Re: [Blue-obelisk] Moleculedatabase of a polish contributor
Le dimanche 5 novembre 2006 16:24, Carsten Niehaus a écrit : > Am Sonntag 05 November 2006 16:14 schrieb Daniel: > > 2006/11/5, Carsten Niehaus <[EMAIL PROTECTED]>: > > Hey Danial, I am CCing this mail to BlueObelisk. > > > > So you are creating a database of properties (density...) of many > > > chemical compounds, basically "Kalzium not for elements but for > > > compounds", right? > > > > Exactly. > > > > > I think after one year, there will be minimum 1000 compounds. > > > > > > > Encyclopedia on hard disc something like links I wrote over. > > > > > > A forum-database sucks, we need to agree on a common file-format. .mol > > > and .cml are the best im my opinion because they are made for this. > > > Many many > > > applications includling Kalzium can handle such files. > > > > I agree with you, that forum-database sucks, so I wanted to make this > > program. > > So, you are doing such database, I would like to create? Something like > > our forum-database? > > We are collecting "molecules" in the form of files in a XML-based language > called CML (Chemical Markup Language). > > > > So you and those other 5999 guys should think about adding files to our > > > database. It is under an opensource-licence and totally free of any > > > restrictions. > > > > How can I get this program? > > There is a public subversion (svn) server for this, look at > www.blueobelisk.org > > This is not a programm, it is just a collections of files, nothing more. > Pretty much every chemistry-application including Kalzium and GChemical can > read those files and for example render it in 3D. > > > How can I add the new files? > > You send a file to the list (see below) or contact the guy who is mainly > maintaining the database. > > > How much weight one file? > > Filesize? Minimal, perhaps 1kb per compound? > > > Is it possible to add inorganic compounds? > > yes > > > Is it difficult to add new compound? > > no, in most cases you just need the SMILES notation and run an app over it. > That app gives you the valid CML-file. Thats it. For the chemical-structures project, you can send ghemical files, as each structure is minimized with MOPAC/PM3 or CML files. You can also send me an email with a list of compounds. I will generate the files. > > Is there polish version? Could we add only polish files? > > Well, only the name is polish, right? Currently, the names are only > available in english, german and french, but that is just because we don't > speak polish. Of course, you are more than welcome to add the polish names! A new language is easy to add. For example, edit the directories.xml file. You will see some lines like Polish. Copy and modify like this: Polski > We coordinate everything on this list: > > [EMAIL PROTECTED] Cheers, Jerome Pansanel ___ Blue-obelisk mailing list [EMAIL PROTECTED] http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Spread Blue Obelisk
Hi, I have added two small icons on BO wiki. This icons (or logo) could be used on website to promote Blue Obelisk. http://wiki.cubic.uni-koeln.de/bowiki/index.php/Logos What are you thinking about ? Jerome Pansanel ___ Blue-obelisk mailing list [EMAIL PROTECTED] http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Java press release
Hi, http://www.sun.com/smi/Press/sunflash/2006-11/sunflash.20061113.1.xml Happy reading ! Jerome Pansanel ___ Blue-obelisk mailing list [EMAIL PROTECTED] http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Lanthanides and actinides in BODR
Hi, Here's a definition taken from the "Handbook of Chemistry and Physics": Lanthanide series (Lanthanides) - Rare earth elements of atomic numbers 57 through 71, which have chemical properties similar to lanthanum (#57). Actinide series - Elements of atomic numbers 89 to 103 analogous to the lanthanide series of the so-called rare earths. Jerome Pansanel Le lundi 8 janvier 2007 03:32, Jordan Mantha a écrit : > Hi all! > > I've been doing a little work on adding various color schemes to the > periodic table app in gchemutils. The first color scheme that I did was > the families (noble gas, alkali metals, etc.) from BODR. Jean Bréfort > noticed that the Actinides were classified as Rare Earths, resulting in > a bug report [0]. I then got to looking at the BODR families a little > bit more. I was wondering if Rare Earths should be replaced with > Lanthoids (or Lanthanides) and Actinoids (or Actinides)? Egon asked me > if I could find any definitive reference (IUPAC or at least a journal > article) that would shed some light but I couldn't find much. A search > of IUPAC's website shows that they use the terms "Actinides" and > "Lanthanides" quite a bit. Wikipedia seemed to have a good family > breakdown [1]. Other resources I found were [2] and [3]. Anybody else > have a definitive resource of idea on getting a more "solid" reference > for the elemental families? > > -Jordan Mantha > > [0] > http://sourceforge.net/tracker/index.php?func=detail&aid=1603063&group_id=2 >0024&atid=120024 [1] http://en.wikipedia.org/wiki/Periodic_table > [2] http://www.webelements.com/ > [3] http://periodic.lanl.gov/default.htm > ___ > Blue-obelisk mailing list > Blue-obelisk@hardly.cubic.uni-koeln.de > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Lanthanides and actinides in BODR
Bibtex entry:
@Book{0849307406,
author = {Weast R.C.},
edition = {1st Student Edition},
editor = {CRC Press, Inc},
title = {Handbook of Chemistry and Physics},
year = {1988},
isbn = {0-8493-0740-6},
note = {A ready-reference book of chemical and physical data}
}
Le lundi 8 janvier 2007 12:27, Egon Willighagen a écrit :
> On Monday 08 January 2007 10:52, Jerome Pansanel wrote:
> > Here's a definition taken from the "Handbook of Chemistry and Physics":
>
> OK, that should do.
