July 1996 - chemweb - imperial.ac.uk

Molecule Editor in Java
by Denis M. Bayada 18 Feb '99

18 Feb '99

Dear all, I have just finished writing a molecule editor in JAVA. If anyone is interested, it is available at : http://www.chem.leeds.ac.uk/ICAMS/people/denis/moledit.html You may freely download the Java source code and modify it. Any comments are indeed welcome. Thank you Denis --------------------------------------------------------------------- Denis M. Bayada e-mail: denis(a)mi.leeds.ac.uk ICAMS voice: (44) (0)113 233 65 95 School of Chemistry fax: (44) (0)113 233 65 63 University of Leeds http://www.chem.leeds.ac.uk/ICAMS/people/denis Leeds LS2 9JT ENGLAND ... but as I proceeded in my labour, it became every day more horrible and irksome to me. Sometimes I could not prevail on myself to enter my laboratory for several days, and at other times I toiled day and night in order to complete my work. It was, indeed, a filthy process in which I was engaged. Frankenstein (Mary Shelley) --------------------------------------------------------------------- ----- 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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Re: Cookie Requests
by Paul Weber 30 Jul '96

30 Jul '96

On Jul 30, 10:25am, Richard Hobson wrote: > Subject: Re: Cookie Requests > > I suppose one can always delete the cookies file on a regular basis. It > certainly doesn't seem to perform any "useful" function as far as the > user is concerned. (Or do I get Club points? :-) Cookies can provide a valuable service to both "user" and "provider," and should not be seen as completely evil and restraining one's freedom. We are using cookies here at Tripos for our Sybyl/Unity beta program, and I think the user will see a definite benefit. In our case, we are using the cookie file to record user name, email address, and phone number, AFTER the user has entered it once in the registration form. The cookie allows us to not have to prompt the user EVERY time they link up to the beta information site -- we get the info from the cookie file. If you do delete or edit the cookie file, then the user must again enter all of the information we require to provide them with beta assistance. Are we asking for private information in the registration? No. All of our user sites are (of course) already known to us, since they have licensed our software. The individuals are all persons who have agreed to work with us, where we receive the benefit of more field testing, and they receive the benefit of early access to a needed software product (plus get direct communication with programmers at Tripos). I can't see how anyone would seriously consider this use of "cookies" to be an invasion of privacy. All of the registrants have willingly volunteered to participate, and we are providing a mechanism that says "Hi, welcome back, no need to enter all that registration info again!" Here is what the cookie file looks like: .tripos.com TRUE / FALSE 849315600 sybun_tester Paul Web er .tripos.com TRUE / FALSE 849315600 sybun_tester_email weber(a)tripos.com .tripos.com TRUE / FALSE 849315600 sybun_tester_phone 6471099 .tripos.com TRUE / FALSE 849315600 sybun_tester_company_nam e tripos Certainly doesn't seem all that menacing now, does it? Cheers, Paul -- --------------------------------------------------------------------- Paul L. Weber, Ph. D. Vice President, Product Development Phone: 314 647 1099 Tripos, Inc. Fax: 314 647 9241 1699 S. Hanley Rd St. Louis MO 63144 USA Email: weber(a)tripos.com --------------------------------------------------------------------- ----- 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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Cookie Requests
by Rzepa, Henry 30 Jul '96

30 Jul '96

Netscape 3, under Options/Network/Protocols allows an alert to be shown if a remote server has asked to write into your "cookie" file. I encountered such a request from e.g. http://structbio.nature.com/1996-April/thesolutionstructureofhivnefre Of course, you can inspect your cookie file to see what it wrote there (if you can make sense of it), and only the originating server can subsequently make use of this information. I still find it interesting to know exactly what information is being saved in this file, and what use the remote service makes of it. Some of it is clearly useful (ie version number of the browser you use etc), some of it may prove useful in your browsing of the site (ie you have visited the config page, and there is no reason to go there again) and some may relate to e.g. the user has viewed this article 3 times previously, so let us act upon this information. I suppose its a bit like the "club" cards in supermarkets, where the supermarket knows more about your weekly shopping habits than you do (I suspect for example that supermarkets must have a pretty good idea of the level of alcoholism in the country. Should your local supermarket alert your doctor if it concludes you are over-doing it for example?) I strongly suspect that the use of "persistent client states" as they are known, is likely to increase dramatically. Perhaps many of us will not mind if the remote server is keeping a "stateful" record of our browsing. But how would visitors from the commercial side of things view this? Is it part of the "e-world", or should we be concerned. i am keeping an open mind on this at the moment! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa(a)ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ (Eudora Pro 3.0) ----- 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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Re: Cookie Requests
by lora＠jhunix.hcf.jhu.edu 29 Jul '96

