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Hi David, hi all,<br>
<br>
I now managed to at least get a test refinement working. What I
mostly changed was the Ubuntu version.<br>
I have no idea why, but I managed to get it to work on Ubuntu 10.04.<br>
<br>
In principle I installed 10.04 freshly in a virtualbox and from
their it worked rather straight-forward.<br>
<br>
Here is how I proceeded in detail for those of you who are
interested:<br>
<br>
1) Setting up a Virtualbox 4.3.2 r90405 on Ubuntu 12.04.3.<br>
2) Installing the 64bit version of Ubuntu 10.04 in a virtualbox (4
processors / 90% speed cap / 4GB Ram /VT-x enabled)<br>
3) Install VBoxAdditions<br>
4) Update ubuntu (<tt>sudo apt-get update</tt>)<br>
5) Installing g++ and zlib library (<tt>sudo apt-get install g++
zlib1g-dev</tt>)<br>
6) Installing binary version of phenix-dev-1525 to
/usr/local/science/phenix-dev-1525 (sudo ./install
--prefix=/usr/local/science)<br>
7) Unpack rosetta_2013_wk42_bundle to
/usr/local/science/rosetta_2013_wk42_bundle<br>
8) set rossetta variables by inserting them at the start of
/usr/local/science/pheninx-dev-1525/phenix_env.sh (just in line
3ff):<br>
<tt>export
PHENIX_ROSETTA_PATH=/usr/local/science/rosetta_2013wk42_bundle</tt><tt><br>
</tt><tt>export
ROSETTA3_DB=/usr/local/science/rosetta_2013wk42_bundle/main/database</tt><tt><br>
</tt><tt>export
PATH=$PATH:/usr/local/science/rosetta_2013wk42_bundle/main/source/bin</tt><br>
9) assign ownership to active user (<tt>sudo chown gebauer:gebauer
/usr/local/science/ -R</tt>)<br>
10) Compile it (phenix.build_phenix_interface nproc=4)<br>
It should run without problems<br>
<br>
Testing:<br>
1) Create a new directory (mkdir test && cd test)<br>
2) Download testset (suggested by Nat: <tt>phenix.fetch_pdb --mtz
1yjp</tt>)<br>
3) Run rosetta_refine (phenix.rosetta_refine 1yjp.pdb 1yjp.mtz
nproc=4)<br>
In my case rFree dropped from 18.21 to 14.90. It's not a low
resolution dataset, but it show that it general works and lowRes
would potentially take to long for a mere testing<br>
<br>
My real data are still being processed so I have no idea how well it
will works... only thing I found out already:<br>
4.5 GB RAM for 4 processes calculating ~500Aa via rosetta seems not
to be enough. I thereby reduced my "real run" to only one
processor...<br>
<br>
Regards,<br>
Jan<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">Am 01.11.2013 08:39, schrieb David
Goldstone:<br>
</div>
<blockquote
cite="mid:294AE645-1159-435C-93BF-5A6A4B9ED772@auckland.ac.nz"
type="cite">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div>Hi Jan, </div>
<div><br>
</div>
<div>I followed the same procedure. The only differences being
that I have installed it to my home directory to keep it
separate from our standard install of phenix and rosetta and I
run the phenix_env.sh separately from the exports. I had to
remove our default init.sh script from my .bashrc (this is our
setup script for all programs ccp4 etc) and now manually source
a different version to ensure it points to the correct version
of phenix. </div>
<div><br>
</div>
<div>I originally had trouble with the python shared libraries but
Nat has fixed this by building them into the binary installer.</div>
<div><br>
</div>
<div>Sorry I can't be more help </div>
<div><br>
</div>
<div>David</div>
<div><br>
<br>
<div>----</div>
<div><span style="background-color: rgba(255, 255, 255, 0);">Dr
David Goldstone<br>
Senior Lecturer<br>
University of Auckland<br>
New Zealand<br>
Ph <a moz-do-not-send="true"
href="tel:+64%209%203737599;84607"
x-apple-data-detectors="true"
x-apple-data-detectors-type="telephone"
x-apple-data-detectors-result="3">+64 9 3737599 x84607</a></span></div>
</div>
<div><br>
On 1/11/2013, at 8:30 PM, Jan Gebauer <<a
moz-do-not-send="true" href="mailto:jan.gebauer@uni-koeln.de">jan.gebauer@uni-koeln.de</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div><span>Dear David,</span><br>
<span></span><br>
<span>thanks for your remark. Indeed my paths are wrong in the
mail; however, this is due to lazy typing... I do set the
Rosetta_DB3 path corretly...</span><br>
<span>I'm still interested to know, how you managed to install
build it. Have you done the same procedure as described by
me? (only with different releases?)</span><br>
<span>Or did you do something differently?</span><br>
<span></span><br>
<span>Regards,</span><br>
<span>Jan</span><br>
<span></span><br>
<span>Am Donnerstag, 31. Oktober 2013 23:11:42 schrieb David
Goldstone:</span><br>
<blockquote type="cite"><span>Dear Jan,</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>I have recently installed phenix
with rosetta refine on Ubuntu 10.04</span><br>
</blockquote>
<blockquote type="cite"><span>using phenix-dev-1515 and
rosetta_wk40_bundle.</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>This install also appears to run
on an Ubuntu 12 install.</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>I think you export commands are
not correct mine are as follows</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>export</span><br>
</blockquote>
