March 1997 - chemweb - imperial.ac.uk

crystal structures with Chime
by RICHARD SINGER 06 Mar '97

06 Mar '97

You may have encountered the following problem when using Chime - when viewing structure files in the XYZ format one is typically offered a blank screen. The reason is that the default display mode is "stick" mode. XYZ files have no connectivity information so no bonds are drawn if the lattice parameter is larger than the threshold value beyond which Chime assumes atoms cannot bond. Of course the structure appears if you change to "ball and stick" but this might not occur to the uninitiated who would assume something was wrong with the structure file. Is there a way round this problem? Richard Singer ----------------------------------------- Dr Richard Singer School of Applied Chemistry Kingston University Penrhyn Road Surrey KT1 2EE UK Tel 0181 547 2000 ext 2471 FAX 0181 547 7562 ----------------------------------------- ----- 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: chime {rotation speed and Chime 1.0...)
by Tim Maffett 06 Mar '97

06 Mar '97

At 05:01 PM 3/5/97 GMT, John R. Nash wrote: >(this message cc:'d to the MOTM page creator as well as sent to ChemWeb) > >Trevor Gilson <T.R.Gilson(a)soton.ac.UK> said: >>The latest motm goes round a bit too fast with chime (is this >>clock-dependent?). Must be close to the epilepsy-inducing rep rate. > >I agree that the molecule spins too quickly, and I think I may know why. >When Chime reached version 1.0, there was a change in the spinrate >parameter, such that "normal" spin rates with older chime versions now spun >a lot faster. The parameter is now "degrees per second," with a 30 degree >spin of the y axis the default. See >http://www.mdli.com/chemscape/chime/chimehelp.html#Dev2 for details. FYI, >the current MOTM page is set with SpinY=360, or one rotation per second. >When I upgraded to 1.0, I had to slow down all of my overly hyperactive >molecules.... (shameless plug: >http://www.chem.wisc.edu/~casey/research.html) > > John is correct here, Chime 1.0 was fixed so that it correctly took the spinX/Y/Z parameter into account and tried to correctly 'match' the requested degrees of rotation to watch actually occurred. Unfortunately one side-effect of this bug fix results in 'overly hyperactive' chimed structures. Chime's rotations should *not* be dependent on the clock speed of the computer. (It is possible that a slower computer would rotate a 'difficult' structure SLOWER, but never a fast computer rotating faster (then requested)). There are several factors that effect rotation: spinFPS: Frames per second that chime will try to display/apply the requested rotation parameters spinX, spinY, spinZ: The degrees per second of rotation for each axis. The degrees of rotation for each 'frame' of the rotation is computed like this: frameX = spinX/spinFPS frameY = spinY/spinFPS frameZ = spinZ/spinFPS For each 'frame' that Chime moves structures the above frameX/Y/Z amount. Chime (as of 1.0) will now try it's best to achieve the requested frame rate, it should never go *faster* then the requested frame rate. The max FPS that can be *achieved* on different machines varies, but in practice no Windows 3.1/95 machine can get more that 17 frames per second because of limitations of the timer on this platform. The SGI should be able to get up to 60 FPS, and a fast PowerMac can probably get near 60 as well. The 'move' command in Chime 1.0's scripting language can be used for a more precise control of rotation/zooms/translates. The command allows the other to specify the amount a 'move' will be 'sped up' on a users machine to compensate for a slower machine. Eric's site has some good examples, and some docs, on the move command. Hope that all made sense... -tim > ..deleted.. > >-john nash > > > >-==-John R. Nash-==-nash(a)chem.wisc.edu-==-UW-Madison Chem. Dept-==- > --- "When in doubt, roll!" --- > ----- 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: chime etc
by Armel Le Bail 05 Mar '97

