As a person who wears two hats- "we- the crystallographers" and "they- the bioinformaticians" it is interesting to see that the world can be divided by one of the most trivial issues- coordinate formats! Enjoying the debate :)
Shekhar On Sun, Jan 6, 2013 at 8:02 PM, Boaz Shaanan <bshaa...@exchange.bgu.ac.il>wrote: > Dear George, > > "Those folks" (bioinformaticiens ?) are not interested in inter-molecular > contacts, as far as I'm aware so they can't bothered less by the orthogonal > coordinates used in pdb files. > > Cheers, > > Boaz > > *Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaa...@bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 * > ** > ** > * > > * > ------------------------------ > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of George > T. DeTitta [deti...@hwi.buffalo.edu] > *Sent:* Sunday, January 06, 2013 3:48 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Who invented PDB format? > > While it is certainly a simple coding job to convert back and forth > between orthogonal and fractional coordinates there is perhaps something > lost in the former and that is the notion of a molecule embedded in a > crystal structure. Generally speaking, it's the latter that we determine. > George may well be right that orthogonalization made it easier for those > non-crystallographers who use structures but I wonder if those folk are > aware of all the information about intermolecular contacts that you lose by > looking at the molecular structure only. Sure, you can recover that > information from orthogonalized coordinates (please consult a > crystallographer if you are in need of guidance) but will you? > Sent via BlackBerry by AT&T > ------------------------------ > *From: *George Sheldrick <gshe...@shelx.uni-ac.gwdg.de> > *Sender: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> > *Date: *Sun, 6 Jan 2013 09:57:28 +0100 > *To: *<CCP4BB@JISCMAIL.AC.UK> > *ReplyTo: *George Sheldrick <gshe...@shelx.uni-ac.gwdg.de> > *Subject: *Re: [ccp4bb] Who invented PDB format? > > Chemical crystallographers have always used fractional coordinates, it > makes it so > much easier to handle symmetry, special positions etc. But if the PDB > hadn't > used orthogonal coordinates, bioinformatics might never have taken off. > > George > > On 01/06/2013 09:34 AM, Eleanor Dodson wrote: > > Some of us resisted using an orthogonal format for coordinates, arguing > that the output from a crystal structure should refer to crystal axes. > And since symmetry was a crystal property it was important that we could > "see" it easily. The PDB format won out, but I still use *coordconv* a > lot > to turn back the orthogonalised PDB style to fractional coordinates - to > see if this heavy atom solution is the same as that one, given an origin > shift, etc etc. > Eleanor > > On 4 Jan 2013, at 20:44, Soisson, Stephen M wrote: > > > -- > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 > > > -- Shekhar C. Mande (शेखर चिं मांडे) Director, National Centre for Cell Science Ganeshkhind, Pune 411 007 Email: shek...@nccs.res.in, direc...@nccs.res.in Phone: +91-20-25708120 Fax:+91-20-25692259
