Obstacle for chemists to use Ubuntu = ChemDraw

[Iridos]

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.

Black box or white box - AFAIK, this is the same problem. I think I have seen both over the time, but cannot remember anymore what I changed (I thought it was colordepth of the Xserver, but when I try to reproduce it now, wine only runs in a 24/32 bit truecolor mode).

One thing, that seems to cause it is the wine-version (or the version of one of the libraries it uses). The problem appeared several years ago - before that, displaying characters worked fine (although there were other gliches - but not as dramatic ones as these boxes which render ChemDraw nearly useles).

I.

[Iridos]

PS. I should probably mention that I use Debian, not Ubuntu - the problem still is exactly the same, but I might have been using wine/chemdraw for longer than Ubuntu actually exists. In regard of this, it is possible that Ubuntu never had a version of wine+libs that did not have the problem

[tak1150]

PS. I should probably mention that I use Debian, not Ubuntu - the problem still is exactly the same, but I might have been using wine/chemdraw for longer than Ubuntu actually exists. In regard of this, it is possible that Ubuntu never had a version of wine+libs that did not have the problem

I have only tried Ubuntu / wine /chemdraw since Ubuntu Edgy (2006 Oct), but for that period what you said about ubuntu is true.

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.

I have emailed CambridgeSoft directly, but have not received any replies (no surprise); I told them that it'd be good for them if they got it working in Linux so that Linux chemists would use their product as well, but oh well.

[Iridos]

(quoting tak1150): I have only tried Ubuntu / wine /chemdraw since Ubuntu Edgy (2006 Oct), but for that period what you said about ubuntu is true.

Hm, perhaps it depended on Chemdraw version? It definitely exists in Chemdraw 6.0.
This is a very long time period, we're discussing and I switched universities etc.
I think the problem appeared when updating some packages, but it is so long ago, I cannot be sure.
I

[Iridos]

I did some research on this. (Had already typed it, but got logged out and it was all lost)
ColorDepth was mentioned here:http://appdb.winehq.org/appview.php?...iTestingId=869
- but that seems to have no effect on ChemDraw.

This seems to be a similar problem:
http://www.winehq.org/pipermail/wine...er/043616.html

connected with this bug report:
http://bugs.winehq.org/show_bug.cgi?id=2737
this bug was fixed in 2006, though.

Seeing all these debug flags in the bug report, I tried to get some useful output myself.

The way I got this output was by starting wine with the debug flags shown below, then adding a bond, then typing a character on the end of the bond, which creates a label and only look at the lines appearing during that action.

WINEDEBUG=+x11drv wine chemdraw.exe gives this output
trace:x11drv:X11DRV_CreateBitmap (0x910) 14x20 1 bpp
trace:x11drv:X11DRV_CreateBitmap (0x914) 1x1 1 bpp
trace:x11drv:X11DRV_CreateBitmap (0x938) 14x20 1 bpp
trace:x11drv:X11DRV_CreateBitmap (0x93c) 1x1 1 bpp
trace:x11drv:X11DRV_CreateBitmap (0x94c) 14x20 1 bpp
trace:x11drv:X11DRV_CreateBitmap (0x95c) 14x20 24 bpp
trace:x11drv:X11DRV_CreateBitmap (0x990) 14x20 1 bpp
trace:x11drv:X11DRV_CreateBitmap (0x994) 1x1 1 bpp
trace:x11drv:X11DRV_CreateBitmap (0x9a4) 14x20 1 bpp
trace:x11drv:X11DRV_CreateBitmap (0x9b4) 14x20 24 bpp
trace:x11drv:X11DRV_SetWindowPos win 0x10026 window (294,10)-(1221,910) client (298,52)-(1217,906) style 16cf0000
trace:x11drv:X11DRV_SetWindowPos win 0x1002c window (1,1)-(922,31) client (2,4)-(921,30) style 50800101
trace:x11drv:X11DRV_SetWindowPos win 0x1002a window (0,835)-(919,854) client (0,835)-(919,854) style 50000000
trace:x11drv:X11DRV_CreateBitmap (0xb2c) 16x16 24 bpp

I also tried WINEDEBUG=+font as well as the options +gdi,+bitmap,+seh,+text
+gdi gave too much output to tell anything useful
+font shows ever-repeating fontchanges
+bitmap showed nothing really new compared to x11drv
and +seh did not create output on adding a character
+text only creates for the menues, but not for typed text (to test that, I wrote some text instead of the single lable using to get output from the other options)

I.



