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Thread: Obstacle for chemists to use Ubuntu = ChemDraw

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  1. #1
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    Obstacle for chemists to use Ubuntu = ChemDraw

    There is ONE thing that stands in the way of chemists who'd like to completely migrate from Windows to Linux...

    It is the 2D Drawing software (or lack thereof)!
    In Windows and Mac, we all use ChemDraw (I should be specific, for all of us who are organic chemists).

    Xdrawchem is really getting there and I'm grateful for the developers, But it is not quite satisfactory (bugs, resolution, stability).

    Some people might be aware that when one tries to install ChemDraw via Wine, it (v. 9, at least) installs but there is a major bug; atoms appear as black boxes.

    I'd like to call on the bright ones who're reading this to help get ChemDraw to work with Wine. For a simpleton like me, all I can do is shuffle around native DLLs to no avail. They got IE6 to work with wine and made IE4Linux package. I'm confident somebody can!

    May God bless you a bunch.

    Tak

  2. #2
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    Re: Obstacle for chemists to use Ubuntu = ChemDraw

    Thought I'd post the screenshot of what I was talking about and the output in the terminal.

    Code:
    libGL warning: 3D driver claims to not support visual 0x4b
    libGL warning: 3D driver claims to not support visual 0x4b
    fixme:ole:OleUIAddVerbMenuA ((nil), (null), 0x280, 16, 65, 66, 0, 0, 0x33fd28): stub
    fixme:ole:OleUIAddVerbMenuA ((nil), (null), 0x280, 16, 65, 66, 0, 0, 0x33df08): stub
    fixme:ole:OleUIAddVerbMenuA ((nil), (null), 0x280, 16, 65, 66, 0, 0, 0x33df08): stub
    fixme:ole:OleUIAddVerbMenuA ((nil), (null), 0x280, 16, 65, 66, 0, 0, 0x33e43c): stub
    Screenshot.png

  3. #3
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    Re: Obstacle for chemists to use Ubuntu = ChemDraw

    I know what you mean. I'm a Physical Chemist, so I don't do much wet chemistry but it seems we have a lot of 2D molecular editors but none that quite stand up to ChemDraw. One you might look at is a Java app called JChemPaint (http://almost.cubic.uni-koeln.de/cdk/jcp). It seems nice.

    This is also why I'm trying to help out as much as I can on a really cool project called gchemutils (http://www.nongnu.org/gchemutils/) that is becoming a whole Chemistry suite (crystal viewer, 3d molecule viewer, periodic table, molecule calculator) and will soon be incorporating GChemPaint (http://www.nongnu.org/gchempaint/) another good 2D molecular editor.

    -LaserJock
    "That's all very well in practice, but will it ever work in theory?" -- G. Hill
    "A tidy laboratory means a lazy chemist." -- Jöns Jacob Berzelius

  4. #4
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    Re: Obstacle for chemists to use Ubuntu = ChemDraw

    Thanks for your tip.
    Does JChemPaint or GChemPaint copy and paste into, say OpenOffice?

    Because for us researchers, the most important use of these softwares is for presentation / publication.

    So if I can't copy / paste into OO Impress or OO Writer, it's not much use (though I know I can save them as pics, etc). I noticed that no other Linux programs I've tried (Chemtool, BK..., a couple others I forgot) does that except for Xdrawchem.

  5. #5
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    Re: Obstacle for chemists to use Ubuntu = ChemDraw

    Quote Originally Posted by tak1150 View Post
    Thanks for your tip.
    Does JChemPaint or GChemPaint copy and paste into, say OpenOffice?

    Because for us researchers, the most important use of these softwares is for presentation / publication.

    So if I can't copy / paste into OO Impress or OO Writer, it's not much use (though I know I can save them as pics, etc). I noticed that no other Linux programs I've tried (Chemtool, BK..., a couple others I forgot) does that except for Xdrawchem.
    While it's not "copy and paste," you can export from BKChem to an OO Draw file, which then integrates just fine into the rest of OO (as well as allowing for some advanced editing, once the structure is in place). I find "copy and paste" solutions to be unreliable anyway when forced to convert a file to an MS format (especially presentations for Powerpoint), as the images often lose a great deal if they were not properly imported. (Incidentally, that is true in Windows as well for OO -> Powerpoint, as well as Powerpoint -> Powerpoint if the version changes from 2000/XP to anything higher or vice versa.)