29 Jul '96

I have been hearing about "Magic Cookies" for a while, but what follows is the best description I have seen. I am using the software Cookie Monster on all of the Macs in our lab, and on my personal computer, as I have already been getting junk mail from some of the sites I have visited. Just depends on whether you want people to know where you are going and where you have been. I have not had any problems with it so far. The URL for this information and to download the software (it is e-mail ware)is: http://www.macworld.com/software/IndexSoftware.NewUploads.html Cookie Monster 1.5.1 The following is the description posted on that page: Author: Nicolas Berloquin Needs: Netscape Navigater or Microsoft Explorer Equipment: Macintosh Fee: e-mail ware File size: 9 K The Magic Cookie is a file created by Microsoft Explorer and Netscape Navigator which resides in the preferences folder. It stores data about you, and enables servers you visit to keep track of what you search for and access. They can store this information in their databases for the purpose of marketing analyses and perhaps to generate mailing lists. Besides commercial uses, it's always possible that some servers out there could use this feature to simply record any of your comings and goings and do with the information what they will. We're trying not to sound too Orwellian, but you get the drift... Cookie Monster trashes the MagicCookie file every time it is launched. Install it in your Startup Items folder and Magic Cookie will do the rest. If for some reason you would like to reinstall the Magic Cookie, simply take Cookie Monster out of your Startup Items folder. For more info, you can lookup: http://pobox.com/~nicolas/monster.html http://www.illuminatus.com/cookie_pages/cookie.cgi http://www.bravado.net/rodgers/InterNetNews.html or netscape's technical page on the cookie standard: http://home.netscape.com/newsref/std/cookie_spec.html On Monday, July 29, Henry Rzepa wrote: >Netscape 3, under Options/Network/Protocols allows an alert to >be shown if a remote server has asked to write into your "cookie" >file. I encountered such a request from e.g. >http://structbio.nature.com/1996-April/thesolutionstructureofhivnefre > >Of course, you can inspect your cookie file to see what it wrote >there (if you can make sense of it), and only the originating server >can subsequently make use of this information. > >I still find it interesting to know exactly what information is being >saved in this file, and what use the remote service makes of it. >Some of it is clearly useful (ie version number of the browser you >use etc), some of it may prove useful in your browsing of the >site (ie you have visited the config page, and there is no reason >to go there again) and some may relate to e.g. >the user has viewed this article 3 times previously, so let us act >upon this information. > >I suppose its a bit like the "club" cards in supermarkets, where >the supermarket knows more about your weekly shopping habits >than you do (I suspect for example that supermarkets must have >a pretty good idea of the level of alcoholism in the country. >Should your local supermarket alert your doctor if it concludes >you are over-doing it for example?) > >I strongly suspect that the use of "persistent client states" >as they are known, is likely to increase dramatically. Perhaps >many of us will not mind if the remote server is keeping a >"stateful" record of our browsing. But how would visitors >from the commercial side of things view this? Is it part of the >"e-world", or should we be concerned. > >i am keeping an open mind on this at the moment! > >Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; >rzepa(a)ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. >URL: http://www.ch.ic.ac.uk/rzepa/ (Eudora Pro 3.0) > > >----- >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) Lora F. Burgess Dept. of Chemistry Johns Hopkins University 34th & Charles Sts. Baltimore, MD 21218 (410) 516-7937 ----- 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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Greek characters
by M.Winter＠Sheffield.ac.uk 26 Jul '96

26 Jul '96

Somehow this didn't get posted when I first wrote it and as I think it important, I'm sending it again Tip of the day Colleagues might like to know that NetScape version 3b5 and InterNet Explorer 2.0.1 (Mac versions, I don't know about other hardware) both support the display of Greek characters. Good news! This is some greek text Where I've written "symbol" you can write a comma delimited list of fonts and if one of them is available, presumably the first, then it gets used by the browser. Could someone please tell me what the font names are on non-Mac platforms that are equivalent to the Mac symbol font (which contains Greek letters)? *** (Extra: Explorer is now at 2.1b1 on the Mac) 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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Re: Greek characters
by Jeffrey.Nauss＠UC.Edu 26 Jul '96

26 Jul '96

On Jul 26, 2:44pm, Mark Winter wrote: > Tip of the day > Colleagues might like to know that NetScape version 3b5 and InterNet > Explorer 2.0.1 (Mac versions, I don't know about other hardware) both > support the display of Greek characters. Good news! > > This is some greek text This is great news! But I have a couple questions: 1) Is there a list of the fonts and other reference material for these symbols? 2) How does the symbol look on non-supported browsers? Anyone know? -- Jeff Nauss *********************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss(a)UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * *********************************************************************** ----- 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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VSEPR tutorial/guide available on WWW
by M.Winter＠Sheffield.ac.uk 26 Jul '96

26 Jul '96

I've just completed a first draft of a VSEPR package at http://www.shef.ac.uk/~chem/vsepr/ The Chime plug-in is preferred but not required. If you have any of Chem3D, Linus Lite, ChemDraw, RasMol, you can use them as helper applications, but these are not required. Browsers versions NetScape 3.0b5 or InterNet Explorer 2.0.1 are preferred but not required (except that earlier version numbers and some other browsers will not display Greek characters and symbols too well). Interactive calculations are a feature. I'd appreciate feedback. 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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Chime and the Netscape Mail Interface
by Rzepa, Henry 23 Jul '96

