Mon Apr  3 11:27:27 CEST 2006
==============================

publish NORMA as a short software tool article

http://journals.iucr.org/d/services/authorservices.html

http://scripts.iucr.org/cgi-bin/iucrid_details?id=3529


inquiry concerning a submission to Acta Cryst D

 
mrn@mbu.iisc.ernet.in


Dear Prof. Dr. Murthy, 

I am writing to you in your function as a co-editor of Acta Cryst D, since 
your areas of expertise listed on the Acta Cryst web site (protein structure 
and function; virus structure and assembly; conformational analysis) 
correspond best to the topic of a short communication that I wish to prepare 
for Acta Cryst D.

However, before formatting the paper for Acta Cryst, I would like to make sure 
that the topic of my paper will be suitable for your journal.

In fact, together with my co-authors Jorge Navaza and Yves-Henri Sanejouand, I 
developped a software tool that allows the flexible (normal mode based) 
fitting of crystallographic protein structure models into reconstructed 
electron densities from cryo-electron microscopy. 

Our tool combines the previously published fitting program URO from Jorge 
Navaza with the normal mode analysis tool from Yves-Henri Sanejouand, both 
published in Acta Cryst D:

Navaza J, Lepault J, Rey FA, Alvarez-Rua C, Borge J.
On the fitting of model electron densities into EM reconstructions: a 
reciprocal-space formulation.
Acta Crystallogr D Biol Crystallogr. 2002:1820-5

and 

Suhre K, Sanejouand YH.
On the potential of normal-mode analysis for solving difficult 
molecular-replacement problems.
Acta Crystallogr D Biol Crystallogr. 2004:796-9.

Recently, I had the opportunity to present this tool at the EMBO Practical 
Course on Combination of Electron Microscopy and X-ray Crystallography in 
Structure Determination, held on 23-29 October 2005 in Gif-sur-Yvette, 
France.

From our discussions with the students at that workshop comes the idea to 
publish a short note on our tool in your journal. 

However, before investing more time into writing up the paper and putting all 
examples in a clear downloadable and auto-executable format, I wish to know 
whether such a paper would be acceptable/interesting for Acta Cryst.

I have to point out that this will be clearly a software article - it does not 
present new scientific results. The general ideas and first exciting examples 
of the application of normal modes to fitting crystal structures into EM 
densities have been published recently by the groups of Brooks& Tama and 
Hinsen et al. 

We will show in our paper that our tool allows to easily reproduce some of 
their results. Thus, our paper will focus on a software tool that will give 
an easy-to-use tool into the hands of a large community protein 
crystallographers. 

I would be very grateful for your oppinion on this project, and in the case of 
a positive reply I would try to submit our paper in about four weeks from 
now.

Looking forward to your kind reply,

Yours sincerely,

Karsten Suhre.

PS: You will find the supporting material for the EMBO course (on which I will 
base my paper) at the following site:

http://www.igs.cnrs-mrs.fr/suhre/NORMA/


Tue Apr  4 20:24:06 CEST 2006
===============================

OK for Jorge

Start with Web-site under elNemo tree

http://www.igs.cnrs-mrs.fr/elNemo/NORMA/

Downloaded URO code for Backup to software/URO

uro_biblio.pdf
uro_BIN_alf_V4.0_f77.tgz
uro_BIN_rh9_g77.tgz
uro_BIN_sgi_6.5_f77.tgz
uro_general.tgz

Tue Apr 11 15:01:49 CEST 2006
------------------------------

NORMA-0.1.tgz  # first version
NORMA-0.2      # replace URO by new sources from Jorge
                 statically linked, 32 bit SuSE 10.0 code