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Re: [Jmol-developers] Abinit reader and crystals
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From: Fabian D. <fab...@wa...> - 2002-09-03 08:53:17
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On Mon, 2002-09-02 at 23:07, Bradley Smith wrote: > My opinion of the patch is that it is difficient in a number of areas, and > is not ready to go into Jmol. > > 1. Crystal properties don't warrant a menu of their own. Rather than having > Crystal/Properties, it should be Extras/Crystal properties... Ok easy to fix > > 2. The menu item is activated regardless of whether crystal information is > read from the file. If caffeine.xyz is read, the crystal properties are > active with defaults that are certianly not going to be related to a crystal > structure of caffeine. In addition, the molecule explodes if the Commit > changes... button is clicked. I can easily disable it but I chose not to do that. Why? I think that the user should be able to load, for instance, a XYZ file containing no crystal information but containing the unit cell atoms and then go the the crystal menu to generate the crystal. For instance, the site http://cst-www.nrl.navy.mil/lattice/ gives the unit cell atomic positions in XYZ format of a lot of crystal. It gives also the basis vector in a separate file. With Jmol and my patch you can easily generate the crystal. I think it is the responsability of the user to chose when to use the crystal dialog. Now you say, that the molecule cafeine "explodes". Its true, but this is the expected behavior. Try to enlarge the crystal box and you will see that the molecule is translated into lattice points. Of course caffeine is a molecule and turning it into a crystal has no sens.... > > 3. Like most of the dialogs in Jmol, it overuses the TitledBorder. Granted > the same design is used throughout Jmol, but better design should be used > for new dialogs. Ok > > 4. Why is the total number of frames listed in the crystal properties? What > does that have to do with crystals properties? Actually nothing. I can remove it. But there is something to say about it. Each frame of the crystal can have it's own crystal properties. I mean the unit cell can change from frame to frame. It is usefull when you do "lattice optimization" with a DFT package for instance. So in the future I would like to add a dialog box that can allow the user to change of "active frame". So far, there is no way to do that in jmol(except when you are in the animate dialog). Thereby, as a starting point, I want to allow the user to change of active frame from inside Crystal-->Properties (not yet implemented). But I think it would be better to design a new dialog bow that can do that and display other usefull information at the same time. > > 5. Values entered into the dialog box are not checked for validity. > Incorrect values cause exceptions to be thrown. Right, I am not yet familiar with execeptions in Java. Will implement it later. Anyway, the way java handles unchecked exceptions keep the program stable even when a field is not valid. > > 6. The crystal properties dialog does not update if a molecule is read while > it is open. Thankx, I didn't notice. > > 7. The space group information is missing. Right, not fully implemented > > These are just the first impressions obtained from using the new code. I > have not looked at the implementation itself. > > Personally, I don't understand the information presented in the crystal > properties. The information is different than that generally used with > protein crystallography, which uses cell dimensions (a, b, c) and angles > (alpha, beta, gamma), and the space group. My class CrystalFile will also support also this notation in the future (interface already implemented). > > Bradley > > Thank you very much for this constructive advice. Don't hesitate to tell me more. Fabian > > ----- Original Message ----- > From: "E.L. Willighagen" <eg...@sc...> > To: "Fabian Dortu" <fab...@wa...>; > <jmo...@li...> > Sent: Monday, September 02, 2002 6:08 AM > Subject: Re: [Jmol-developers] Abinit reader and crystals > > > > On Monday 02 September 2002 14:31, E.L. Willighagen wrote: > > > On Monday 02 September 2002 16:16, Fabian Dortu wrote: > > > > The files are not given in attachement because it is too big > > > > (size must no exceed 40kb in this mailing list) so I put it in > > > > the patches section of Sourceforge. > > > > > > Acknoledged. I am now trying to merge your changes with a local > > > copy of Jmol in CVS... > > > > Done that. Works without any problems. > > > > The patch does not view the cell axis, does it? > > Fabian, what are your futher plans? > > > > Bradley, what is your opinion on this patch? There was did patch about > > crystal in the past (for Jmol 1.1) but never got included... I've never > had > > time to port that patch to current CVS... Should Jmol be able to view > crystal > > structures? > > > > Egon > > > > > > ------------------------------------------------------- > > This sf.net email is sponsored by: OSDN - Tired of that same old > > cell phone? Get a new here for FREE! > > https://www.inphonic.com/r.asp?r=sourceforge1&refcode1=vs3390 > > _______________________________________________ > > Jmol-developers mailing list > > Jmo...@li... > > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > -- Contrary to popular belief, Unix is user friendly. It just happens to be selective about who it makes friends with. --Dave Parnas ********** Fabian Dortu Collegeberg 16 .~. 3000 Leuven /V\ Belgium /( )\ ^^-^^ Phone : 32-475-599268 e-mails : Fab...@wa... Fab...@st... *********************************************** |