Obstacle for chemists to use Ubuntu = ChemDraw

[barbarosreis]

hey;
I am very new to linux-almost 30 mins- and i first checked chem draw or any equivalent program at ubuntu. and read your posts but i couldt get what should i do.

as i understand we can use chemdraw but we should do something tricky.

if someone tell what should i do. i will be very close to uninstall win.

thanks

[canakas]

Hello there,

Wow 30min you are brave! =)
it took me a year of much frustration to gain the knowledge I needed to be able to get ChemDraw11 to work...I also had help from mister_pink here on the forum.

I think a little searching around the ubuntu/wine guides should help you understand the recipe in a better way than I am able to explain...sorry about that.

but I would recommend that you go for something a little less unstable if you want to do some serious chemistry work in linux...

Several nice softwares were mentioned earlier in this thread I believe
Maybe the Marvin-bundle suits your needs...

by the way
CD 12 is out.. I will post back here when I do try it in Wine.

mister_pink: have you installed it yet?

cheers

[barbarosreis]

I even didnt know how diffucult to use chemdraw on ubuntu.

I checked bkchem and gchempaint. they are nice but i cant something i easy do in chemdraw.

in bkchem you cant rotate a part of molecule even if you select a part of molecule program rotate all of it.

sometimes bond angles not so correct i know chemdraw not a genius for that but it's much better especially when heteroatom is encounter.

and nmr predict is a good properties for chem draw sometimes help me to faster decisions.

converting molecule name to structure and structure to name also is very useful.

sure, one of the biggest problem is that these softwares cannot open or save cdx format -chemdraw-

are there any more option i can check

[canakas]

I completely agree with you.
I don't know of any native linux chemistry application that can do what we can do in ChemBioDraw...

You can try MarvinSketch from the JChem-suite from ChemAxon... it is free you just have to register and a few things... It is not as good a GUI as CD, but it has some nice features like pKa-estimation. It also works pretty well with its brother MarvinSpace (like a simple Chem3D), although the structure optimization algorithms are not the strongest.

[mister_pink]

Unfortunately I no longer do chemistry, so I don't have access to chemdraw. Would be interested to know if anyone gets it working properly though.

[rutulian]

Just noticed this thread. My $0.02....

I'm writing my dissertation. The Marvin-suite is awesome!!!! Yes, ChemDraw is the standard, but I've been doing some cheminformatics work, and the Marvin tools are far better suited to the task then the Cambridgesoft stuff. ChemDraw itself is nice, but I've always hated everything else from them: Chem3D, ChemFinder, etc.... And the constant activation nagging really irks me. It's designed to be Windows-only software, so it has a lot of annoying Windows-isms. MarvinSketch is a bit different. If you're used to ChemDraw, it might be a bit frustrating at first. But when you get used to the flow, the interface is actually very efficient and nice. And the figures it generates are very nice (high resolution bitmaps or vector-based, your choice).

My current workflow:
1) Structures drawn in MarvinSketch --> Stored in an InstantJChem database
2) With the database I can easily sort and query for particular structures and add metadata like entry #'s and NMR data. If you process your NMRs with MestRec (yes, it works in Linux too!) and store them as a .png or whatever, you can link them to your records in InstantJChem so that you can quickly retrieve the NMR for any given compound in the database.
3) Use MarvinSketch again to assemble the reaction schemes
4) Use the included MolConverter program to export the .mrv files to .svg files, and then use Inkscape to convert those to .eps files
5) Use latex with the chemstyle package to automatically manage the compound numbering and referencing

There are some issues....
1) MarvinSketch doesn't have precision alignment tools, so the schemes can be a little painful. I guess it depends on how OCD you are. I was able to manage, but some more of the common vector illustration tools would be nice (keyboard positioning, alignment and distribution of groups, rulers, guides, snap to grid, etc). Maybe those will come in a future release.

2) Also, MarvinSketch doesn't export directly to EPS. It does export to PDF, but depending on what you are doing, that may not be good enough. The chemstyle package, for example, uses the PSFrag utility which, of course, only works on postscript files. The SVG route is a usable workaround, but then you have to add Inkscape processing to your workflow. Every additional step is more time....

3) InstantJChem doesn't support fields with rich text. In many cases this is just aesthetic, but it really helps when you are storing NMR data.

Anyhow, that's a bit longwinded, but I just thought I should put in a plug for ChemAxon. Running programs critical for my work under WINE is not particularly desirable to me. Of the available tools that run natively under Linux, ChemAxon's are definitely the best. Yes, I've tried them all. GChempaint is promising, but it needs a lot more work.

[lastpook]

Hello, everyone
Does anybody know if GChemPaint works with Karmic Koala? I have totally failed with installation (it seems like package 'gcu' is named 'gcu-bin' now and therefore ./configure returns error all the time)

As for Marvine. Really rocks after I have realized how to use shortcuts for radicals

[jbrefort]

Seems there is no gchempaint package in karmic. You might try one from debian (testing has 0.10.9 which is ways better than 0.8.6, but you will need to update gcu-bin at least to the same version).

Replying to the previous post, I'd say that I agree that gchempaint needs a lot more work. May be it will never reach a full-featured state just because it is a one man project. I failed to find other interested developers.

[lastpook]

Seems there is no gchempaint package in karmic. You might try one from debian (testing has 0.10.9 which is ways better than 0.8.6, but you will need to update gcu-bin at least to the same version).

I have installed 0.10.9 and 0.10.8 in Karmic but unfortunatelly after installation none of the applications can be launched.

gchempaint-0.10: error while loading shared libraries: libgchempaint-0.10.so.0: cannot open shared object file: No such file or directory
gchem3d-0.10: error while loading shared libraries: libgcu-0.10.so.0: cannot open shared object file: No such file or directory
gchemcalc-0.10: error while loading shared libraries: libgcu-0.10.so.0: cannot open shared object file: No such file or directory

Where one can get these libraries for Ubuntu 9.10?

After using Marvin for a while I've found that there is no way to draw multistep retrosynthetic schemes. weird, isn't it?

[LaserJock]

For people wanting GChemPaint for Ubuntu 9.10, I've just uploaded it to the Debichem PPA. If you're running Ubuntu go to the Software Sources and add ppa:debichem/ppa in the third party tab. Reload the repositories and install/upgrade gchempaint. For command line users you can use the following:

sudo add-apt-repository ppa:debichem/ppa
sudo apt-get update
sudo apt-get install gchempaint

That repository also has Avogadro, the awesome 3D molecular editor, that people might also find useful.

Hope that helps,

LaserJock