>
> What is the full bibtex entry for that book?
>
> Egon
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Re: [Blue-obelisk] A BODR project on SF?
Hi Egon, Great idea ! Go on ! Jerome Le mercredi 7 février 2007 07:58, Egon Willighagen a écrit : > Hi all, > > a number of bugs have been reported in the past for BODR, and a few more > reports were announced earlier this week. While the BO mailing list is the > obvious and true ML to use, and we also have SVN, BODR really needs a BTS > too. > > I have been thinking of simply setting up a SF project for just the BODR > project. Now that it is entering the first Linux distribution (Debian), and > that it even is mentioned in LinuxFormat, it really seems to take off now, > and a separate project page does not seem too bad. > > If no one disagrees within the next few days, I'll go ahead. If you support > this proposal, please let that be know too :) > > Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] KOpenBabel: a new building block for a chemistry-aware desktop
Hi, KOpenBabel is a graphical interface to Open Babel. It permits the conversion of chemical files (more than 70 file formats are supported). KOpenBabel is divided in three parts: - KOpenBabel3: a KDE3 interface - KOpenBabel4: a KDE4 interface - QOpenBabel: a Qt4 interface KOpenBabel3 and QOpenBabel are the most advanced projects. Translastions are available in french and german. All basic features are working (file conversion, format guessing). All packages are released under the GNU Public License. QOpenBabel has been successfully compiled on Microsoft Windows XP. The compilation on Mac OS X must be also possible, but no test has been done. You can find further details about this project on: http://kopenbabel.sourceforge.net/ Here's also an interesting hack for KDE: Place in your konqueror/servicemenus directory the file "chemical-cml-convert.desktop": [Desktop Entry] Encoding=UTF-8 ServiceTypes=chemical/x-cml Actions=Convert [Desktop Action Convert] Name=Convert chemical file Exec=kopenbabel Icon=background This permits you to directly add a new item "Convert chemical file" in the Actions menu when you right-click on a CML file. Cheers, Jerome Pansanel ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Chemical Structures: release v2.0
Hi, The new version 2.0.0 of Chemical Structures released today. This release has many new features and fixes: - the project contains 524 structures - the build system is based on CMake - the user interface has been improved by using a new html design - SMILES string is displayed on the molecule page - Python scripts are used to generate html pages (instead of XSLT) - name and formula indexes are available - many bug fixes - ... For an online version, visit the project home page: http://chem-file.sourceforge.net/ The last version can be downloaded on this page: https://sourceforge.net/project/showfiles.php?group_id=169897 About Chemical Structures: The Chemical Structures project aims to provide a complete set of molecular structures. The version 2.0 contains over 500 structures of organic compounds. In addition to structural data, each file contains complementary informations, like molecular weight, boiling point, melting point or InChI code. Chemical Structures is part of the Blue Obelisk Data Repository. Cheers, Jerome Pansanel ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] From APBS/PyMOL to Jmol and the web
A message from the PyMOL list (many occurences of Jmol). Jerome -- Message transmis -- Hi everyone, Today the American Chemical Society's Chemical Biology published their second set of interactive structure figures (disclosure: adapted for Jmol by yours truly) in their March issue. These figures incorporate molecular electrostatic potential maps calculated with the APBS plug-in for PyMOL, written by Michael Lerner. This is thanks to Michael's ready cooperation and Bob Hanson's tireless development of Jmol. The figures are available at the following URL (subscription required): http://pubs.acs.org/cgi-bin/article.cgi/acbcct/2007/2/i03/html/ cb700012y.html The paper is Mechanistic and Structural Basis of Stereospecific Cβ- Hydroxylation in Calcium-Dependent Antibiotic, a Daptomycin-Type Lipopeptide, by Matthias Strieker et al. See figures 4 and 7. ACS Chemical Biology is leading the way in providing interactive 3D renderings of authors' structure figures, complete with custom controls that make use of many powerful aspects of Jmol and 3D visualization in general. If you'd like to support Chemical Biology's efforts, please spread the word to colleagues about the journal and their commitment to this technology. Thank to the PyMOL community for answering my posts so promptly and helpfully, making the MEP figures possible. Best, Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// --- ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] promoting Blue Obelisk
