Re: import bib refs to show in pdf?
Am Monday 13 July 2009 05:44:23 schrieb Sebastian Stolzenberg: Hi rh, Hi All, Thanks for the reply; attached, please find my test files, that do not work now on my ubuntu machine with LyX 1.6.0. I found the command bibtex in test.lyx, so I manually ran bibtex on test.bib, with the error message that test.bib.aux is not found. I am not even close to the actual problem, am I? ;-) should'nt it be test.aux ? run bibtex test and not bibtex test.bib manually Wolfgang Thank you Sebastian Sebastian Stolzenberg wrote: Dear All, I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 Everything behaves normal, in particular, I can export pdfs and easily import a *.bib into my Bibliography section and LyX recognizes all the references in it. However, trying to export this document with references into pdf, the references do not appear and all my citation show question tags. Any help is much appreciated, Sebastian -- - Wolfgang Engelmann Schlossgartenstrasse 22 D-72070 Tübingen Tel 07071 68325
Re: import bib refs to show in pdf?
On 07/12/2009 11:44 PM, Sebastian Stolzenberg wrote: Hi rh, Hi All, Thanks for the reply; attached, please find my test files, that do not work now on my ubuntu machine with LyX 1.6.0. I found the command bibtex in test.lyx, so I manually ran bibtex on test.bib, with the error message that test.bib.aux is not found. I am not even close to the actual problem, am I? ;-) As someone else said, you have to run bibtex test, not bibtex test.bib. (You can also run latex test rather than latex test.tex, though you don't HAVE to do so.) As far as these files go, there are no citations in the test file you sent. If I add one, it works for me. Try putting the files into /tmp and see if they work there. rh Thank you Sebastian Sebastian Stolzenberg wrote: Dear All, I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 Everything behaves normal, in particular, I can export pdfs and easily import a *.bib into my Bibliography section and LyX recognizes all the references in it. However, trying to export this document with references into pdf, the references do not appear and all my citation show question tags. Any help is much appreciated, Sebastian
Re: import bib refs to show in pdf?
Hi rh, Hi Murat, Hi All, let's define $tmp=/tmp/lyx_tmpdir.TJ6542/lyx_tmpbuf2 There is 1 reference in the test.bib I attached, but looking into the $tmp/test.log file, I get this error message here: LaTeX Warning: Empty `thebibliography' environment on input line 3. since $tmp/test.bbl has no references. However, there exists $tmp/0_home_sebastian_test.bib, including my 1 reference. The files test.aux, test.tex, and test.tex.dep-pdf (all in $tmp) refer to this bib file. @rh: As a workaround, did you add a reference to a *.bib or a *.bbl file to make things work? If *.bbl, could you kindly send me the *.bbl file so that I can learn, how to these references manually? @Murat: How can I set a Latex path in Lyx? Only through the Preference-PATH prefix line? Thanks a zillion, Sebastian rgheck wrote: On 07/12/2009 11:44 PM, Sebastian Stolzenberg wrote: Hi rh, Hi All, Thanks for the reply; attached, please find my test files, that do not work now on my ubuntu machine with LyX 1.6.0. I found the command bibtex in test.lyx, so I manually ran bibtex on test.bib, with the error message that test.bib.aux is not found. I am not even close to the actual problem, am I? ;-) As someone else said, you have to run bibtex test, not bibtex test.bib. (You can also run latex test rather than latex test.tex, though you don't HAVE to do so.) As far as these files go, there are no citations in the test file you sent. If I add one, it works for me. Try putting the files into /tmp and see if they work there. rh Thank you Sebastian Sebastian Stolzenberg wrote: Dear All, I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 Everything behaves normal, in particular, I can export pdfs and easily import a *.bib into my Bibliography section and LyX recognizes all the references in it. However, trying to export this document with references into pdf, the references do not appear and all my citation show question tags. Any help is much appreciated, Sebastian
Re: import bib refs to show in pdf?
