chemistry Dept. +44 020 7594 5774 (Office) +44 020 7594 5804 (Fax) 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)

1 0

Fwd: Re: Elsevier's ChemWeb Preprint Archive
by Rzepa, Henry 17 Aug '01

17 Aug '01

I forward this exchange on another list since it relates to chemistry! >Approved-By: harnad(a)COGLIT.SOTON.AC.UK >X-Sender: till(a)corona.oci.utoronto.ca >MIME-Version: 1.0 >Date: Wed, 15 Aug 2001 14:42:16 -0400 >Reply-To: September 1998 American Scientist Forum > <SEPTEMBER98-FORUM(a)LISTSERVER.SIGMAXI.ORG> >Sender: September 1998 American Scientist Forum > <SEPTEMBER98-FORUM(a)LISTSERVER.SIGMAXI.ORG> >From: Jim Till <till(a)UHNRES.UTORONTO.CA> >Subject: Re: Elsevier's ChemWeb Preprint Archive >To: SEPTEMBER98-FORUM(a)LISTSERVER.SIGMAXI.ORG >Status: U > >On Tue, 29 May 2001, I posted message to this Forum which included this >criticism of the Chemistry Preprint Server (CPS): > >[jt]>Another flaw [is that the CPS isn't] on the list of "Open Archives" >[jt]>(at: http://oaisrv.nsdl.cornell.edu/Register/BrowseSites.pl) >[jt]>So, the CPS archive doesn't meet an "inter-operability" criterion. > >I've just received a copy of Volume 4, Issue 33 of the ChemWeb.com News >Bulletin (distributed to subscribers via email on August 15, 2001). It's >a special issue in recognition of the establishment of the CPS, a year ago >(on August 21, 2000 - the CPS is at: http://preprint.chemweb.com) > >An excerpt from this newsletter: > >> The CPS was developed by closely following the Los Alamos archives >> (http://arxiv.org) which cover physics and related disciplines. In >> setting up the service ChemWeb.com has constantly referred to the Open >> Archive Initiative (http://www.openarchives.org) for e-print archives. > >In this excerpt, it's emphasized that the design of the CPS server has >been guided by the Open Archives Initiative. But, it seems to me that a >crucial element, inter-operability of OAI-compliant eprint archives, >probably still isn't being met by the CPS server. > >I've just visited the current list of registered OAI-conforming >repositories (see: >http://oaisrv.nsdl.cornell.edu/Register/BrowseSites.pl) > >The CPS isn't listed. So, either it's registered but doesn't appear yet >on the list, it isn't registered, or it isn't fully OAI-conforming. I >suspect that it isn't fully OAI-conforming. > >Have I missed something? > >Jim Till >University of Toronto The definitive answer is that CPS has not filled out the registration form at openarchives.org. If they did, we would be happy to validate their site. Donna Bergmark Cornell Digital Library Research Group (and Open Archives Initiative) -- Henry Rzepa. Imperial College, Chemistry Dept. +44 020 7594 5774 (Office) +44 020 7594 5804 (Fax) 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)

1 0

Visualisaion of chemical process...more
by Paul May 17 Aug '01

17 Aug '01

Hi, Forgot to say that apparently there's a free version of the article at: http://xlink.rsc.org/?DOI=10.1039/b103982m and a pdf version coming soon. Regards, ----------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 928-9927, fax: +44 (0)117 925-1295 <mailto:paul.may@bris.ac.uk> ICQ: 107669629 Home URL: <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> Molecule of the Month: <http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm> "I am sorry, you have reached an imaginary number. Please rotate your phone ninety degrees and try again." ------------------------------------------------------------------------------ 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)

2 1

webmolecules.com - warning
by Dr Mary Masson 16 Aug '01

16 Aug '01

Hi, Does anyone know what has happened to www.webmolecules.com? I was going to ask this question last week, because the link had been dead for some weeks, and it had been very useful. Today, I had a deputation from our postgrads saying that the url is alive again, but it has now been taken over by a page that begins "If you are under 18 years of age or if it is illegal to view adult material in your community, please leave now." I have to get the link off all my web pages pronto - some of you may want to do the same. Regards Mary ---------------------- Dr Mary Masson Department of Chemistry University of Aberdeen Meston Walk, Aberdeen AB24 3UE Tel 01224 272931 Fax 01224 272921 email m.masson(a)abdn.ac.uk 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)

4 3

The visualisation of chemical processes for electronic publishing
by Paul May 16 Aug '01

