Obstacle for chemists to use Ubuntu = ChemDraw

[lastpook]

Thanks!

[Captain_Rage]

Many thanks for posting the PPA address! Though I wonder why GChemPaint isn't in the official Ubuntu repositories...

[LaserJock]

Many thanks for posting the PPA address! Though I wonder why GChemPaint isn't in the official Ubuntu repositories...

It is in the official Ubuntu repositories (gchempaint) but we use the PPA to provide newer versions where we can for stable Ubuntu releases. Ubuntu's update policy is fairly strict and doesn't generally allow completely new software releases, only critical bug fixes.

[repunante]

For years and years I was using all the list of software available in Linux to draw structures of molecules, changing from one to another again and again. It was impossible to find a proper one: not enough features, annoying interfaces, poor quality of the results,...
So at the end I was using chemdraw for windows with wine, having good results but feeling a bit uncomfortable, you know, I don't like to run something from Windows in Linux, call it scrupulousness maybe.

Today I tried Bkchem, I think this it is the 4th time I tried it in several years. I always had problems with it, maybe because I run it with Gnome the lines are crap (the letters are nice though). The main problem was the stability, it always crashed for no apparent reason.
Today it didn't crash, it wash smooth and stable, I couldn't change the kde feeling but at least it was working. My surprise was that I could do everything I needed, write heteroatoms directly to the structure, scale some molecules leaving the others with the original size, put brackets, move the structures easily, rotate them ... in the chemdraw way: intuitive and easy.

The only bad thing was that I couldn't copy the scheme directly to openoffice but I save it to a svg file and I pasted it in the document with an excellent quality. It was strange for me, because the lines looked awful in Bkchem but in openoffice looked quite neat. I printed it out and now I have it in front of me: I cannot believe the result, just perfect.
Bkchem made my day.

PS. sorry about the possible mistakes in my narration, I'm learning slowly.

[billyjmc]

@repunante,

This is very similar to my experience. BKchem doesn't look too nice on-screen, but you can't argue with the results. I love that it natively saves the product in SVG. It makes it easy to process into something else, like PDF or PS for inclusion in a LaTeX document. (Also, the project has recently been taken over by a new programmer, so it's likely to see some more updates in the near future. Woo!)

I've found that MarvinSketch is too clever for its own good. Sometimes I want to simply write free-form labels instead of actual atoms or functional groups. And I don't like how the "atoms" are centered in their locations -- left-align, please. Finally, converting them to a reasonable vector graphic form that I'm satisfied with has been somewhat painful, but certainly not insurmountable.

With that all said, I have scripts and makefiles for doing the heavy lifting for all these conversions. Maybe someone will find them useful...

http://people.tamu.edu/~bjmcculloch/

[billyjmc]

I'm now using ChemDraw on Linux. My version of Wine (1.1.42) works fine (if a but slow on startup) for CD7, which is sufficient for my purposes.

Perhaps more interestingly, though, for all those fans of TeX et al., is that I've managed to script the conversion from native CDX format to any filetype ChemDraw is capable of.

I've detailed the procedure at my website (URL below), but will give a summary here for archival purposes.

http://people.tamu.edu/~bjmcculloch/

cdx2eps.pl

#!/path/to/windows/version/of/ActivePerl/perl.exe
# Usage: cdx2eps.pl <input document 1> [input document 2] [...]

use strict;
use warnings;

use Win32::OLE;
use File::Basename;
use Cwd 'abs_path';

my $ChemDraw = Win32::OLE->new('ChemDraw.Application', 'Quit');

foreach ( @ARGV ) {
    my $absolute = abs_path($_);
    my ($filename, $directory, $suffix) = fileparse($absolute, ".cdx");
    my $input = $directory . $filename . $suffix;
    my $output = $directory . $filename . ".eps";
    $ChemDraw->Application->Documents->Open($input)->SaveAs($output);
}

One caveat here is that even though I've given the "Quit" command to Chemdraw, it never does (Wine has a few bugs when working with COM Automation, apparently). You can kill it of course, but that's a pain. You also can't, as far as I can tell, specify options for the save process, e.g. resolution of a PNG. Otherwise, this works great. ChemDraw is smart enough to output the proper filetype based on the output filename.

[mfomich]

Hi!
My problem is that the window of ChemDraw 7 under Wine is almost totally invisible. It means I see only a kind of refraction. Any suggestions please?

Ubuntu 11.04
Wine 1.2.2
ChemDraw 7.0

UPD. Sorry. I had to wait more. The start was quite sluggish. Finally, it worked fine.

[repunante]

@repunante,

This is very similar to my experience. BKchem doesn't look too nice on-screen, but you can't argue with the results. I love that it natively saves the product in SVG. It makes it easy to process into something else, like PDF or PS for inclusion in a LaTeX document. (Also, the project has recently been taken over by a new programmer, so it's likely to see some more updates in the near future. Woo!)

I've found that MarvinSketch is too clever for its own good. Sometimes I want to simply write free-form labels instead of actual atoms or functional groups. And I don't like how the "atoms" are centered in their locations -- left-align, please. Finally, converting them to a reasonable vector graphic form that I'm satisfied with has been somewhat painful, but certainly not insurmountable.

With that all said, I have scripts and makefiles for doing the heavy lifting for all these conversions. Maybe someone will find them useful...

http://people.tamu.edu/~bjmcculloch/

I tried ChemDoodle for Linux and it is awesome. Not free but very very cheap.

[yeayea]

Hey All,

For those of you who are still interested in running ChemDraw in Ubuntu, I have ChemDraw 12 up and running with Wine 1.4 in Ubuntu 12.04!

Check out the WineHQ page on ChemDraw 12

I followed the instructions and installed from the .msi file and everything is working fine! The anti-aliasing was not working at first, but after installing .NET 2.0 with winetricks the structures look pretty good.