Thanks guys for your help. It turned out to be an encoding problem: BibTex does not support unicode yet. Cheers, Sebastian rgheck wrote: On 07/13/2009 10:22 AM, Sebastian Stolzenberg wrote: Hi rh, Hi Murat, Hi All, let's define $tmp=/tmp/lyx_tmpdir.TJ6542/lyx_tmpbuf2 There is 1 reference in the test.bib I attached, but looking into the $tmp/test.log file, I get this error message here: LaTeX Warning: Empty `thebibliography' environment on input line 3. since $tmp/test.bbl has no references. However, there exists $tmp/0_home_sebastian_test.bib, including my 1 reference. The files test.aux, test.tex, and test.tex.dep-pdf (all in $tmp) refer to this bib file. @rh: As a workaround, did you add a reference to a *.bib or a *.bbl file to make things work? If *.bbl, could you kindly send me the *.bbl file so that I can learn, how to these references manually? No, I didn't do anything but add a footnote to your LyX file. Without it, of course there will be no references, since nothing is cited. Normally, LyX (and, for that matter, LaTeX) includes only cited material in the bibliography. This allows you to have a single, huge bib file that you use with all your documents, and only the ones you cite get output. If you want to output everything in the bib file, then click on the bibliography inset and then, at the bottom, where it says Content, choose All references. rh
Re: import bib refs to show in pdf?
On 07/13/2009 01:18 PM, Sebastian Stolzenberg wrote: Thanks guys for your help. It turned out to be an encoding problem: BibTex does not support unicode yet. This is a fairly common problem. You might try BibLaTeX if you really need unicode. rh Cheers, Sebastian rgheck wrote: On 07/13/2009 10:22 AM, Sebastian Stolzenberg wrote: Hi rh, Hi Murat, Hi All, let's define $tmp=/tmp/lyx_tmpdir.TJ6542/lyx_tmpbuf2 There is 1 reference in the test.bib I attached, but looking into the $tmp/test.log file, I get this error message here: LaTeX Warning: Empty `thebibliography' environment on input line 3. since $tmp/test.bbl has no references. However, there exists $tmp/0_home_sebastian_test.bib, including my 1 reference. The files test.aux, test.tex, and test.tex.dep-pdf (all in $tmp) refer to this bib file. @rh: As a workaround, did you add a reference to a *.bib or a *.bbl file to make things work? If *.bbl, could you kindly send me the *.bbl file so that I can learn, how to these references manually? No, I didn't do anything but add a footnote to your LyX file. Without it, of course there will be no references, since nothing is cited. Normally, LyX (and, for that matter, LaTeX) includes only cited material in the bibliography. This allows you to have a single, huge bib file that you use with all your documents, and only the ones you cite get output. If you want to output everything in the bib file, then click on the bibliography inset and then, at the bottom, where it says Content, choose All references. rh
Re: import bib refs to show in pdf?
Am Monday 13 July 2009 05:44:23 schrieb Sebastian Stolzenberg: Hi rh, Hi All, Thanks for the reply; attached, please find my test files, that do not work now on my ubuntu machine with LyX 1.6.0. I found the command bibtex in test.lyx, so I manually ran bibtex on test.bib, with the error message that test.bib.aux is not found. I am not even close to the actual problem, am I? ;-) should'nt it be test.aux ? run bibtex test and not bibtex test.bib manually Wolfgang Thank you Sebastian Sebastian Stolzenberg wrote: Dear All, I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 Everything behaves normal, in particular, I can export pdfs and easily import a *.bib into my Bibliography section and LyX recognizes all the references in it. However, trying to export this document with references into pdf, the references do not appear and all my citation show question tags. Any help is much appreciated, Sebastian -- - Wolfgang Engelmann Schlossgartenstrasse 22 D-72070 Tübingen Tel 07071 68325
Re: import bib refs to show in pdf?