05 Mar '97

Trevor Gilson writes : >The latest motm goes round a bit too fast with chime (is this >clock-dependent?). Must be close to the epilepsy-inducing rep rate. >No doubt time will allow refinement of the parameters, but would it >not be better if using the mouse were to shut down the externally >induced spin? Presumably someone going in with a mouse wants to >examine still orientations. With the right button of the mouse, select "rotation stop". Rotation is useless in this case, just a demo of the power of chime in inducing epilepsy :-). I don't know if the rotation is clock-dependent, it is surely model-size and computer-power -dependent. Just another more complaint and I stop the rotation :-| Armel Le Bail, Laboratoire des Fluorures URA CNRS 449 Faculte des Sciences, Universite du Maine, F-72017 Le Mans, France http://fluo.univ-lemans.fr:8001/ and/or http://pcb4122.univ-lemans.fr/ ----- 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: chime etc
by John R. Nash 05 Mar '97

05 Mar '97

(this message cc:'d to the MOTM page creator as well as sent to ChemWeb) Trevor Gilson <T.R.Gilson(a)soton.ac.UK> said: >The latest motm goes round a bit too fast with chime (is this >clock-dependent?). Must be close to the epilepsy-inducing rep rate. I agree that the molecule spins too quickly, and I think I may know why. When Chime reached version 1.0, there was a change in the spinrate parameter, such that "normal" spin rates with older chime versions now spun a lot faster. The parameter is now "degrees per second," with a 30 degree spin of the y axis the default. See http://www.mdli.com/chemscape/chime/chimehelp.html#Dev2 for details. FYI, the current MOTM page is set with SpinY=360, or one rotation per second. When I upgraded to 1.0, I had to slow down all of my overly hyperactive molecules.... (shameless plug: http://www.chem.wisc.edu/~casey/research.html) >No doubt time will allow refinement of the parameters, but would it >not be better if using the mouse were to shut down the externally >induced spin? Presumably someone going in with a mouse wants to >examine still orientations. Well, it is simple to turn off the rotation using the popup menu, and IMHO it it useful to be able to "tweak" a rotating molecule with the mouse to adjust its spinning orientation. Your mileage may vary, of course... -john nash -==-John R. Nash-==-nash(a)chem.wisc.edu-==-UW-Madison Chem. Dept-==- --- "When in doubt, roll!" --- ----- 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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Paperless Submission of Student Projects/Coursework
by Rzepa, Henry 05 Mar '97

05 Mar '97

For the first time this year, we have operated a "paperless" undergraduate course, and the results seeming sufficiently interesting to post here The course was Chemical IT, http://www.ch.ic.ac.uk/local/it/ and assessment was by course project. 15 topics were suggested, and students had to select one and notify us of their selection by e-mail They were given 2 months to complete the project; access to computers being during the free time from lectures, tutorials etc.Because there was no printing requirement, the usual last minute rush to use overheated (and in our case broken) printers with no paper or ink cartridges did not occur. Around 70 projects were submited, which represents a high completion rate, of which 2 actually were on paper, around 50 on floppy disk, and about 20 as e-mail enclosures. One was "received" as a URL pointer to a private Web page from an Internet service provider (ie it did not actually reside on campus at all!) Around 50 projects were in word processor format, and 20 were in HTML + images. Several of the better ones can be seen on http://www.ch.ic.ac.uk/local/projects/ Assesment was on-screen, and the use of good indexing and structuring by many students made this process rapid and quick. We were not able to cover the scripts however with copious remarks in red ink! Overall the process seems to have motivated the students, who on average displayed docukent creation skills that many of the staff here do not have, and seems certain to be repeated on a larger scale in our dept in the future. If anyone else has any experiences to report on the paperless UG environment, do please post here. 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/ ----- 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 etc
by Trevor Gilson 05 Mar '97

05 Mar '97

The latest motm goes round a bit too fast with chime (is this clock-dependent?). Must be close to the epilepsy-inducing rep rate. No doubt time will allow refinement of the parameters, but would it not be better if using the mouse were to shut down the externally induced spin? Presumably someone going in with a mouse wants to examine still orientations. 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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Re: JavaScript
by Nikodem Miranowicz 05 Mar '97

