r17825 - in /branches/frame_order_testing: ./ docs/latex/ -- October 16, 2012 - 10:15

Author: bugman
Date: Tue Oct 16 10:15:02 2012
New Revision: 17825

URL: http://svn.gna.org/viewcvs/relax?rev=17825&view=rev
Log:
Merged revisions 17361-17365 via svnmerge from 
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk

........
  r17361 | bugman | 2012-08-28 17:28:52 +0200 (Tue, 28 Aug 2012) | 3 lines
  
  Added the Fushman 1999 reference and a few formatting fixes in other 
references.
........
  r17362 | bugman | 2012-08-28 17:29:48 +0200 (Tue, 28 Aug 2012) | 5 lines
  
  Created the new 'Citations' chapter of the relax user manual.
  
  This is to clearly outline to the user the citations required for the 
various components of relax.
........
  r17363 | bugman | 2012-08-28 18:46:56 +0200 (Tue, 28 Aug 2012) | 5 lines
  
  Modified the relax LaTeX bibliography style file relax.bst to convert DOI 
numbers to hyperlinks.
  
  This is to add links to the references within the relax user manual.
........
  r17364 | bugman | 2012-08-28 18:57:01 +0200 (Tue, 28 Aug 2012) | 3 lines
  
  Slight modification of the DOI hyperlink formatting bibliography style for 
the user manual.
........
  r17365 | bugman | 2012-08-28 19:14:29 +0200 (Tue, 28 Aug 2012) | 5 lines
  
  The LaTeX bibliography style for PhD theses now includes the DOI hyperlink.
  
  This is for the user manual.
........

Added:
    branches/frame_order_testing/docs/latex/cite.tex
      - copied unchanged from r17365, trunk/docs/latex/cite.tex
Modified:
    branches/frame_order_testing/   (props changed)
    branches/frame_order_testing/docs/latex/bibliography.bib
    branches/frame_order_testing/docs/latex/relax.bst
    branches/frame_order_testing/docs/latex/relax.tex

Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Oct 16 10:15:02 2012
@@ -1,1 +1,1 @@
-/trunk:1-17274,17295-17359
+/trunk:1-17274,17295-17359,17361-17365

Modified: branches/frame_order_testing/docs/latex/bibliography.bib
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/latex/bibliography.bib?rev=17825&r1=17824&r2=17825&view=diff
==============================================================================
--- branches/frame_order_testing/docs/latex/bibliography.bib (original)
+++ branches/frame_order_testing/docs/latex/bibliography.bib Tue Oct 16 
10:15:02 2012
@@ -426,7 +426,7 @@
 @Article{Bieri11,
    Author = {Bieri, Michael and d’Auvergne, Edward and Gooley, Paul},
    Affiliation = {Department of Biochemistry and Molecular Biology, Bio21 
Molecular Science and Biotechnology Institute, The University of Melbourne, 
Parkville, VIC 3010, Australia},
-   Title = {relaxGUI: a new software for fast and simple NMR relaxation data 
analysis and calculation of ps-ns and μs motion of proteins},
+   Title = {relax{GUI}: a new software for fast and simple {NMR} relaxation 
data analysis and calculation of ps-ns and $\mu$s motion of proteins},
    Journal = jbnmr,
    Publisher = {Springer Netherlands},
    issn = {0925-2738},
@@ -1807,7 +1807,7 @@
 }
 