On 07/12/2009 11:44 PM, Sebastian Stolzenberg wrote: Hi rh, Hi All, Thanks for the reply; attached, please find my test files, that do not work now on my ubuntu machine with LyX 1.6.0. I found the command bibtex in test.lyx, so I manually ran bibtex on test.bib, with the error message that test.bib.aux is not found. I am not even close to the actual problem, am I? ;-) As someone else said, you have to run bibtex test, not bibtex test.bib. (You can also run latex test rather than latex test.tex, though you don't HAVE to do so.) As far as these files go, there are no citations in the test file you sent. If I add one, it works for me. Try putting the files into /tmp and see if they work there. rh Thank you Sebastian Sebastian Stolzenberg wrote: Dear All, I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 Everything behaves normal, in particular, I can export pdfs and easily import a *.bib into my Bibliography section and LyX recognizes all the references in it. However, trying to export this document with references into pdf, the references do not appear and all my citation show question tags. Any help is much appreciated, Sebastian
Re: import bib refs to show in pdf?
Hi rh, Hi Murat, Hi All, let's define $tmp=/tmp/lyx_tmpdir.TJ6542/lyx_tmpbuf2 There is 1 reference in the test.bib I attached, but looking into the $tmp/test.log file, I get this error message here: LaTeX Warning: Empty `thebibliography' environment on input line 3. since $tmp/test.bbl has no references. However, there exists $tmp/0_home_sebastian_test.bib, including my 1 reference. The files test.aux, test.tex, and test.tex.dep-pdf (all in $tmp) refer to this bib file. @rh: As a workaround, did you add a reference to a *.bib or a *.bbl file to make things work? If *.bbl, could you kindly send me the *.bbl file so that I can learn, how to these references manually? @Murat: How can I set a Latex path in Lyx? Only through the Preference-PATH prefix line? Thanks a zillion, Sebastian rgheck wrote: On 07/12/2009 11:44 PM, Sebastian Stolzenberg wrote: Hi rh, Hi All, Thanks for the reply; attached, please find my test files, that do not work now on my ubuntu machine with LyX 1.6.0. I found the command bibtex in test.lyx, so I manually ran bibtex on test.bib, with the error message that test.bib.aux is not found. I am not even close to the actual problem, am I? ;-) As someone else said, you have to run bibtex test, not bibtex test.bib. (You can also run latex test rather than latex test.tex, though you don't HAVE to do so.) As far as these files go, there are no citations in the test file you sent. If I add one, it works for me. Try putting the files into /tmp and see if they work there. rh Thank you Sebastian Sebastian Stolzenberg wrote: Dear All, I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 Everything behaves normal, in particular, I can export pdfs and easily import a *.bib into my Bibliography section and LyX recognizes all the references in it. However, trying to export this document with references into pdf, the references do not appear and all my citation show question tags. Any help is much appreciated, Sebastian
Re: import bib refs to show in pdf?
Thanks guys for your help. It turned out to be an encoding problem: BibTex does not support unicode yet. Cheers, Sebastian rgheck wrote: On 07/13/2009 10:22 AM, Sebastian Stolzenberg wrote: Hi rh, Hi Murat, Hi All, let's define $tmp=/tmp/lyx_tmpdir.TJ6542/lyx_tmpbuf2 There is 1 reference in the test.bib I attached, but looking into the $tmp/test.log file, I get this error message here: LaTeX Warning: Empty `thebibliography' environment on input line 3. since $tmp/test.bbl has no references. However, there exists $tmp/0_home_sebastian_test.bib, including my 1 reference. The files test.aux, test.tex, and test.tex.dep-pdf (all in $tmp) refer to this bib file. @rh: As a workaround, did you add a reference to a *.bib or a *.bbl file to make things work? If *.bbl, could you kindly send me the *.bbl file so that I can learn, how to these references manually? No, I didn't do anything but add a footnote to your LyX file. Without it, of course there will be no references, since nothing is cited. Normally, LyX (and, for that matter, LaTeX) includes only cited material in the bibliography. This allows you to have a single, huge bib file that you use with all your documents, and only the ones you cite get output. If you want to output everything in the bib file, then click on the bibliography inset and then, at the bottom, where it says Content, choose All references. rh
Re: import bib refs to show in pdf?
