Killustrator for Chemistry
Hi Jerry (and SuSE users): I am discovering that Killustrator is well adapted to drawing Chemical compounds. The fact that the moving, rotating and resizing of the drawing elements are all done with the mouse, as opposed to using pull down menus, greatly speeds up the process. Getting used to the mouse clicks to change from movement to rotation is a little tedious at first but well worth the practice. I must say Killustrator is remarkably efficient. I should have some more substituents drawn up in the next few weeks, if you are interested. -- Cheers, Jonathan
Jonathan
I am discovering that Killustrator is well adapted to drawing Chemical compounds. The fact that the moving, rotating and resizing of the drawing elements are all done with the mouse, as opposed to using pull down menus, greatly speeds up the process. Getting used to the mouse clicks to change from movement to rotation is a little tedious at first but well worth the practice. I must say Killustrator is remarkably efficient. I should have some more substituents drawn up in the next few weeks, if you are interested.
Over the years I have tried to get more programmers and chemists interested in molecular modelling through software and computers. There are now some free packages out there as well as the usual stuff like Gaussian for Linux. I'm not sure that Killustrator is the real answer for this. However, an add on package for scientific and mathematical use is desperately needed. I did try and make weak attempts at getting people interested in this but so far there hasn't been much response. Reason I think that this would work very well is because of the large army of chemistry and medical students I've seen out there who either can't afford the software or haven't got the time to be a beta tester. They just need to use it to get their first or second degree. One of the other factors is that they want software that looks and feels like Mac or MS Windows such as Chemoffice or Molecules 3D or Iris Draw for Windows. I suppose that more time will change things eventually :)) Richard
On Sunday 28 January 2001 04:26, you wrote:
Jonathan
I'm not sure that Killustrator is the real answer for this. However, an add on package for scientific and mathematical use is desperately needed. I did try and make weak attempts at getting people interested in this but so far there hasn't been much response.
I don't think Killustrator is all that bad. The nice thing is that you can insert the finished drawing into Kword. Jerry and I have tried Khemical and it's just not ready yet. Gnome has Ghemical but I could not get it to compile. I also looked on SAL (Scientific Applications for Linux) and there are some other rendering programs but alas I could not get them to install. When you apeak of an add on package for mathematics, have you considered Octave, Scilab or MuPad?
Reason I think that this would work very well is because of the large army of chemistry and medical students I've seen out there who either can't afford the software or haven't got the time to be a beta tester.
You are right. A fellow student paid $800.00 for a M$ compatible drawing suite that renders molecules. The drawings are reminiscent of *.pdb files.
They just need to use it to get their first or second degree. One of the other factors is that they want software that looks and feels like Mac or MS Windows such as Chemoffice or Molecules 3D or Iris Draw for Windows.
Well I am a firm believer that Linux (open source in general) should not make fidelity to existing M$ proprietary software a priority. In general the Open Source stuff should be crafted to exploit the advantages offered by UNIX. I could say more about this but one example will suffice. Octave, an open source high level language, that has a vague resemblance to MatLab, has been the object of a good bit of coercion by users to have it mimic the features, look and feel of MatLab. The reason why? MatLab users don't want to pay the $1500.00 for the closed source software. The point is making software that is a clone of a closed source product is an invitation for complete fidelity to some closed source paradigm. John Eaton, the chief developer of Octave, retorted to one requester for full MatLab compliance: "Should I also include all the programming mistakes that are in MatLab" (or words to that effect) Linux and Open Source have to go their own way.
I suppose that more time will change things eventually :))
Richard
-- Cheers, Jonathan
Jonathan On Sun, 28 Jan 2001, Jonathan Drews wrote:
I don't think Killustrator is all that bad. The nice thing is that you can insert the finished drawing into Kword. Jerry and I have tried Khemical and it's just not ready yet. Gnome has Ghemical but I could not get it to compile.
Yes, this is the problem that I've been faced with for a complete year now. I know that if want to compile the Gnome stuff from source in the SuSE distro than you are facing an uphill struggle. I tried to put this to some of the Red Hat people earlier this year. That was like standing in the bottom a trench in Germany with a gun pointed at me. Well, I have done that for a job so I know what it feels like ? :)) I know Miguel de Icaza reasonably well. Enough to have a pleasant conversation with him anyway. I might talk to him about this later this year. Thing about Gtk+ is that it's just made for a molecular modelling app. Got the right feel to it.
.I also looked on SAL (Scientific Applications for Linux) and there are some other rendering programs but alas I could not get them to install. When you apeak of an add on package for mathematics, have you considered Octave, Scilab or MuPad?
Well, looked into them at first and then I got used to Mathematica for Linux. I'm sure that's all very well but not many people can afford it and I only got it when Wolfram Research offered it to me so that I could demo it to other people. That fell over when the local University decided that they could only use MS Windows for anything in future. Of course, that means that once again the students can't afford to pay for any of it and time on the computer in the department is short. So, academic results are affected. TBH, I don't really like the apps above but I would use them if I had to. I like easy to use GUIs like Mathcad etc. So, if I do anything to help GPL'd software along it would have to be an extensive GUI project of some sort.
You are right. A fellow student paid $800.00 for a M$ compatible drawing suite that renders molecules. The drawings are reminiscent of *.pdb files.