 
-@article{Erdelyi11,
+@Article{Erdelyi11,
 Author = {Erdelyi, Mate and d'Auvergne, Edward and Navarro-Vazquez, Armando 
and
    Leonov, Andrei and Griesinger, Christian},
 Title = {{Dynamics of the Glycosidic Bond: Conformational Space of Lactose}},
@@ -2181,6 +2181,20 @@
   medline-stat   = {MEDLINE},
   url            = 
{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=9054979},
   year           = 1997
+}
+
+@article{Fushman99,
+  author = {Fushman, D. and Tjandra, N. and Cowburn, D.},
+  title = {An Approach to Direct Determination of Protein Dynamics from 
{15N} {NMR} Relaxation at Multiple Fields, Independent of Variable {15N} 
Chemical Shift Anisotropy and Chemical Exchange Contributions},
+  journal = jacs,
+  volume = {121},
+  number = {37},
+  pages = {8577-8582},
+  year = {1999},
+  doi = {10.1021/ja9904991},
+  URL = {http://pubs.acs.org/doi/abs/10.1021/ja9904991},
+  eprint = {http://pubs.acs.org/doi/pdf/10.1021/ja9904991},
+  abstract = { An approach to protein dynamics analysis from 15N relaxation 
data is demonstrated, based on multiple-field relaxation data. This provides 
a direct, residue-specific determination of both the spectral density 
components, the 15N chemical shift anisotropy (CSA) and the conformational 
exchange contribution to the 15N line width. Measurements of R1, R2, and 
15N{1H} NOE are used. The approach is free from any assumption about the 
values of the CSA or of the conformational exchange. Using this approach, the 
spectral densities, the values of 15N CSA, and the conformational exchange 
contribution to the 15N line width are directly determined from the 
relaxation data for human ubiquitin, collected at 360, 500, and 600 MHz. The 
spectral densities are analyzed in terms of the order parameter and the 
correlation time of local motion, using an axially symmetric overall 
rotational diffusion model. The residue-specific values of 15N CSA and the 
spectral densities obtained using this approach are in agreement with those 
derived previously [Fushman, Tjandra, and Cowburn. J. Am. Chem. Soc. 1998, 
120, 10947−10952] from CSA/dipolar cross-correlation analysis. Accurate 
determination of spectral densities and order parameters from 15N relaxation 
may be accomplished by analysis of multiple-field data without assumption of 
constant CSA or zero chemical exchange contributions. }
 }
 
 @Article{Gagne98,

Modified: branches/frame_order_testing/docs/latex/relax.bst
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/latex/relax.bst?rev=17825&r1=17824&r2=17825&view=diff
==============================================================================
--- branches/frame_order_testing/docs/latex/relax.bst (original)
+++ branches/frame_order_testing/docs/latex/relax.bst Tue Oct 16 10:15:02 2012
@@ -46,6 +46,7 @@
     author
     booktitle
     chapter
+    doi
     edition
     editor
     howpublished
@@ -269,6 +270,14 @@
   if$
 }
 
+FUNCTION {format.doi}
+{
+  doi empty$
+    { "" }
+    { "(\href{http://dx.doi.org/"; doi * "}{" * doi * "})" * }
+  if$
+}
+
 FUNCTION {format.title}
 { title empty$
     { "" }
@@ -508,6 +517,8 @@
     }
   if$
   new.block
+  format.doi output
+  new.block
   note output
   fin.entry
 }
@@ -710,6 +721,8 @@
   "PhD thesis" format.thesis.type output.nonnull
   school "school" output.check
   address output
+  new.block
+  format.doi output
   new.block
   note output
   fin.entry

Modified: branches/frame_order_testing/docs/latex/relax.tex
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/latex/relax.tex?rev=17825&r1=17824&r2=17825&view=diff
==============================================================================
--- branches/frame_order_testing/docs/latex/relax.tex (original)
+++ branches/frame_order_testing/docs/latex/relax.tex Tue Oct 16 10:15:02 2012
@@ -71,6 +71,10 @@
 
 % Natbib Citation format.
 \bibpunct{(}{)}{;}{a}{,}{,}
+
+% Inline citations.
+\usepackage{bibentry}
+\nobibliography*
 
 % Allow the maths blocks to be broken!!!
 \allowdisplaybreaks[1]
@@ -201,6 +205,7 @@
 %%%%%%%%%%%%%%%
 
 \include{intro}
+\include{cite}
 \include{install}
 \include{infrastruct}
 \include{data_model}