On 07/13/2009 01:18 PM, Sebastian Stolzenberg wrote: Thanks guys for your help. It turned out to be an encoding problem: BibTex does not support unicode yet. This is a fairly common problem. You might try BibLaTeX if you really need unicode. rh Cheers, Sebastian rgheck wrote: On 07/13/2009 10:22 AM, Sebastian Stolzenberg wrote: Hi rh, Hi Murat, Hi All, let's define $tmp=/tmp/lyx_tmpdir.TJ6542/lyx_tmpbuf2 There is 1 reference in the test.bib I attached, but looking into the $tmp/test.log file, I get this error message here: LaTeX Warning: Empty `thebibliography' environment on input line 3. since $tmp/test.bbl has no references. However, there exists $tmp/0_home_sebastian_test.bib, including my 1 reference. The files test.aux, test.tex, and test.tex.dep-pdf (all in $tmp) refer to this bib file. @rh: As a workaround, did you add a reference to a *.bib or a *.bbl file to make things work? If *.bbl, could you kindly send me the *.bbl file so that I can learn, how to these references manually? No, I didn't do anything but add a footnote to your LyX file. Without it, of course there will be no references, since nothing is cited. Normally, LyX (and, for that matter, LaTeX) includes only cited material in the bibliography. This allows you to have a single, huge bib file that you use with all your documents, and only the ones you cite get output. If you want to output everything in the bib file, then click on the bibliography inset and then, at the bottom, where it says Content, choose All references. rh
Re: import bib refs to show in pdf?
Am Monday 13 July 2009 05:44:23 schrieb Sebastian Stolzenberg: > Hi rh, Hi All, > > Thanks for the reply; attached, please find my test files, that do not > work now on my ubuntu machine with LyX 1.6.0. > > I found the command "bibtex" in test.lyx, so I manually ran bibtex on > test.bib, with the error message that "test.bib.aux" is not found. I am > not even close to the actual problem, am I? ;-) should'nt it be test.aux ? run bibtex test and not bibtex test.bib manually Wolfgang > > Thank you > Sebastian > > Sebastian Stolzenberg wrote: > > Dear All, > > > > I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 > > > > Everything behaves normal, in particular, I can export pdfs and easily > > import a *.bib into my Bibliography section and LyX recognizes all the > > references in it. > > > > However, trying to export this document with references into pdf, the > > references do not appear and all my citation show question tags. > > > > Any help is much appreciated, > > Sebastian -- - Wolfgang Engelmann Schlossgartenstrasse 22 D-72070 Tübingen Tel 07071 68325
Re: import bib refs to show in pdf?
On 07/12/2009 11:44 PM, Sebastian Stolzenberg wrote: Hi rh, Hi All, Thanks for the reply; attached, please find my test files, that do not work now on my ubuntu machine with LyX 1.6.0. I found the command "bibtex" in test.lyx, so I manually ran bibtex on test.bib, with the error message that "test.bib.aux" is not found. I am not even close to the actual problem, am I? ;-) As someone else said, you have to run "bibtex test", not "bibtex test.bib". (You can also run "latex test" rather than "latex test.tex", though you don't HAVE to do so.) As far as these files go, there are no citations in the test file you sent. If I add one, it works for me. Try putting the files into /tmp and see if they work there. rh Thank you Sebastian Sebastian Stolzenberg wrote: Dear All, I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 Everything behaves normal, in particular, I can export pdfs and easily import a *.bib into my Bibliography section and LyX recognizes all the references in it. However, trying to export this document with references into pdf, the references do not appear and all my citation show question tags. Any help is much appreciated, Sebastian
Re: import bib refs to show in pdf?