16 Aug '01

Hi, I'm not normally one to blow my own trumpet, but I thought publicising this might be of use to some of you trying to write interactive web-based chemistry reports. It's a paper in PhysChemComm (the RSC on-line Journal) that I've written to tell you the basics of how to jazz up chemical reports or presentations using Chime, VRML, animated gifs, etc, etc. To get the link, your organisation needs to have access to the RSC online Journals. http://hotdog.rsc.org/ej/qu/2001/B103982M/index.htm Regards, ----------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 928-9927, fax: +44 (0)117 925-1295 <mailto:paul.may@bris.ac.uk> ICQ: 107669629 Home URL: <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> Molecule of the Month: <http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm> ------------------------------------------------------------------------------ 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)

2 1

Re: Chemical formulas as gifs
by Jerzy Krol-Bogomilski 13 Aug '01

13 Aug '01

Hi, I thank to all who responded. You have helped me very much! Now I am able to save organic chemical formulas as GIFs. Regards, Jerzy. Jerzy Kr�l-Bogomilski Ph.D. http://www.geocities.com/jerzor jerzor(a)yahoo.com __________________________________________________ Do You Yahoo!? Send instant messages & get email alerts with Yahoo! Messenger. http://im.yahoo.com/ 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)

1 0

RE: IE and "plugins": correction
by Bachrach, Steven 13 Aug '01

13 Aug '01

I apologize for jumping in here late but I was on vacation this past week WITHOUT my laptop (I recommend this to all!) In any event, I want to clarify one item that Henry mentioned and that is concerning the Microsoft Antitrust lawsuit. Microsoft has not WON this suit, in fact they LOST - the appeals court has simply thrown out the penalty (which was to break up microsoft into two pieces). In fact, Microsoft just lost an appeal to have the original verdict thrown out. So the status is now what will be the penalty - likely not to be busting up Microsoft! But this whole plug-in issue is VERY disconcerning. It would be nice to hear something useful from MDL on the matter! Open source chemistry is of course a very real option, but without the browser framework this becomes a serious development problem. However, the GCC compiler is a major development project so perhaps we can encourage a project to develop an open source browser that supports XML, plugins, java, javascript? Steve -- Steven Bachrach ph: (210)999-7379 Department of Chemistry fax: (210)999-7569 Trinity University 715 Stadium Drive San Antonio, TX 78212 steven.bachrach(a)trinity.edu > -----Original Message----- > From: Rzepa, Henry [mailto:h.rzepa@ic.ac.uk] > Sent: Monday, August 06, 2001 10:57 AM > To: chemweb(a)ic.ac.uk > Subject: IE and "plugins": correction > > > Correction to my earlier posting. I had noted that Adobe "plugins' > do work with IE 5.5 SP2 and IE 6, XP. This is because they are not > plugins but pure ActiveX controls (this from a developer who > should know!) > > So I suppose the next question is whether the "chemically important" > plugins will be upgraded by their developers to ActiveX controls. > MDL presumably will do so, but how many others are out there, > and will they get upgraded? > > Netscape of course will continue to work, but then again the cost > of producing one "plugin" and one "activeX" control for Windows > might mean some developers will chose one or the other but perhaps not > both. With less than 30% of the use and still decreasing, > this might mean the final nail in the coffin > for Netscape. A similar issue confronts "non" Windows platforms. > > It really is difficult to avoid the conclusion that having won its > anti-trust case in the courts in the USA, Microsoft is going to get > even more monopolistic. > -- > > Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0870) 132-3747 (eFax) > Dept. Chemistry, Imperial College, London, SW7 2AY, UK. > http://www.ch.ic.ac.uk/rzepa/ > > > 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) > 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)

4 5

RE: IE and "plugins": correction
by Miller, Mitch 06 Aug '01

06 Aug '01

Hello, Any idea about where the Java plug-in stands in this? This plug-in was to be the only way to run Java applets in I.E. as there won't native support for Java long-term in I.E. Mitch -----Original Message----- From: Rzepa, Henry [mailto:h.rzepa@ic.ac.uk] Sent: Monday, August 06, 2001 9:57 AM To: chemweb(a)ic.ac.uk Subject: IE and "plugins": correction Correction to my earlier posting. I had noted that Adobe "plugins' do work with IE 5.5 SP2 and IE 6, XP. This is because they are not plugins but pure ActiveX controls (this from a developer who should know!) So I suppose the next question is whether the "chemically important" plugins will be upgraded by their developers to ActiveX controls. MDL presumably will do so, but how many others are out there, and will they get upgraded? Netscape of course will continue to work, but then again the cost of producing one "plugin" and one "activeX" control for Windows might mean some developers will chose one or the other but perhaps not both. With less than 30% of the use and still decreasing, this might mean the final nail in the coffin for Netscape. A similar issue confronts "non" Windows platforms. It really is difficult to avoid the conclusion that having won its anti-trust case in the courts in the USA, Microsoft is going to get even more monopolistic. -- Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0870) 132-3747 (eFax) Dept. Chemistry, Imperial College, London, SW7 2AY, UK. http://www.ch.ic.ac.uk/rzepa/ 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) 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)

3 2