<div dir="ltr">This is still much too convoluted a procedure to be practical, of course. 狢 promise I'll get around to looking at Ubuntu 12 this week but the VM setup was fiasco and we're somewhat short-handed.<div>
<br></div><div>For what it's worth, your data ran fine on our systems, although it overfit somewhat - I still need to try running phenix.refine as well to see if it actually improved anything, but it's definitely an issue with the build on your specific system. 狢'll send the results separately.</div>
<div><br></div><div style>-Nat</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Nov 5, 2013 at 5:26 AM, Jan Gebauer <span dir="ltr"><<a href="mailto:jan.gebauer@uni-koeln.de" target="_blank">jan.gebauer@uni-koeln.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
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>Am 01.11.2013 08:39, schrieb David
Goldstone:<br>
</div>
<blockquote type="cite">
<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 href="tel:+64%209%203737599;84607" target="_blank">+64 9 3737599 x84607</a></span></div>
</div>
<div><br>
On 1/11/2013, at 8:30 PM, Jan Gebauer <<a href="mailto:jan.gebauer@uni-koeln.de" target="_blank">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><div><div class="h5">
<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: <a href="tel:%2B49%20%28221%29%20470%203212" value="+492214703212" target="_blank">+49 (221) 470 3212</a> � �</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Fax: <a href="tel:%2B49%20%28221%29%20470%205066" value="+492214705066" target="_blank">+49 (221) 470 5066</a></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span><a href="http://px.uni-koeln.de/" target="_blank">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>
</div></div><div class="im"><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 href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span><a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">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>
</div><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 <a href="tel:%2B64%209%203737599%20x84607" value="+6493737599" target="_blank">+64 9 3737599 x84607</a></span><br>
</blockquote>
</div>
</blockquote>
</blockquote><div class="im">
<br>
<pre cols="72">--
Dr. Jan Gebauer
AG Prof. Baumann
Institut für Biochemie / Uni-Köln
Otto-Fischer-Str. 12-14 / 50674 Köln
Fon: <a href="tel:%2B49%20%28221%29%20470%203212" value="+492214703212" target="_blank">+49 (221) 470 3212</a>        
Fax: <a href="tel:%2B49%20%28221%29%20470%205066" value="+492214705066" target="_blank">+49 (221) 470 5066</a>
<a href="http://px.uni-koeln.de/" target="_blank">http://px.uni-koeln.de/</a></pre>
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