Hi rh, Hi Murat, Hi All, let's define $tmp=/tmp/lyx_tmpdir.TJ6542/lyx_tmpbuf2 There is 1 reference in the test.bib I attached, but looking into the $tmp/test.log file, I get this error message here: LaTeX Warning: Empty `thebibliography' environment on input line 3. since $tmp/test.bbl has no references. However, there exists $tmp/0_home_sebastian_test.bib, including my 1 reference. The files test.aux, test.tex, and test.tex.dep-pdf (all in $tmp) refer to this bib file. @rh: As a workaround, did you add a reference to a *.bib or a *.bbl file to make things work? If *.bbl, could you kindly send me the *.bbl file so that I can learn, how to these references manually? @Murat: How can I set a Latex path in Lyx? Only through the "Preference"->"PATH prefix" line? Thanks a zillion, Sebastian rgheck wrote: On 07/12/2009 11:44 PM, Sebastian Stolzenberg wrote: Hi rh, Hi All, Thanks for the reply; attached, please find my test files, that do not work now on my ubuntu machine with LyX 1.6.0. I found the command "bibtex" in test.lyx, so I manually ran bibtex on test.bib, with the error message that "test.bib.aux" is not found. I am not even close to the actual problem, am I? ;-) As someone else said, you have to run "bibtex test", not "bibtex test.bib". (You can also run "latex test" rather than "latex test.tex", though you don't HAVE to do so.) As far as these files go, there are no citations in the test file you sent. If I add one, it works for me. Try putting the files into /tmp and see if they work there. rh Thank you Sebastian Sebastian Stolzenberg wrote: Dear All, I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 Everything behaves normal, in particular, I can export pdfs and easily import a *.bib into my Bibliography section and LyX recognizes all the references in it. However, trying to export this document with references into pdf, the references do not appear and all my citation show question tags. Any help is much appreciated, Sebastian
Re: import bib refs to show in pdf?
Thanks guys for your help. It turned out to be an encoding problem: BibTex does not support unicode yet. Cheers, Sebastian rgheck wrote: On 07/13/2009 10:22 AM, Sebastian Stolzenberg wrote: Hi rh, Hi Murat, Hi All, let's define $tmp=/tmp/lyx_tmpdir.TJ6542/lyx_tmpbuf2 There is 1 reference in the test.bib I attached, but looking into the $tmp/test.log file, I get this error message here: LaTeX Warning: Empty `thebibliography' environment on input line 3. since $tmp/test.bbl has no references. However, there exists $tmp/0_home_sebastian_test.bib, including my 1 reference. The files test.aux, test.tex, and test.tex.dep-pdf (all in $tmp) refer to this bib file. @rh: As a workaround, did you add a reference to a *.bib or a *.bbl file to make things work? If *.bbl, could you kindly send me the *.bbl file so that I can learn, how to these references manually? No, I didn't do anything but add a footnote to your LyX file. Without it, of course there will be no references, since nothing is cited. Normally, LyX (and, for that matter, LaTeX) includes only cited material in the bibliography. This allows you to have a single, huge bib file that you use with all your documents, and only the ones you cite get output. If you want to output everything in the bib file, then click on the bibliography inset and then, at the bottom, where it says "Content", choose "All references". rh
Re: import bib refs to show in pdf?
On 07/13/2009 01:18 PM, Sebastian Stolzenberg wrote: Thanks guys for your help. It turned out to be an encoding problem: BibTex does not support unicode yet. This is a fairly common problem. You might try BibLaTeX if you really need unicode. rh Cheers, Sebastian rgheck wrote: On 07/13/2009 10:22 AM, Sebastian Stolzenberg wrote: Hi rh, Hi Murat, Hi All, let's define $tmp=/tmp/lyx_tmpdir.TJ6542/lyx_tmpbuf2 There is 1 reference in the test.bib I attached, but looking into the $tmp/test.log file, I get this error message here: LaTeX Warning: Empty `thebibliography' environment on input line 3. since $tmp/test.bbl has no references. However, there exists $tmp/0_home_sebastian_test.bib, including my 1 reference. The files test.aux, test.tex, and test.tex.dep-pdf (all in $tmp) refer to this bib file. @rh: As a workaround, did you add a reference to a *.bib or a *.bbl file to make things work? If *.bbl, could you kindly send me the *.bbl file so that I can learn, how to these references manually? No, I didn't do anything but add a footnote to your LyX file. Without it, of course there will be no references, since nothing is cited. Normally, LyX (and, for that matter, LaTeX) includes only cited material in the bibliography. This allows you to have a single, huge bib file that you use with all your documents, and only the ones you cite get output. If you want to output everything in the bib file, then click on the bibliography inset and then, at the bottom, where it says "Content", choose "All references". rh
import bib refs to show in pdf?
