Chemistry software

[ionophore]

Anyone know of a good chem-draw type of thing for linux? I am a chemistry graduate student and need to be able to draw structures.

[MetalMusicAddict]

Gnome Chemistry Utils (http://www.nongnu.org/gchemutils/) might help you. Our very own MOTU great LaserJock helps on this project. It should end up in Feisty.

[jpkotta]

https://help.ubuntu.com/community/UbuntuScientists

[mips]

http://www.ubuntuforums.org/forumdisplay.php?f=169

Look at the Sticky Threads

[matthew]

Anyone know of a good chem-draw type of thing for linux? I am a chemistry graduate student and need to be able to draw structures.
Look at a package called "chemtool" and see if it does what you need.

from a terminal:
sudo apt-get install chemtool

[newbie2]

http://xdrawchem.sourceforge.net/
http://sourceforge.net/softwaremap/trove_list.php?form_cat=384

[LaserJock]

Here's what I'd use in order of preference:
1. BKchem (not in Ubuntu quite yet, but really good) - http://bkchem.zirael.org/
2. xdrawchem
3. chemtool

You might just try them and see which you like best.

MetalMusicAddict was a little premature in his recommendation of gchemutils. I am indeed working with the author on that project but it hasn't incorporated it's sister project gchempaint yet. gchempaint is a really good molecular drawing app but the Ubuntu version is very outdated. The next release of Ubuntu in April should have it though.

-LaserJock

[RAV TUX]

Anyone know of a good chem-draw type of thing for linux? I am a chemistry graduate student and need to be able to draw structures.
you could use the live DVD's Quantian (http://dirk.eddelbuettel.com/quantian.html) or XPLORA (http://rds.yahoo.com/_ylt=A0oGkljqr4RFKHYBXlFXNyoA;_ylu=X3oDMTB2ZjQ4dDE xBGNvbG8DdwRsA1dTMQRwb3MDMgRzZWMDc3IEdnRpZAM-/SIG=12f5d01f2/EXP=1166410090/**http%3a//www.xplora.org/ww/en/pub/xplora/library/software.htm) they will have every imaginable science program you need...

[RAV TUX]

also try VigyaanCD:

Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry.
http://www.vigyaancd.org/
http://www.vigyaancd.org/chem.html
http://www.vigyaancd.org/download.html



What is Vigyaan? What is VigyaanCD?
Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry. It has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling software. VigyaanCD v1.0 is based on KNOPPIX (http://www.knoppix.org/) v3.7.
Note: Users do not need to change anything on their hard disk (and do not need to install Linux) to use VigyaanCD.

What is the latest version?
Stable version is: v 1.0 (20050907)

What software is available on VigyaanCD?
At present the following ready to use software comes on VigyaanCD: Arka/GP, Artemis, Bioperl, BLAST (NCBI-tools), ClustalW/ClustalX, Cn3D, EMBOSS tools, Garlic, Glimmer, GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, Jmol, MPQC, MUMer, NJPlot, Open Babel, Octave, PSI3, PyMOL, Ramachandran plot viewer, Rasmol, Raster3D, Seaview, TINKER, XDrawChem, Xmgr and Xfig. GNU C/C++/Fortran compilers and additional Linux tools (such as ps2pdf) are also available.

VigyaanCD also provides tools required to compile and install other applications (from source). Therefore, making testing of 'Linux' applications possible on computers with other OS.

Do you have Demos and Tutorials?
Yes. Instructions and sample files required for quick start are available on CD. Detailed tutorials are also available.

How much does it cost?
VigyaanCD is free. Obtain your free copy from here (http://www.vigyaancd.org/download.html).

Do I need to install VigyaanCD on my computer to run it?
No. You can directly run VigyaanCD by booting the computer from CD-ROM without installing anything on your hard-disk. When done, simply remove the VigyaanCD and reboot the computer. Your computer will boot normally.

What do I need to run VigyaanCD?
You need to download the latest Vigyaan ISO and burn it on to a CD. (If you have not burned a bootable ISO image onto a CD before or are having problems buring image on Windows computer, please read this (http://www.vigyaancd.org/faqs.html#burn).) The hardware requirements are as following:
Intel-compatible CPU (i486 or later),
20 MB of RAM for text mode, at least 96 MB for graphics mode (256 MB recommended to use the various graphical software),
bootable CD-ROM drive, or a boot floppy and standard CD-ROM (IDE/ATAPI or SCSI),
standard SVGA-compatible graphics card,
serial or PS/2 standard mouse or IMPS/2-compatible USB-mouse. Do I need to have/install Windows or Linux on my computer to use VigyaanCD?
No. All the software needed to start the workbench are present on the CD.

I don't have root/administrative privilege for the computer, is that a problem?
No. All you need to do is boot the computer from CD.

What about VigyaanCD license?
If not otherwise specified, the software on the CD falls under the GNU GENERAL PUBLIC LICENSE (GPL) (http://www.gnu.org/copyleft/gpl.html). Similar to other Open Source licenses, this means that you can copy, modify, redistribute and even resell the CD without restrictions, as long as the recipient receives the same license. The source code of the standard packages on the CD are available from their respective original providers.

[spendrup]

I use a tool called Marvin, which is free for academic purposes.
The molecule structures look much better than those of Xdrawchem and Chemtool and it's very easy to use. You can export to various formats like png or jpeg.

You can download it here:
www.chemaxon.com/

I think the stand-alone program is called MarvinBeans

(Isis Draw also works on Linux)

[lbyrd33]

Im also a grad student in chemistry and I have used xdrawchem which is nice because one can directly export the files to ChemDraw. Actually, last week I was able to install ChemDraw office using Crossover Office.

[kayvee]

I got to this thread after googling for chem draw alternatives for linux and I should say, MarvinSketch looks very good followed by BK Chem for the purpose to making chemistry structures. Thank you for the suggestion

[RichardLinx]

You might like kalzium:
http://edu.kde.org/kalzium/screenshots.php

It contains information about 103 chemical elements, including mass, charge, picture, discovery information, chemical and energy data, and a model of the atom. The table itself can be configured to display numeration, state of matter, and colour-coding in various ways. Additionally, a date index is available, allowing only elements discovered up to a defined year to be shown.

[Hallvor]

http://www.redbrick.dcu.ie/~noel/linux4chemistry/

[xjian77]

Not really related. But pymol crashed after upgrade to maverick. I got the X-windows restarted after trying to run pymol. I had tried to build from the source. The build process went through rather smoothly. However, the same thing happened again.
I would like to see whether other people would see the same thing or not.