[phenixbb] Structure minimization for model with rigid body

Alexandre OURJOUMTSEV sacha at igbmc.fr
Fri Jan 18 00:27:58 PST 2013

Dear all,

Since nobody else reacted (maybe I missed some mails), I would like to refer to Dana's mail to address NOT the scientific part of her question but the linguistic one.

(since there was no suite of Dana's request in phenixbb, I suppose that people understood her question and answered her in private; good luck to Dana).

It makes me unhappy (saying politely) when, frequently enough, I see/hear the expression "structure minimization" even when it became a part of jargon.


One can minimize energy or some other FUNCTION of a model, one can OPTIMIZE a structural model (in the sense that the model fits better some data), but please not "minimize a structure".

Such an expression is not really innocent, especially for young researchers, because when talking about minimization (rather optimization) problems, one should have clear in his mind :

- what is the model, which parameters can be modified (like Dana said, rigid body)

- what is the score function, what will be minimized or maximized (definitely NOT a structure :))

- by which minimization method will we achieve this.

and "structure minimization" makes a confusing of all this.

I would wish that we (I mean our community as a whole) "minimize" :) using wrong expressions like that. Sorry for my intervention.

With best wishes,

Sacha Urzhumtsev

-----Message d'origine-----
De : phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> [mailto:phenixbb-bounces at phenix-online.org] De la part de danashah at post.tau.ac.il<mailto:danashah at post.tau.ac.il>
Envoyé : mardi 15 janvier 2013 08:34
À : phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
Objet : [phenixbb] Structure minimization for model with rigid body


We're interesting in performing a structure minimization for a model, while treating a part of the model as a rigid body.



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