Dear All, I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 Everything behaves normal, in particular, I can export pdfs and easily import a *.bib into my Bibliography section and LyX recognizes all the references in it. However, trying to export this document with references into pdf, the references do not appear and all my citation show question tags. Any help is much appreciated, Sebastian
Re: import bib refs to show in pdf?
Hi rh, Hi All,
Thanks for the reply; attached, please find my test files, that do not
work now on my ubuntu machine with LyX 1.6.0.
I found the command bibtex in test.lyx, so I manually ran bibtex on
test.bib, with the error message that test.bib.aux is not found. I am
not even close to the actual problem, am I? ;-)
Thank you
Sebastian
Sebastian Stolzenberg wrote:
Dear All,
I installed the latest Lyx version 1.6.3 on my Mac 10.4.11
Everything behaves normal, in particular, I can export pdfs and easily
import a *.bib into my Bibliography section and LyX recognizes all the
references in it.
However, trying to export this document with references into pdf, the
references do not appear and all my citation show question tags.
Any help is much appreciated,
Sebastian
% This file was created with JabRef 2.3.1.
% Encoding: UTF-8
@ARTICLE{Brooks1983,
author = {Brooks, Bernard R. and Bruccoleri, Robert E. and Olafson, Barry D.
and States, David J. and Swaminathan, S. and Karplus, Martin},
title = {CHARMM: A program for macromolecular energy, minimization, and dynamics
calculations},
journal = {Journal of Computational Chemistry},
year = {1983},
volume = {4},
pages = {187--217},
number = {2},
abstract = {CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly
flexible computer program which uses empirical energy functions to
model macromolecular systems. The program can read or model build
structures, energy minimize them by first- or second-derivative techniques,
perform a normal mode or molecular dynamics simulation, and analyze
the structural, equilibrium, and dynamic properties determined in
these calculations. The operations that CHARMM can perform are described,
and some implementation details are given. A set of parameters for
the empirical energy function and a sample run are included.},
file = {Brooks1983_CHARMM- A program for macromolecular energy, minimization,
and dynamics calculations.pdf:pdf-refs/Brooks1983_CHARMM- A program
for macromolecular energy, minimization, and dynamics calculations.pdf:PDF},
owner = {sebastian},
timestamp = {2009.05.24},
url = {http://dx.doi.org/10.1002/jcc.540040211}
}
@comment{jabref-meta: selector_publisher:}
@comment{jabref-meta: selector_author:}
@comment{jabref-meta: selector_journal:}
@comment{jabref-meta: selector_keywords:}
@comment{jabref-meta: groupsversion:3;}
@comment{jabref-meta: groupstree:
0 AllEntriesGroup:;
1 ExplicitGroup:GluT\;2\;;
2 ExplicitGroup:Scaffolding proteins\;2\;Waxman2007\;;
3 ExplicitGroup:C-terminals\;2\;Gonzalez2003\;Gonzalez2004a\;Jackson20
01\;Kalandadze2002\;Lin2001\;;
3 ExplicitGroup:N-terminals\;2\;Marie2002\;;
3 ExplicitGroup:general\;2\;Gonzalez2004\;Torres2007\;;
2 ExplicitGroup:Cluster Formation\;2\;Nakagawa2008\;Peacey2009\;Zhou20
04\;;
2 ExplicitGroup:Recycling\;2\;Voglmaier2006\;;
2 ExplicitGroup:Hotspot Residues\;2\;Zhang1999\;;