    Personally I've found BKChem to be better for my purposes than ChemDraw (the recent versions spend too much time trying to change my structures for me!), but I only need it occasionally. It also seems more reliable (stable) than most of the other tools (though I've not tried the Java-based ones). I have hope for GChemPaint, but I don't think it's quite there yet. Of course, I'm also partial to Python solutions, as I regularly use the language.

  6. #6
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    Re: Obstacle for chemists to use Ubuntu = ChemDraw

    Hi there! As yet another physical chemist (and a spectroscopist as you might imagine) I don't need chemical drawing programs as much as some. However, I too, still need them. I was poking around the internets one day and found the following review:

    http://groundstate.ca/chemdraw

    It is fairly old (2004), but the reviewer does specifically address importing drawings into Open Office. Hope it helps some.

  7. #7
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    Re: Obstacle for chemists to use Ubuntu = ChemDraw

    Quote Originally Posted by tak1150 View Post
    There is ONE thing that stands in the way of chemists who'd like to completely migrate from Windows to Linux...

    It is the 2D Drawing software (or lack thereof)!
    In Windows and Mac, we all use ChemDraw (I should be specific, for all of us who are organic chemists).

    Xdrawchem is really getting there and I'm grateful for the developers, But it is not quite satisfactory (bugs, resolution, stability).

    Some people might be aware that when one tries to install ChemDraw via Wine, it (v. 9, at least) installs but there is a major bug; atoms appear as black boxes.

    I'd like to call on the bright ones who're reading this to help get ChemDraw to work with Wine. For a simpleton like me, all I can do is shuffle around native DLLs to no avail. They got IE6 to work with wine and made IE4Linux package. I'm confident somebody can!

    May God bless you a bunch.

    Tak
    I have a similar problem with installing Chemoffice 9 using crossover office. I dont have the black box problems as I can see all carbon-carbon bonds; however, when you want to put in a heteroatom I am left with just a blank white box where the atom should be. Everything else seems to work fine. Even though I cannot see the atom, the program does notice it as I can see the change in the mass.

  8. #8
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    Re: Obstacle for chemists to use Ubuntu = ChemDraw

    Quote Originally Posted by lbyrd33 View Post
    I dont have the black box problems as I can see all carbon-carbon bonds; however, when you want to put in a heteroatom I am left with just a blank white box where the atom should be.
    I meant to say that I only have problems with the heteroatoms as well. Also any text that you type in will be all black boxes!

    This person claims on WINE App DB that s/he got it to work after installing "gdiplus.dll" I have tried that and it didn't work...

    I don't have crossover (yet) but maybe if you put gdiplud.dll in your ~/.wine/drive_c/windows/system32 folder, w/ all the Crossover stuff it might work...?

  9. #9
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    Re: Obstacle for chemists to use Ubuntu = ChemDraw

    Quote Originally Posted by tak1150 View Post
    I meant to say that I only have problems with the heteroatoms as well. Also any text that you type in will be all black boxes!

    This person claims on WINE App DB that s/he got it to work after installing "gdiplus.dll" I have tried that and it didn't work...

    I don't have crossover (yet) but maybe if you put gdiplud.dll in your ~/.wine/drive_c/windows/system32 folder, w/ all the Crossover stuff it might work...?
    Thanks, Ill give it a try later.

  10. #10
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    Re: Obstacle for chemists to use Ubuntu = ChemDraw

    If it currently doesn't work in Wine even without tweaking then you could speak to Codeweavers about it and see how much they'd charge to get it fully working and supported. If you all chipped in then it may be affordable, just depends how much effort it would take and how many people want it.

    One sidenote though, DO NOT use native DLLs unless you know it specifically needs them. Feeding Wine/CO native DLLs will normally break it unless there is good reason to use them.
    Wine FAQ and Newbie Guide - http://wiki.winehq.org/FAQ
    Please read This Page on how to install Wine.

    RetroTracks.net - Classic Game Music Tracks

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