Yes, I was hoping that someone might say that :))
Octave, an open source high level language, that has a vague resemblance to MatLab, has been the object of a good bit of coercion by users to have it mimic the features, look and feel of MatLab. The reason why? MatLab users don't want to pay the $1500.00 for the closed source software. The point is making software that is a clone of a closed source product is an invitation for complete fidelity to some closed source paradigm. John Eaton, the chief developer of Octave, retorted to one requester for full MatLab compliance:
mmm.. I dunno :) Maybe something different will come out of this eventually ? Thanks Richard
On Sunday 28 January 2001 13:27, you wrote:
I tried to put this to some of the Red Hat people earlier this year. That was like standing in the bottom a trench in Germany with a gun pointed at me. Well, I have done that for a job so I know what it feels like ? :))
The Red Hat folks are just incomprehensible.
I know Miguel de Icaza reasonably well. Enough to have a pleasant conversation with him anyway. I might talk to him about this later this year. Thing about Gtk+ is that it's just made for a molecular modelling app. Got the right feel to it.
GNOME shows a great deal of promise. The problem is, IMHO, that they just can't seem to complete anything. I am also not happy that they have decided to abandon Abiword as their main Word Processor. Abiword is a terrific word processor. Still the gnome environment is very good. However development for Glade, Gnumeric and some other projects appears to be at a standstill. I mention Glade because I would like to find a GUI creation tool other than TCL/Tk.
Well, looked into them at first and then I got used to Mathematica for Linux. I'm sure that's all very well but not many people can afford it and I only got it when Wolfram Research offered it to me so that I could demo it to other people. That fell over when the local University decided that they could only use MS Windows for anything in future. Of course, that means that once again the students can't afford to pay for any of it and time on the computer in the department is short. So, academic results are affected.
Well Open Source doesn't have anything like Mathematica or Maple yet. I urge you to look at MuPad (http://www.mupad.de/). I have Mathematica for Linux also and it runs just great on SuSE. The problem I have found with the closed source software is that it just doesn't run as good as the GNU/Kde/Gnome stuff. Despite the command line syntax, Octave, is quite good. It has a very elegant way for getting the roots of polynomials. You just enter a list of coefficients and it finds the roots. No initial guesses are needed. The down side is that creating functions is somewhat obscure when compared to doing it in Mathematica. The syntax of Octave might be an impediment to science students already burdened with new material.
TBH, I don't really like the apps above but I would use them if I had to. I like easy to use GUIs like Mathcad etc. So, if I do anything to help GPL'd software along it would have to be an extensive GUI project of some sort.
I think the best thing in that case is just have the students buy Maple or Mathematica. I used Maple on my old DOS computer and it worked very well. In fact MuPad is reminiscent of the old DOS Maple. -- Cheers, Jonathan
On Sunday 28 January 2001 14:27, Jonathan Drews wrote :
Well, looked into them at first and then I got used to Mathematica for Linux. I'm sure that's all very well but not many people can afford it and I only got it when Wolfram Research offered it to me so that I could demo it to other people.
Jonathan, is that the student edition for Linux? How much? ;-) And, how does it compaire visually with MuPAD or MathCad? JLK -- Scientific theories, according to Sir Karl Popper, can be "falsified," or proven wrong, by experiment. Unscientific theories -Marxist dialectical history and Freudian psychology were Popper's favorites- are formed in such a way that they cannot be falsified by data.
mmm.... a sudden thought.... A GPL collection of templates... On Sunday 28 January 2001 00:29, Jonathan Drews wrote:
Hi Jerry (and SuSE users):
I am discovering that Killustrator is well adapted to drawing Chemical compounds. The fact that the moving, rotating and resizing of the drawing elements are all done with the mouse, as opposed to using pull down menus, greatly speeds up the process. Getting used to the mouse clicks to change from movement to rotation is a little tedious at first but well worth the practice. I must say Killustrator is remarkably efficient. I should have some more substituents drawn up in the next few weeks, if you are interested.
-- Scientific theories, according to Sir Karl Popper, can be "falsified," or proven wrong, by experiment. Unscientific theories -Marxist dialectical history and Freudian psychology were Popper's favorites- are formed in such a way that they cannot be falsified by data.
Jerry On Sun, 28 Jan 2001, Jerry Kreps wrote:
mmm.... a sudden thought.... A GPL collection of templates...
Yes, don't know if this fits in with anyone else's way of thinking about it but I though Gtk+ was the ultimate programming tool for producing something of that sort. In the MS Windows versions the whole thing is based around VB (yuk), Java components and ODBC. So, something similar for Linux might work ? Thanks Richard
On Sunday 28 January 2001 11:32, Richard wrote:
Jerry
On Sun, 28 Jan 2001, Jerry Kreps wrote:
mmm.... a sudden thought.... A GPL collection of templates...
Yes, don't know if this fits in with anyone else's way of thinking about it but I though Gtk+ was the ultimate programming tool for producing something of that sort.
Doesn't fit with mine. I've got other things to do beside program GUI math interfaces. That's why I've been following KOffice so closely. Jonathan's KIllustrator examples are very nice! JLK -- Scientific theories, according to Sir Karl Popper, can be "falsified," or proven wrong, by experiment. Unscientific theories -Marxist dialectical history and Freudian psychology were Popper's favorites- are formed in such a way that they cannot be falsified by data.
participants (3)
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Jerry Kreps -
Jonathan Drews -
Richard