05 Mar '97

>Does anybody know chemical applications of JavaScript ? >Thanks, > If you take a look at http://www.chem.cmu.edu/djsoft/java/index.html you will find some Java Applets: (Spectroscopic Simulator, Statistical Mechanics, Simulator, The Periodic Table, Data Fitting, Particle in a Box, Money Flow Graph). Try also http://yip5.chem.wfu.edu/yip/organic/nt.html where you will probably find some more applets (Acid Base Titration-Interactive Weak Acid Strong Base Titration Simulation 1 - 3 ) as well as Shockwave apps. good luck Nikodem Miranowicz ************************************************************************** * * * mgr Nikodem Miranowicz * * * * Mailto:nmiran@chem.amu.edu.pl * * http://chem.amu.edu.pl/~nmiran/ * * * ************************************************************************** * Zaklad Dydaktyki Chemii * Laboratory of Chemical Education * * Wydzial Chemii * Institute of Chemistry * * Uniwersytet im.A.Mickiewicza * Adam Mickiewicz University * * Ul.Grunwaldzka 6, Poznan * Ul.Grunwaldzka 6, Poznan, Poland * ************************************************************************** * * * tel 48 (61) 699-181 ext.379 fax 48 (61) 658-008 * * * ************************************************************************** ----- 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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Guidelines for this List
by Rzepa, Henry 05 Mar '97

05 Mar '97

A message from the list coordinator In 15 months of operation, this list appears to have managed to steer the difficult path between obscure arcane queries, and very general queries about any topic in chemistry. Might I remind people that we do try to focus on "chemical applications of the Internet", and that perhaps questions about general chemistry are best sent to other lists. It is not my current intention to turn the list into a moderated one (requiring me to make a decision on each posting), so I would ask for everyone's co-operation in trying to keep the noise level down (and thus making noise such as this message unnecessary). 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/ ----- 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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chemistry problem...
by Keith Wilkinson 04 Mar '97

04 Mar '97

a small chemistry problem! I'd like to know why catalytic reforming raises the octane number by creating branched isomers. The real question is why does a branched isomer burn more slowly than the straight chain version. Would anyone know? Many thanks, keith wilkinson ----- 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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Electronic conferences
by Janet Ash 04 Mar '97

04 Mar '97

On behalf of the Chemical Structure Association Executive Committee, I should like to respond to Bernard Blessington's message about the Chemical Structure Association organising local meetings in preference to electronic conferences. The CSA was co-organiser of the 4th international conference on Chemical Structures in the Netherlands last June, at which the latest research in chemical structure information handling was presented. This was attended by around 130 people from many different nationalities, all of whom benefitted greatly not only from the lectures, poster session and exhibition, but also from numerous informal discussions which took place daily in the coffee breaks, over meals and at the bar. At the other end of the spectrum, the CSA aims to provide introductory courses for people who have little or no experience in the field. The Internet Workshop to be held in April in Sheffield is a teaching workshop, and, as it is designed for people who are not familiar with using the internet, would obviously be inappropriate as an electronic conference. One of the current aims of the CSA is to extend the membership worldwide and we hope that the new Web site at http://www.chem-structure.org will help to achieve this aim. We already have a new member in India. Organising an electronic conference would be an excellent way to enable all our members to take part, and also to attract the schools, the undergraduate and postgraduate students that, as Bernard Blessington points out, can afford neither the time nor money to attend local meetings. However, what are people's experience with electronic meetings? What resources are required to set up an electronic conference? The CSA does not have the resources to organise such a conference on its own. We would need to work in conjunction with an academic organisation, for example, which has spare Web space available and students who have the time spend on setting up an electronic conference. There is often a registration fee for electronic conferences. Does this severely restrict the number of people who take part? If you have taken part in an electronic conference, has it been of great benefit to you, or do you have recollections of Web pages you never got round to looking at, and e-mail messages you never read properly because of the pressing distractions of your day-to-day work which surrounded you? Is it better to get away from the office for a day or two to meet with other people in a focussed environment? We would very much welcome your response to the above questions. Janet Ash CSA Chairman ------------------------------------------- Janet Ash Herengracht 14E 1015 BK Amsterdam The Netherlands Tel/Fax: +31 20 6269610 e-mail: ash(a)euronet.nl or 100547.562(a)compuserve.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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