Re: [ccp4bb] Alternatives to ChemDraw 3D
You can build any 3D molecule easily in Discovery Studio Visualizer - It is free but not for Mac OS I have been pretty impressed with Discovery Studio Visualizer and feel that it can serve as a nice compliment to Pymol. I wrote up a brief overview and comparison between the two programs here: http://bit.ly/QgvNL I also covered the selection feature in DSV: http://bit.ly/4UIzcd Cheers, Sean
Re: [ccp4bb] Alternatives to ChemDraw 3D?
On Feb 7, 2010, at 11:13 PM, Wataru Kagawa wrote: Hi all, I would like to create a pdb file for a chemical compound (FW ~600) that was created in our chemistry department. ChemDraw 3D appears capable of doing this, but I would like to know if there are free alternatives that work great on Macs. Any info would be greatly appreciated. Thanks. Wataru Hi Wataru-san: Three easy steps: 1. Define a SMILES string for your compound. The java molecular editor makes this easy: http://www.molinspiration.com/jme/ 2. Paste the smiles string into COOT, or feed it into phenix.elbow 3. Output the pdb file. COOT is faster but phenix.elbow allows you to minimize the structure, even using third-party QM programs like GAMESS. I trust all is well. Bill
Re: [ccp4bb] Alternatives to ChemDraw 3D? Yes, Chemdoodle!
Alternatives to ChemDraw 3D? Yes, ChemDoodle! I installed XDrawChem on Mac OSX 10.4.11 but it crashes all the time which is somewhat annoying. Then I finally stumbled upon ChemDoodle *which is not for free* but the trial version solved my problem at that time. Having worked with it, I really liked it so much that I finally purchased it for 60 US$. You only pay this amount once, software updates are for free. Hope this helps. - Jeroen - Wataru Kagawa wrote: Hi all, I would like to create a pdb file for a chemical compound (FW ~600) that was created in our chemistry department. ChemDraw 3D appears capable of doing this, but I would like to know if there are free alternatives that work great on Macs. Any info would be greatly appreciated. Thanks. Wataru ~ Wataru Kagawa, Ph. D. Waseda University Graduate School of Advanced Science Engineering 2-2 Wakamatsu-cho, Shinjuku-ku Tokyo, Japan 162-8480 tel. 03-5369-7369 (ext. 3241) fax. 03-5367-2820 ~ -- Dr. Jeroen R. Mesters Gruppenleiter Strukturelle Neurobiologie und Kristallogenese Institut für Biochemie, Universität zu Lübeck Zentrum für Medizinische Struktur- und Zellbiologie Ratzeburger Allee 160, D-23538 Lübeck Tel: +49-451-5004065, Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
Re: [ccp4bb] Alternatives to ChemDraw 3D
This may be somewhat convoluted but for this exact purpose try ZINC. For other drawing things then yes use one of the other packages http://zinc.docking.org/ Draw the molecule using the widget, save the smiles file and let their server make the 3D version for you, properly protonated etc. And you get things like logP, and other descriptors as well. true you get it as .mol2.gz or .sdf.gz but babel is your friend -Martin
Re: [ccp4bb] Alternatives to ChemDraw 3D
There are several more options to create 3D coordinates from it's 2D drawing: You can build any 3D molecule easily in Discovery Studio Visualizer - It is free but not for Mac OS there is nice server called Frog, that convert 2D to 3D and can build set of conformers http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog2 Corina is another server that do simple 2D to 3D conversion http:// www.molecular-networks.com/online_demos/corina_demo and you have the PRODRG server http://davapc1.bioch.dundee.ac.uk/ prodrg/ that can convert 2D to 3D and in addition can create topology file in many formats (e.g GROMACS, CNS...). PRODRG support only common atom types (N, C, O, S, P, Cl, I, Br, F) Rotem - Rotem Sertchook, Ph.D. Bioinformatics Unit, Biological Services Weizmann Institute of Science, Rehovot 76100, Israel. -
[ccp4bb] Alternatives to ChemDraw 3D?
Hi all, I would like to create a pdb file for a chemical compound (FW ~600) that was created in our chemistry department. ChemDraw 3D appears capable of doing this, but I would like to know if there are free alternatives that work great on Macs. Any info would be greatly appreciated. Thanks. Wataru ~ Wataru Kagawa, Ph. D. Waseda University Graduate School of Advanced Science Engineering 2-2 Wakamatsu-cho, Shinjuku-ku Tokyo, Japan 162-8480 tel. 03-5369-7369 (ext. 3241) fax. 03-5367-2820 ~