2 ExplicitGroup:Reviews\;2\;Torres2007\;Tzingounis2007\;Vandenberg2008
\;;
2 ExplicitGroup:experimental hints\;2\;Seal2001\;Shachnai2005\;Tao2007
\;Zerangue1996\;Zhang1998\;;
3 ExplicitGroup:near HP2b tip\;2\;Kavanaugh1997\;Tao2007\;;
3 ExplicitGroup:NA3binding site\;2\;Rosental2006\;Tao2006\;;
3 ExplicitGroup:Proton transport\;2\;Fairman1998\;;
3 ExplicitGroup:Chloride conductance\;2\;Fairman1995\;;
3 ExplicitGroup:Substrate Transport\;2\;Ryan2009\;;
2 ExplicitGroup:other MD sims\;2\;Gu2009\;Huang2008\;Huang2009\;Shriva
stava2008\;;
2 ExplicitGroup:Sodium binding\;2\;Gouaux2005\;Noskov2007\;;
2 ExplicitGroup:Boudker and Structure\;2\;Boudker2007\;Gendreau2004\;G
roeneveld2007\;Yernool2003\;Yernool2004\;;
2 ExplicitGroup:useful parameters for MD\;2\;Fuchs2006\;;
1 ExplicitGroup:NMA\;2\;Bahar2005\;Niv2008\;Riccardi2009\;Schulz2009\;
Sherwood2008\;Suhre2004\;Tozzini2005\;;
2 ExplicitGroup:unread\;2\;Bahar2005\;Chu2007\;Franklin2007\;Schroeder
2007\;Schulz2009\;Sherwood2008\;Yang2007\;Zheng2007a\;Zheng2007b\;;
2 ExplicitGroup:reviews\;2\;Tozzini2005\;;
2 ExplicitGroup:clap-motions\;2\;Zheng2007\;;
2 ExplicitGroup:Structure-refinements\;2\;Schroeder2007\;;
2 ExplicitGroup:perturbed NMA\;2\;Ming2006\;Ming2008\;Schuyler2009\;Te
hver2008\;Zheng2009\;;
2 ExplicitGroup:Willy R. Wriggers\;2\;Jeong2006\;;
2 ExplicitGroup:Spencer Erickson\;2\;Sanejouand2004\;Tama2001\;;
2 ExplicitGroup:multiple-basin-interpolation\;2\;Best2005\;Clementi200
0\;Maragakis2005\;Nakamura2004\;Okazaki2006\;Pan2008\;Ueda1978\;Yang20
09\;;
2 ExplicitGroup:NMA-MD\;2\;Sweet2008\;;
2 ExplicitGroup:general\;2\;Ma2005\;Monod1965\;Rzehak2002\;;
1 ExplicitGroup:MD\;2\;Kandt2007\;Maragakis2008\;Shaw2005\;;
2 ExplicitGroup:unread\;2\;Maragakis2008\;Sankararamakrishnan2000\;;
2 ExplicitGroup:Trajectories\;2\;Raveh2009\;;
2 ExplicitGroup:Nose\;2\;Evans1985\;Nose1984\;;
2 ExplicitGroup:PMF\;2\;Allen2006\;;
2 ExplicitGroup:General\;2\;Harvey1998\;Mackerell2004\;;
2 ExplicitGroup:Lipids (i think i got this from anshu)\;2\;;
2 ExplicitGroup:Protein Folding\;2\;Scheraga2007\;;
1
import bib refs to show in pdf?
Dear All, I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 Everything behaves normal, in particular, I can export pdfs and easily import a *.bib into my Bibliography section and LyX recognizes all the references in it. However, trying to export this document with references into pdf, the references do not appear and all my citation show question tags. Any help is much appreciated, Sebastian
Re: import bib refs to show in pdf?
Hi rh, Hi All,
Thanks for the reply; attached, please find my test files, that do not
work now on my ubuntu machine with LyX 1.6.0.
I found the command bibtex in test.lyx, so I manually ran bibtex on
test.bib, with the error message that test.bib.aux is not found. I am
not even close to the actual problem, am I? ;-)
Thank you
Sebastian
Sebastian Stolzenberg wrote:
Dear All,
I installed the latest Lyx version 1.6.3 on my Mac 10.4.11
Everything behaves normal, in particular, I can export pdfs and easily
import a *.bib into my Bibliography section and LyX recognizes all the
references in it.
However, trying to export this document with references into pdf, the
references do not appear and all my citation show question tags.
Any help is much appreciated,
Sebastian
% This file was created with JabRef 2.3.1.