23 Jul '96

I have hitherto only tried the Chime plug-in for viewing pdb files in the regular "HTML" Netscape browser window. Today I decided to see what it would do in the Mail window. 1. Firstly, if one attaches a PDB file as "source" from the send mail feature, it correctly attaches the chemical/x-pdb MIME header. 2. Using Netscape 2.02 (Mac), one can read this file, and it comes over as an attachment with the MIME type correct. I was rather hoping against hope that the molecule itself would be in-lined into the mail message body. But although it makes an attempt to read it (the pdb is 191K in size, and it takes about 3 seconds to read this in) no molecule appears. Clicking on the "Attachment" hyperlink produces a "loading plug-in" message, but no molecule appears in the mail windows, although it does go black in preparation. The usual Chime pull down menus only partially appear. If exactly the same attached pdb file is opened instead in the usual browser window, a fully working Chimed molecule appears 3. Using Netscape 3.0b5 produces different behaviour, on exactly the same mailbox entries. Rather than labelling the attachment as such, the file name appears with a random name apparently associated with an earlier e-mail attachment. Clicking on the hyperlink now does produce a Chimed molecule, but this appears in the regular browser window rather than the Mail Window. The purpose of this message is (a) to find out whether all this behaviour is reproducible on other peoples systems, and using other versions of Netscape browsers. (b) To bring to peoples attention that "active" molecules can be sent with e-mail messages and viewed with Chime as a plug-in. Shame that Eudora does not support Netscape plug-ins! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa(a)ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ (Eudora Pro 3.0) ----- 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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CGI problems with Netscape 2.x and up on Macintosh
by Terry M. Gray 20 Jul '96

20 Jul '96

For two years we have been developing a web interface to some quantum chemistry programs developed at Calvin. We're preparing a manuscript for J. Chem. Ed. describing these. The approach that we took was to keep the original FORTRAN programs intact but to develop a web-form based interface calling a CGI script that runs the progroams and prepares numerical and graphical output that is returned to the user. We also have a quantum chem primer and excerises on on-line to support these. The URL's for the forms are given below. The main URL for the site is http://www.calvin.edu/chemistry/computational/computationalTOC.html You are welcome to check these out and comment if you like. My main reason for writing, however, is not to promote the site, but rather to get some help with a problem that we are having. I recently submitted this problem to the comp.infosystems.www.authoring.cgi newsgroup, but have not received any help yet. So, since this was a chemistry based web-group, I thought I might get some help here. The CGI scripts worked under Netscape 1.12. They still work with Netscape 2.0.2 on a UNIX box (Sun and SGI). BUT they don't work with Netscape 2.x and up (even 3.0b4) on the Mac. I think that they work okay under Windows and Windows 95, but I haven't tested them extensively there. Has anybody heard of such weirdness? They are fairly complicated CGI's that take some form data and then run some computational chemistry programs on the data. Here are some of the form URL's for anyone who wants to try them out: http://www.calvin.edu/chemistry/computational/begatom/begform.html http://www.calvin.edu/chemistry/computational/atom/atomform.html http://www.calvin.edu/chemistry/computational/atomplus/atomplusform.html http://www.calvin.edu/chemistry/computational/ion/ionform.html http://www.calvin.edu/chemistry/computational/webgauss/webform.html http://www.calvin.edu/chemistry/computational/webadvgauss/webadvform.html The problem seems to be in the parsing step, which is a C program. The rest of the CGI script seems to work fine. In other words, it takes the default values from the form or old input files from a previous run and works on them. Of course, this is disastrous because the user thinks that the data returned is for the data input in the original form submission, but is not. Thanks for anyone who can help. Terry M. Gray _____________________________________________________________ Terry M. Gray, Ph.D. Department of Chemistry and Biochemistry Calvin College 3201 Burton SE Grand Rapids, MI 40546 Office: (616) 957-7187 FAX: (616) 957-6501 Email: grayt(a)calvin.edu http://www.calvin.edu/~grayt *This mission critical message was written on a Macintosh with Eudora Pro* A special message for Macintosh naysayers: http://www.macworld.com/pages/july.96/Column.2204.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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the *correct* Windows 3.1 0.9c version of chime is now available
by Tim Maffett 09 Jul '96

09 Jul '96

I am *very* sorry, but due to a mistake on our webmaster's part the correct files were *NOT* available for download until early this morning. I should have verified the availability of the file before sending my message, and I errored by not doing so. The corrected, bug fixed, version of Chime 0.9c for Windows 3.1 is now available on our website: http://www.mdli.com/chemscape/chime/download.html This time I downloaded and installed this version myself to verify that it is the correct version. Again, we apologize for the inconvenience that we may have caused for many of you. -tim Tim Maffett tim(a)mdli.com Principal Architect, Internet Technologies MDL Information Systems, Inc. ----- 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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