<blockquote type="cite"><span>PHENIX_ROSETTA_PATH=/mnt/home/dgol002/programs/rosetta_2013wk40_bundle</span><br>
</blockquote>
<blockquote type="cite"><span>export</span><br>
</blockquote>
<blockquote type="cite"><span>ROSETTA3_DB=/mnt/home/dgol002/programs/rosetta_2013wk40_bundle/main/database</span><br>
</blockquote>
<blockquote type="cite"><span>export</span><br>
</blockquote>
<blockquote type="cite"><span>PATH=$PATH:/mnt/home/dgol002/programs/rosetta_2013wk40_bundle/main/source/bin</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>ie you are exporting ROSETTA_BIN
twice rather than ROSETTA3_DB.</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>Hope this helps</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>David</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>On 1/11/2013 4:48 a.m., Jan
Gebauer wrote:</span><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Dear all,</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>I'm trying to get
rosetta_refine working on ubuntu 12.04 LTS.</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>This was the (latest) way I
tried it:</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>1) Downloaded phenix-dev-1523
binary & installed it via installer in</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>/usr/local/science/phenix4rosetta/phenix-dev-1523</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>2) Downloaded rosetta 2031wk42
and extracted it in</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>3) Inserted into phenix_env.sh</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>export</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>export</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>PHENIX_ROSETTA_PATH=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>export</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/database</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>4) sources phenix_env.sh</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>5) build the interface via</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>rosetta.build_phenix_interface
nproc=4</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>6) exceute the refinement via
phenix.rosetta_refine phasermodel.pdb</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>data.mtz nproc=4</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>The programm runs fine, up to
the point where it should generate</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>models via rosetta, it then
stops and crashes.</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>I have attached some logfiles</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Has anyone managed to run
rosetta_refine on Ubuntu? Which phenix and</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>rosetta versions did you use?
Ist there anything wrong on my above</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>mentioned build protocol?</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>I'm thankful for any help.</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Regards,</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Jan Gebauer</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>--</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Dr. Jan Gebauer</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>AG Prof. Baumann</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Institut für Biochemie /
Uni-Köln</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Otto-Fischer-Str. 12-14 /
50674 Köln</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Fon: +49 (221) 470 3212 </span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Fax: +49 (221) 470 5066</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span><a moz-do-not-send="true"
href="http://px.uni-koeln.de/">http://px.uni-koeln.de/</a></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>_______________________________________________</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>phenixbb mailing list</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span><a moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span><a moz-do-not-send="true"
href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a></span><br>
</blockquote>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>--</span><br>
</blockquote>
<blockquote type="cite"><span>Dr David Goldstone</span><br>
</blockquote>
<blockquote type="cite"><span>Senior Lecturer & Rutherford
Discovery Fellow</span><br>
</blockquote>
<blockquote type="cite"><span>Structural Biology</span><br>
</blockquote>
<blockquote type="cite"><span>University of Auckland</span><br>
</blockquote>
<blockquote type="cite"><span>New Zealand</span><br>
</blockquote>
<blockquote type="cite"><span>Ph +64 9 3737599 x84607</span><br>
</blockquote>
</div>
</blockquote>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dr. Jan Gebauer
AG Prof. Baumann
Institut für Biochemie / Uni-Köln
Otto-Fischer-Str. 12-14 / 50674 Köln
Fon: +49 (221) 470 3212        
Fax: +49 (221) 470 5066
<a class="moz-txt-link-freetext" href="http://px.uni-koeln.de/">http://px.uni-koeln.de/</a></pre>
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