Le lundi 26 mars 2007 15:35, Dr P. Murray-Rust a écrit : > I'm looking forward to meeting on Tuesday. One thing I would like to > promote is the use of the Blue Obelisk in our activties. Yes, I haven't > done anything yet either. This could be in readme files, an additional logo > on the home page of software, etc., links from our home pages. > > Any suggestions before the meeting... > > P. There is a logo available on: http://wiki.cubic.uni-koeln.de/bowiki/index.php/Logos A good way to promote Blue Obelisk would be to have a link to BO papers. This week, I'm installing a Free Software for chemical library management (CLM) at Toronto SGC group. It use JChemPaint and Jmol applets. I'll add links to the software websites and to BO home page on this CLM system. Cheers, Jerome Pansanel ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Re: Chemical test file repository
Le lundi 16 avril 2007 19:35, Geoffrey Hutchison a écrit : > On Apr 16, 2007, at 12:10 PM, Daniel Leidert wrote: > [...] > >> If this sounds good, perhaps we should add a new directory to the > >> BODR for this and start importing from OB and other projects. Perhaps > >> Peter can contribute a variety of CML examples (including both old > >> and new ones)? > > > > FACK. Base structure > > ... This can be really useful for other projects managed by BO members, like KFile-Chemical. So, it would be good idea to include them into BODR. Jerome Pansanel > > > or similar, as you suggested? > > I have some "invalid" examples which are just random binary data and > I use them on every file reader. It's a great way to be sure it > rejects invalid data and doesn't crash. Similarly, I have an empty > file -- in some formats, this is valid, but most it is not. > > That's why I was suggesting something like: > > valid/pdb_2.2 > valid/mdl_2000 > valid/xyz > valid/cml_2.0 > invalid/ > nonstandard/mdl > nonstandard/pdb > > Cheers, > -Geoff > ___ > Blue-obelisk mailing list > Blue-obelisk@hardly.cubic.uni-koeln.de > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Relocation of mailing list?
Hi, I can provide also hosting at the Department of Chemistry, Strasbourg University. Jerome Pansanel Le mardi 8 mai 2007 02:54, Geoffrey Hutchison a écrit : > On May 7, 2007, at 5:39 PM, Noel O'Boyle wrote: > > Do others agree? Several universities (e.g. Cambridge) provide Mailman > > mailing lists so it shouldn't be difficult to find a suitable location > > with zero maintenance required. > > I've also offered to host either the mailing lists or whole > blueobelisk.org domain (SVN, wiki, etc.). My hosting plan for my > personal domain is pretty much unlimited. (I also think they're more > reliable than SourceForge generally.) > > But it's definitely something we should consider pretty soon. > > Cheers, > -Geoff > ___ > Blue-obelisk mailing list > Blue-obelisk@hardly.cubic.uni-koeln.de > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Blue Obelisk SF project approved. Ready to start moving.
Le mercredi 16 mai 2007 15:58, Christoph Steinbeck a écrit : > Our SF project blueobelisk.sf.net has been approved and we now have a > SF-based platform. > Let me know who wants to take responsibilities. I'm using daily the SF website, so I can and I would like help the BO project on SF. My username is pansanel. > I have added PeterMR and EgonW to the project as project admins, but > clearly, we need more here. > > A minor question: Is [EMAIL PROTECTED] ok for our new > mailing list. It needs to be [EMAIL PROTECTED] We can > only choose the "something" part :-) That's a fine name. OpenBabel has the same suffix. > I' going to submit a support request regarding the move of the archives. > Hope that'll work, but since both systems are mailman based, it might. > > Cheers, > > Chris Cheers, Jerome Pansanel ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