% Encoding: UTF-8
@ARTICLE{Brooks1983,
author = {Brooks, Bernard R. and Bruccoleri, Robert E. and Olafson, Barry D.
and States, David J. and Swaminathan, S. and Karplus, Martin},
title = {CHARMM: A program for macromolecular energy, minimization, and dynamics
calculations},
journal = {Journal of Computational Chemistry},
year = {1983},
volume = {4},
pages = {187--217},
number = {2},
abstract = {CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly
flexible computer program which uses empirical energy functions to
model macromolecular systems. The program can read or model build
structures, energy minimize them by first- or second-derivative techniques,
perform a normal mode or molecular dynamics simulation, and analyze
the structural, equilibrium, and dynamic properties determined in
these calculations. The operations that CHARMM can perform are described,
and some implementation details are given. A set of parameters for
the empirical energy function and a sample run are included.},
file = {Brooks1983_CHARMM- A program for macromolecular energy, minimization,
and dynamics calculations.pdf:pdf-refs/Brooks1983_CHARMM- A program
for macromolecular energy, minimization, and dynamics calculations.pdf:PDF},
owner = {sebastian},
timestamp = {2009.05.24},
url = {http://dx.doi.org/10.1002/jcc.540040211}
}
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import bib refs to show in pdf?
Dear All, I installed the latest Lyx version 1.6.3 on my Mac 10.4.11 Everything behaves normal, in particular, I can export pdfs and easily import a *.bib into my Bibliography section and LyX recognizes all the references in it. However, trying to export this document with references into pdf, the references do not appear and all my citation show question tags. Any help is much appreciated, Sebastian
Re: import bib refs to show in pdf?
Hi rh, Hi All,
Thanks for the reply; attached, please find my test files, that do not
work now on my ubuntu machine with LyX 1.6.0.
I found the command "bibtex" in test.lyx, so I manually ran bibtex on
test.bib, with the error message that "test.bib.aux" is not found. I am
not even close to the actual problem, am I? ;-)
Thank you
Sebastian
Sebastian Stolzenberg wrote:
Dear All,
I installed the latest Lyx version 1.6.3 on my Mac 10.4.11
Everything behaves normal, in particular, I can export pdfs and easily
import a *.bib into my Bibliography section and LyX recognizes all the
references in it.
However, trying to export this document with references into pdf, the
references do not appear and all my citation show question tags.
Any help is much appreciated,
Sebastian
% This file was created with JabRef 2.3.1.
% Encoding: UTF-8
@ARTICLE{Brooks1983,
author = {Brooks, Bernard R. and Bruccoleri, Robert E. and Olafson, Barry D.
and States, David J. and Swaminathan, S. and Karplus, Martin},
title = {CHARMM: A program for macromolecular energy, minimization, and dynamics
calculations},
journal = {Journal of Computational Chemistry},
year = {1983},
volume = {4},
pages = {187--217},
number = {2},
abstract = {CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly
flexible computer program which uses empirical energy functions to
model macromolecular systems. The program can read or model build
structures, energy minimize them by first- or second-derivative techniques,
perform a normal mode or molecular dynamics simulation, and analyze
the structural, equilibrium, and dynamic properties determined in
these calculations. The operations that CHARMM can perform are described,
and some implementation details are given. A set of parameters for
the empirical energy function and a sample run are included.},
file = {Brooks1983_CHARMM- A program for macromolecular energy, minimization,
and dynamics calculations.pdf:pdf-refs/Brooks1983_CHARMM- A program
for macromolecular energy, minimization, and dynamics calculations.pdf:PDF},
owner = {sebastian},
timestamp = {2009.05.24},
url = {http://dx.doi.org/10.1002/jcc.540040211}
}
@comment{jabref-meta: selector_publisher:}
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3 ExplicitGroup:N-terminals\;2\;Marie2002\;;
3 ExplicitGroup:general\;2\;Gonzalez2004\;Torres2007\;;
2 ExplicitGroup:Cluster Formation\;2\;Nakagawa2008\;Peacey2009\;Zhou20
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2 ExplicitGroup:Recycling\;2\;Voglmaier2006\;;
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1
