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: [log in to unmask]
Phone: 972-8-647-2220  Skype: boaz.shaanan                 
Fax:   972-8-647-2992 or 972-8-646-1710    

 

 

                

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From: CCP4 bulletin board [[log in to unmask]] on behalf of George T. DeTitta [[log in to unmask]]
Sent: Sunday, January 06, 2013 3:48 PM
To: [log in to unmask]
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

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From: George Sheldrick <[log in to unmask]>

Sender: CCP4 bulletin board <[log in to unmask]>

Date: Sun, 6 Jan 2013 09:57:28 +0100

To: <[log in to unmask]>

ReplyTo: George Sheldrick <[log in to unmask]>

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