Now I forgot to mention it - these 1 bpp (bits per pixel) entries seem strange - although they are followed by a 24 bpp entry.
It seems x11 first tries to clear the area, using 1 bit color depth, then overwrite this with the real image. Seems we are somehow stuck with the 2-color version (?)
Also creating 1x1 bitmaps seems strange. If these were scaled, they'd definitely be black or white boxes (or perhaps better rectangles) :)

[mortenkjeldgaard]

Another GPL chemistry drawing program is BKchem, written in Python. I haven't used it, but it looks very nice.
Check it out! (http://freshmeat.net/projects/bkchem/)

Cheers,
Morten

[eZtaR]

I just came across this totally at random and thought you might find it interesting:
http://code.google.com/soc/kde/appin...BDFAAF85EFFA00

It's a student named Marcus Hanwell who's gonna devote his summer to writing a 3d molecular editor. In his article he also mentions various other apps that might help you in your journey of finding a 2d chemical drawer.


Oh btw: Have you guys checked out if ChemSketch works with wine? Seems to me that it does practically the same as chemdraw

[tak1150]

Oh btw: Have you guys checked out if ChemSketch works with wine? Seems to me that it does practically the same as chemdraw

Yes, I have tried Chemsketch and it does work under wine
Drawing features of it are not as good (in my opinion) as Chemdraw and the files are not very portable to other linux applications. That's why I've abandoned it.

Biggest reason why I need ChemDraw:
Most communications between collaborators are done in ChemDraw files (windows or mac) and therefore, I really need ChemDraw and nothing else to work in my Ubuntu computer.

-I am aware that Xdrawchem is supposed to support chemdraw files, but I've never been able to read any Chemdraw files in xdrawchem.


Software I've tried: (well either way, I still need chemdraw, but had to try these for my curiosity)

1. BKChem - great portability, but bad resolution, somewhat unstable, ok drawability
2. GChempaint - so so portability, ok resolution, good drawability, but bad when it comes to heteroatoms
3. EasyChem - too weird
4. XDrawchem - excellent portability, bad resolution, unstable, good drawability, but unacceptable because the development seems to have ceased
5. JChempaint - can't remember ... but there must have been some reason why I'm not using it

Again, I'm very grateful for these developers, but I'm in a situation where I'm forced to be picky! And I admit I'm picky in general.

Hope this list is somewhat useful...
My favorite is GChempaint even though it's not very usable for the reasons stated. GUI is excellent. BKChem is nice and probably most promising in my eyes.

[tak1150]

Oh, I have tried ISISDraw with Wine as well. But it has the same problems as ChemSketch.

My philosophy is that if a software has all of the needed features, I don't mind running it under Wine. But if there is one feature missing, it's not really worth it for me to have to resort to Wine (because of the inherent instability from having another layer). Whereas a Linux native software may be tolerated with one missing feature or so.

[LaserJock]

<snip>
Softwares I've tried: (well either way, I still need chemdraw, but had to try these for my curiosity)

1. BKChem - great portability, but bad resolution, somewhat unstable, ok drawability
2. GChempaint - so so portability, ok resolution, good drawability, but bad when it comes to heteroatoms
3. EasyChem - too weird
4. XDrawchem - excellent portability, bad resolution, unstable, good drawability, but unacceptable because the development seems to have ceased
5. JChempaint - can't remember ... but there must have been some reason why I'm not using it

Again, I'm very grateful for these developers, but I'm in a situation where I'm forced to be picky! And I admit I'm picky in general.

Hope this list is somewhat useful...
My favorite is GChempaint even though it's not very usable for the reasons stated. GUI is excellent. BKChem is nice and probably most promising in my eyes.

Thanks for the review, I'm often amazed at how many apps we have for essentially the same task, and yet many just seem to fall short of the "standard". I'm curious, what version of gchempaint did you try? I'm a contributor to gchemutils (which has now incorporated gchempaint) and an Ubuntu developer so I'm especially interested in getting gchempaint in better shape in Ubuntu.

The latest release of gchempaint, 0.8, has quite a few improvements and I think the 0.10 release will be a significant leap forward. In the CVS branch we are working on more/better templates, better reaction rendering, OpenOffice.org copy-n-paste support, Wikipedia image integration, similar structure searches and CAS lookup for starters. As you can imagine right now all of this is a bit unstable do I don't recommend using gchempaint from CVS for production work, but testers are always welcome and the lead developer is quite responsive.

Anyway, my $0.02

-LaserJock